Science.gov

Sample records for acinetobacter genomic species

  1. Genomic and phenotypic characterization of the species Acinetobacter venetianus

    PubMed Central

    Fondi, Marco; Maida, Isabel; Perrin, Elena; Orlandini, Valerio; La Torre, Laura; Bosi, Emanuele; Negroni, Andrea; Zanaroli, Giulio; Fava, Fabio; Decorosi, Francesca; Giovannetti, Luciana; Viti, Carlo; Vaneechoutte, Mario; Dijkshoorn, Lenie; Fani, Renato

    2016-01-01

    Crude oil is a complex mixture of hydrocarbons and other organic compounds that can produce serious environmental problems and whose removal is highly demanding in terms of human and technological resources. The potential use of microbes as bioremediation agents is one of the most promising fields in this area. Members of the species Acinetobacter venetianus have been previously characterized for their capability to degrade n-alkanes and thus may represent interesting model systems to implement this process. Although a preliminary experimental characterization of the overall hydrocarbon degradation capability has been performed for five of them, to date, the genetic/genomic features underlying such molecular processes have not been identified. Here we have integrated genomic and phenotypic information for six A. venetianus strains, i.e. VE-C3, RAG-1T, LUH 13518, LUH 7437, LUH 5627 and LUH 8758. Besides providing a thorough description of the A. venetianus species, these data were exploited to infer the genetic features (presence/absence patterns of genes) and the short-term evolutionary events possibly responsible for the variability in n-alkane degradation efficiency of these strains, including the mechanisms of interaction with the fuel droplet and the subsequent catabolism of this pollutant. PMID:26902269

  2. Genomic and phenotypic characterization of the species Acinetobacter venetianus.

    PubMed

    Fondi, Marco; Maida, Isabel; Perrin, Elena; Orlandini, Valerio; La Torre, Laura; Bosi, Emanuele; Negroni, Andrea; Zanaroli, Giulio; Fava, Fabio; Decorosi, Francesca; Giovannetti, Luciana; Viti, Carlo; Vaneechoutte, Mario; Dijkshoorn, Lenie; Fani, Renato

    2016-02-23

    Crude oil is a complex mixture of hydrocarbons and other organic compounds that can produce serious environmental problems and whose removal is highly demanding in terms of human and technological resources. The potential use of microbes as bioremediation agents is one of the most promising fields in this area. Members of the species Acinetobacter venetianus have been previously characterized for their capability to degrade n-alkanes and thus may represent interesting model systems to implement this process. Although a preliminary experimental characterization of the overall hydrocarbon degradation capability has been performed for five of them, to date, the genetic/genomic features underlying such molecular processes have not been identified. Here we have integrated genomic and phenotypic information for six A. venetianus strains, i.e. VE-C3, RAG-1(T), LUH 13518, LUH 7437, LUH 5627 and LUH 8758. Besides providing a thorough description of the A. venetianus species, these data were exploited to infer the genetic features (presence/absence patterns of genes) and the short-term evolutionary events possibly responsible for the variability in n-alkane degradation efficiency of these strains, including the mechanisms of interaction with the fuel droplet and the subsequent catabolism of this pollutant.

  3. Draft genome sequence of an Acinetobacter genomic species 3 strain harboring a bla(NDM-1) gene.

    PubMed

    Chen, Yong; Cui, Yujun; Pu, Fei; Jiang, Guoqin; Zhao, Xiangna; Yuan, Yanting; Zhao, Wei; Li, Dongfang; Liu, Hui; Li, Yin; Liang, Ting; Xu, Li; Wang, Yan; Song, Qing; Yang, Jiyong; Liang, Long; Yang, Ruifu; Han, Li; Song, Yajun

    2012-01-01

    Here we report the draft genome sequence of one Acinetobacter genomic species 3 strain, D499, which harbors the bla(NDM-1) gene. The total length of the assembled genome is 4,103,824 bp, and 3,896 coding sequences (CDSs) were predicted within the genome. A previously unreported bla(NDM-1)-bearing plasmid was identified in this strain.

  4. Genome Sequence of Airborne Acinetobacter sp. Strain 5-2Ac02 in the Hospital Environment, Close to the Species of Acinetobacter towneri.

    PubMed

    Barbosa, Beathriz G V; Fernandez-García, Laura; Gato, Eva; López, Maria; Blasco, Lucia; Leão, Robson Souza; Albano, Rodolpho M; Fernández, Begoña; Cuenca, Felipe-Fernández; Pascual, Álvaro; Bou, German; Marques, Elizabeth A; Tomás, María

    2016-12-08

    Acinetobacter spp. are found in 53% of air colonization samples from the hospital environment. In this work, we sequenced all the genome of airborne Acinetobacter sp. strain 5-2Ac02. We found important features at the genomic level in regards to the rhizome. By phylogenetic analysis, A. towneri was the species most closely related to Acinetobacter sp. 5-2Ac02.

  5. Genome Sequence of Airborne Acinetobacter sp. Strain 5-2Ac02 in the Hospital Environment, Close to the Species of Acinetobacter towneri

    PubMed Central

    Barbosa, Beathriz G. V.; Fernandez-García, Laura; Gato, Eva; López, Maria; Blasco, Lucia; Leão, Robson Souza; Albano, Rodolpho M.; Fernández, Begoña; Cuenca, Felipe-Fernández; Pascual, Álvaro; Bou, German; Marques, Elizabeth A.

    2016-01-01

    Acinetobacter spp. are found in 53% of air colonization samples from the hospital environment. In this work, we sequenced all the genome of airborne Acinetobacter sp. strain 5-2Ac02. We found important features at the genomic level in regards to the rhizome. By phylogenetic analysis, A. towneri was the species most closely related to Acinetobacter sp. 5-2Ac02. PMID:27932646

  6. Taxonomy of haemolytic and/or proteolytic strains of the genus Acinetobacter with the proposal of Acinetobacter courvalinii sp. nov. (genomic species 14 sensu Bouvet & Jeanjean), Acinetobacter dispersus sp. nov. (genomic species 17), Acinetobacter modestus sp. nov., Acinetobacter proteolyticus sp. nov. and Acinetobacter vivianii sp. nov.

    PubMed

    Nemec, Alexandr; Radolfova-Krizova, Lenka; Maixnerova, Martina; Vrestiakova, Eliska; Jezek, Petr; Sedo, Ondrej

    2016-04-01

    We aimed to define the taxonomic status of 40 haemolytic and/or proteolytic strains of the genus Acinetobacter which were previously classified into five putative species termed as genomic species 14BJ (n=9), genomic species 17 (n=9), taxon 18 (n=7), taxon 19 (n=6) and taxon 20 (n=9). The strains were recovered mostly from human clinical specimens or soil and water ecosystems and were highly diverse in geographical origin and time of isolation. Comparative analysis of the rpoB and gyrB gene sequences of all strains, and the whole-genome sequences of selected strains, showed that these putative species formed five respective, well-supported clusters within a distinct clade of the genus Acinetobacter which typically, although not exclusively, encompasses strains with strong haemolytic activity. The whole-genome-based average nucleotide identity (ANIb) values supported the species status of each of these clusters. Moreover, the distinctness and coherence of the clusters were supported by whole-cell profiling based on MALDI-TOF MS. Congruent with these findings were the results of metabolic and physiological testing. We conclude that the five putative taxa represent respective novel species, for which the names Acinetobacter courvalinii sp. nov. (type strain ANC 3623T=CCUG 67960T=CIP 110480T=CCM 8635T), Acinetobacter dispersus sp. nov. (type strain ANC 4105T=CCUG 67961T=CIP 110500T=CCM 8636T), Acinetobacter modestus sp. nov. (type strain NIPH 236T=CCUG 67964T=CIP 110444T=CCM 8639T), Acinetobacter proteolyticus sp. nov. (type strain NIPH 809T=CCUG 67965T=CIP 110482T = CCM 8640T) and Acinetobacter vivianii sp. nov. (type strain NIPH 2168T=CCUG 67967T=CIP 110483T=CCM 8642T) are proposed.

  7. Draft Genome Sequence of JVAP01T, the Type Strain of the Novel Species Acinetobacter dijkshoorniae

    PubMed Central

    Fernández-Orth, Dietmar; Cosgaya, Clara; Telli, Murat; Mosqueda, Noraida; Marí-Almirall, Marta

    2017-01-01

    ABSTRACT Here, we report the draft genome sequence of the type strain of Acinetobacter dijkshoorniae, a novel human pathogen within the Acinetobacter calcoaceticus–Acinetobacter baumannii (ACB) complex. Strain JVAP01T has an estimated genome size of 3.9 Mb, exhibits a 38.8% G+C content, and carries a plasmid with the blaNDM-1 carbapenemase gene. PMID:28082506

  8. Development and Evaluation of Species-Specific PCR for Detection of Nine Acinetobacter Species.

    PubMed

    Li, Xue Min; Choi, Ji Ae; Choi, In Sun; Kook, Joong Ki; Chang, Young-Hyo; Park, Geon; Jang, Sook Jin; Kang, Seong Ho; Moon, Dae Soo

    2016-05-01

    Molecular methods have the potential to improve the speed and accuracy of Acinetobacter species identification in clinical settings. The goal of this study is to develop species-specific PCR assays based on differences in the RNA polymerase beta-subunit gene (rpoB) to detect nine commonly isolated Acinetobacter species including Acinetobacter baumannii, Acinetobacter calcoaceticus, Acinetobacter pittii, Acinetobacter nosocomialis, Acinetobacter lwoffii, Acinetobacter ursingii, Acinetobacter bereziniae, Acinetobacter haemolyticus, and Acinetobacter schindleri. The sensitivity and specificity of these nine assays were measured using genomic DNA templates from 55 reference strains and from 474 Acinetobacter clinical isolates. The sensitivity of A. baumannii-specific PCR assay was 98.9%, and the sensitivity of species-specific PCR assays for all other species was 100%. The specificities of A. lwoffii- and A. schindleri-specific PCR were 97.8 and 98.9%, respectively. The specificity of species-specific PCR for all other tested Acinetobacter species was 100%. The lower limit of detection for the nine species-specific PCR assays developed in this study was 20 or 200 pg of genomic DNA from type strains of each species. The Acinetobacter species-specific PCR assay would be useful to determine the correct species among suggested candidate Acinetobacter species when conventional methods including MALDI-TOF MS identify Acinetobacter only to the genus level. The species-specific assay can be used to screen large numbers of clinical and environmental samples obtained for epidemiologic study of Acinetobacter for the presence of target species.

  9. Identification, Genotypic Relation, and Clinical Features of Colistin-Resistant Isolates of Acinetobacter Genomic Species 13BJ/14TU from Bloodstreams of Patients in a University Hospital

    PubMed Central

    Lee, Seung Yeob; Shin, Jong Hee; Park, Kyung Hwa; Kim, Ju Hee; Shin, Myung Geun; Suh, Soon Pal; Ryang, Dong Wook

    2014-01-01

    Colistin resistance remains rare among clinical isolates of Acinetobacter species. We noted the emergence of colistin-resistant bloodstream isolates of the Acinetobacter genomic species (GS) 13BJ/14TU from patients at a university hospital between 2003 and 2011. We report here, for the first time, the microbiological and molecular characteristics of these isolates, with clinical features of Acinetobacter GS 13BJ/14TU bacteremia. All 11 available patient isolates were correctly identified as Acinetobacter GS 13BJ/14TU using partial rpoB gene sequencing but were misidentified using the phenotypic methods Vitek 2 (mostly as Acinetobacter baumannii), MicroScan (mostly as A. baumannii/Acinetobacter haemolyticus), and the API 20 NE system (all as A. haemolyticus). Most isolates were susceptible to commonly used antibiotics, including carbapenems, but all were resistant to colistin, for which it is unknown whether the resistance is acquired or intrinsic. However, the fact that none of the patients had a history of colistin therapy strongly suggests that Acinetobacter GS 13BJ/14TU is innately resistant to colistin. The phylogenetic tree of multilocus sequence typing (MLST) showed that all 11 isolates formed a separate cluster from other Acinetobacter species and yielded five sequence types. However, pulsed-field gel electrophoresis (PFGE) revealed 11 distinct patterns, suggesting that the bacteremia had occurred sporadically. Four patients showed persistent bacteremia (6 to 17 days), and all 11 patients had excellent outcomes with cleared bacteremia, suggesting that patients with Acinetobacter GS 13BJ/14TU-associated bacteremia show a favorable outcome. These results emphasize the importance of precise species identification, especially regarding colistin resistance in Acinetobacter species. In addition, MLST offers another approach to the identification of Acinetobacter GS 13BJ/14TU, whereas PFGE is useful for genotyping for this species. PMID:24403305

  10. Identification, genotypic relation, and clinical features of colistin-resistant isolates of Acinetobacter genomic species 13BJ/14TU from bloodstreams of patients in a university hospital.

    PubMed

    Lee, Seung Yeob; Shin, Jong Hee; Park, Kyung Hwa; Kim, Ju Hee; Shin, Myung Geun; Suh, Soon Pal; Ryang, Dong Wook; Kim, Soo Hyun

    2014-03-01

    Colistin resistance remains rare among clinical isolates of Acinetobacter species. We noted the emergence of colistin-resistant bloodstream isolates of the Acinetobacter genomic species (GS) 13BJ/14TU from patients at a university hospital between 2003 and 2011. We report here, for the first time, the microbiological and molecular characteristics of these isolates, with clinical features of Acinetobacter GS 13BJ/14TU bacteremia. All 11 available patient isolates were correctly identified as Acinetobacter GS 13BJ/14TU using partial rpoB gene sequencing but were misidentified using the phenotypic methods Vitek 2 (mostly as Acinetobacter baumannii), MicroScan (mostly as A. baumannii/Acinetobacter haemolyticus), and the API 20 NE system (all as A. haemolyticus). Most isolates were susceptible to commonly used antibiotics, including carbapenems, but all were resistant to colistin, for which it is unknown whether the resistance is acquired or intrinsic. However, the fact that none of the patients had a history of colistin therapy strongly suggests that Acinetobacter GS 13BJ/14TU is innately resistant to colistin. The phylogenetic tree of multilocus sequence typing (MLST) showed that all 11 isolates formed a separate cluster from other Acinetobacter species and yielded five sequence types. However, pulsed-field gel electrophoresis (PFGE) revealed 11 distinct patterns, suggesting that the bacteremia had occurred sporadically. Four patients showed persistent bacteremia (6 to 17 days), and all 11 patients had excellent outcomes with cleared bacteremia, suggesting that patients with Acinetobacter GS 13BJ/14TU-associated bacteremia show a favorable outcome. These results emphasize the importance of precise species identification, especially regarding colistin resistance in Acinetobacter species. In addition, MLST offers another approach to the identification of Acinetobacter GS 13BJ/14TU, whereas PFGE is useful for genotyping for this species.

  11. Molecular Characterization of the Gene Encoding a New AmpC β-Lactamase in a Clinical Strain of Acinetobacter Genomic Species 3

    PubMed Central

    Beceiro, Alejandro; Dominguez, Lourdes; Ribera, Anna; Vila, Jordi; Molina, Francisca; Villanueva, Rosa; Eiros, Jose Maria; Bou, German

    2004-01-01

    A presumptive chromosomal cephalosporinase (pI, 9.0) from a clinical strain of Acinetobacter genomic species 3 (AG3) is reported. The nucleotide sequence of this β-lactamase shows for the first time the gene encoding an AmpC enzyme in AG3. In addition, the biochemical properties of the novel AG3 AmpC β-lactamase are reported PMID:15047547

  12. Acinetobacter Species Infections among Navy and Marine Corps Beneficiaries: 2012 Annual Report

    DTIC Science & Technology

    2013-11-18

    phenotypic tests, several other Acinetobacter species are difficult to distinguish from A. baumannii , namely A. calcoaceticus, Acinetobacter genomic...the A. baumannii -calcoaceticus complex, or ABC. 1-4 Geographic distribution contributes to the growing concern surrounding Acinetobacter . The... Acinetobacter cases was A. baumannii in the DON (42.7%) and ABC in the DOD (38.8%). In the DON, 9.3% of Acinetobacter isolates were MDR and 1.3% were XDR

  13. Identification of genetic recombination between Acinetobacter species based on multilocus sequence analysis.

    PubMed

    Kim, Dae Hun; Park, Young Kyoung; Choi, Ji Young; Ko, Kwan Soo

    2012-07-01

    During multilocus sequence analysis of Acinetobacter calcoaceticus-Acinetobacter baumannii complex, we identified the evidence of recent genetic recombination between 2 Acinetobacter species. While 3 isolates belonged to A. nosocomialis based on 16S rRNA, gyrB, fusA, gdhB, and rplB gene sequences, they showed close relationships with Acinetobacter genomic species 'close to 13TU' in rpoB, recA, cpn60, rpoD, and gltA gene trees.

  14. Reservoirs of Non-baumannii Acinetobacter Species

    PubMed Central

    Al Atrouni, Ahmad; Joly-Guillou, Marie-Laure; Hamze, Monzer; Kempf, Marie

    2016-01-01

    Acinetobacter spp. are ubiquitous gram negative and non-fermenting coccobacilli that have the ability to occupy several ecological niches including environment, animals and human. Among the different species, Acinetobacter baumannii has evolved as global pathogen causing wide range of infection. Since the implementation of molecular techniques, the habitat and the role of non-baumannii Acinetobacter in human infection have been elucidated. In addition, several new species have been described. In the present review, we summarize the recent data about the natural reservoir of non-baumannii Acinetobacter including the novel species that have been described for the first time from environmental sources and reported during the last years. PMID:26870013

  15. [Frequency and antimicrobial resistance of Acinetobacter species in a university hospital of Buenos Aires City].

    PubMed

    Rodríguez, Carlos Hernán; Nastro, Marcela; Dabos, Laura; Vay, Carlos; Famiglietti, Angela

    2014-01-01

    Two-hundred Acinetobacter isolates belonging to 200 patients admitted to Hospital de Clínicas José de San Martín during the period March 2013-June 2014 were analyzed. The identification was performed by mass spectrometry and was confirmed by molecular methods. Susceptibility to antimicrobials was studied by the Vitek-2 system. A 94% correlation of both identification methods was found. Multidrug resistant Acinetobacter baumannii was the predominant genomic species (92.6%) in hospital-acquired infections, whereas Acinetobacter pitti and Acinetobacter nosocomialis accounted for 3.5% and 0.5% of the isolates recovered, respectively. In community-acquired infections a major predominance of the different genomic species was observed. Acinetobacter johnsonii and A. baumannii are the most frequent species, accounting for 45.9% of the isolates recovered. Resistance to carbapenems and minocycline was only observed in A. baumannii. Mass spectrophotometry was an effective tool for the identification of the different genomic species.

  16. First Genome Sequence of a Mexican Multidrug-Resistant Acinetobacter baumannii Isolate

    PubMed Central

    Graña-Miraglia, Lucía; Lozano, Luis; Castro-Jaimes, Semiramis; Cevallos, Miguel A.; Volkow, Patricia

    2016-01-01

    Acinetobacter baumannii has emerged as an important nosocomial pathogen worldwide. Here, we present the draft genome of the first multidrug-resistant A. baumannii isolate, sampled from a tertiary hospital in Mexico City. This genome will provide a starting point for studying the genomic diversity of this species in Mexico. PMID:27013043

  17. Genome organization of epidemic Acinetobacter baumannii strains

    PubMed Central

    2011-01-01

    Background Acinetobacter baumannii is an opportunistic pathogen responsible for hospital-acquired infections. A. baumannii epidemics described world-wide were caused by few genotypic clusters of strains. The occurrence of epidemics caused by multi-drug resistant strains assigned to novel genotypes have been reported over the last few years. Results In the present study, we compared whole genome sequences of three A. baumannii strains assigned to genotypes ST2, ST25 and ST78, representative of the most frequent genotypes responsible for epidemics in several Mediterranean hospitals, and four complete genome sequences of A. baumannii strains assigned to genotypes ST1, ST2 and ST77. Comparative genome analysis showed extensive synteny and identified 3068 coding regions which are conserved, at the same chromosomal position, in all A. baumannii genomes. Genome alignments also identified 63 DNA regions, ranging in size from 4 o 126 kb, all defined as genomic islands, which were present in some genomes, but were either missing or replaced by non-homologous DNA sequences in others. Some islands are involved in resistance to drugs and metals, others carry genes encoding surface proteins or enzymes involved in specific metabolic pathways, and others correspond to prophage-like elements. Accessory DNA regions encode 12 to 19% of the potential gene products of the analyzed strains. The analysis of a collection of epidemic A. baumannii strains showed that some islands were restricted to specific genotypes. Conclusion The definition of the genome components of A. baumannii provides a scaffold to rapidly evaluate the genomic organization of novel clinical A. baumannii isolates. Changes in island profiling will be useful in genomic epidemiology of A. baumannii population. PMID:21985032

  18. Distribution of Acinetobacter species on human skin: comparison of phenotypic and genotypic identification methods.

    PubMed Central

    Seifert, H; Dijkshoorn, L; Gerner-Smidt, P; Pelzer, N; Tjernberg, I; Vaneechoutte, M

    1997-01-01

    At least 19 genomic species are recognized as constituting the genus Acinetobacter. However, little is known about the natural reservoirs of the various members of the genus. An epidemiological study was therefore performed to investigate the colonization with Acinetobacter spp. of the skin and mucous membranes of 40 patients hospitalized in a cardiology ward and 40 healthy controls. Single samples were obtained once from each of nine different body sites, i.e., forehead, ear, nose, throat, axilla, hand, groin, perineum, and toe web. Identification of Acinetobacter isolates was achieved by using phenotypic properties and was compared to identification by amplified ribosomal DNA restriction analysis. Selected isolates were further investigated with sodium dodecyl sulfate-polyacrylamide gel electrophoresis, ribotyping, and DNA-DNA hybridization. Plasmid profile analysis was used for epidemiological typing. Thirty patients (75%) and 17 controls (42.5%) were found to be colonized with Acinetobacter spp., and the colonization rates of patients increased during their hospital stay. The most frequently isolated species were Acinetobacter lwoffii (47%), A. johnsonii (21%), A. radioresistens (12%), and DNA group 3 (11%). In contrast, A. baumannii and DNA group 13TU, the most important nosocomial Acinetobacter spp., were found only rarely on human skin (0.5 and 1%, respectively) and their natural habitat remains to be defined. A good correlation between phenotypic and genotypic methods for identification of Acinetobacter spp. was observed, and only two isolates could not be assigned to any of the known DNA groups. PMID:9350741

  19. Identification of NDM-1 in a Putatively Novel Acinetobacter Species ("NB14") Closely Related to Acinetobacter pittii.

    PubMed

    Espinal, Paula; Mosqueda, Noraida; Telli, Murat; van der Reijden, Tanny; Rolo, Dora; Fernández-Orth, Dietmar; Dijkshoorn, Lenie; Roca, Ignasi; Vila, Jordi

    2015-10-01

    In this study, we describe the molecular characterization of a plasmid-located blaNDM-1 harbored by an Acinetobacter clinical isolate recovered from a patient in Turkey that putatively constitutes a novel Acinetobacter species, as shown by its distinct ARDRA (amplified 16S ribosomal DNA restriction analysis) profile and molecular sequencing techniques. blaNDM-1 was carried by a conjugative plasmid widespread among non-baumannii Acinetobacter isolates, suggesting its potential for dissemination before reaching more clinically relevant Acinetobacter species.

  20. Acinetobacter seifertii Isolated from China: Genomic Sequence and Molecular Epidemiology Analyses.

    PubMed

    Yang, Yunxing; Wang, Jianfeng; Fu, Ying; Ruan, Zhi; Yu, Yunsong

    2016-03-01

    Clinical infections caused by Acinetobacter spp. have increasing public health concerns because of their global occurrence and ability to acquire multidrug resistance. Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex encompasses A. calcoaceticus, A. baumannii, A. pittii (formerly genomic species 3), and A nosocomial (formerly genomic species 13TU), which are predominantly responsible for clinical pathogenesis in the Acinetobacter genus. In our previous study, a putative novel species isolated from 385 non-A. baumannii spp. strains based on the rpoB gene phylogenetic tree was reported. Here, the putative novel species was identified as A. seifertii based on the whole-genome phylogenetic tree. A. seifertii was recognized as a novel member of the ACB complex and close to A. baumannii and A. nosocomials. Furthermore, we studied the characteristics of 10 A. seifertii isolates, which were distributed widely in 6 provinces in China and mainly caused infections in the elderly or children. To define the taxonomic status and characteristics, the biochemical reactions, antimicrobial susceptibility testing, pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and whole-genome sequence analysis were performed. The phenotypic characteristics failed to distinguish A. serfertii from other species in the ACB complex. Most of the A. seifertii isolates were susceptible to antibiotics commonly used for nosocomial Acinetobacter spp. infections, but one isolate (strain A362) was resistant to ampicillin/sulbactam, ceftazidime and amikacin. The different patterns of MLST and PFGE suggested that the 10 isolates were not identical and lacked clonal relatedness. Our study reported for the first time the molecular epidemiological and genomic features of widely disseminated A. seifertii in China. These observations could enrich the knowledge of infections caused by non-A. baumannii and may provide a scientific basis for future clinical treatment.

  1. The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences.

    PubMed

    Touchon, Marie; Cury, Jean; Yoon, Eun-Jeong; Krizova, Lenka; Cerqueira, Gustavo C; Murphy, Cheryl; Feldgarden, Michael; Wortman, Jennifer; Clermont, Dominique; Lambert, Thierry; Grillot-Courvalin, Catherine; Nemec, Alexandr; Courvalin, Patrice; Rocha, Eduardo P C

    2014-10-13

    Bacterial genomics has greatly expanded our understanding of microdiversification patterns within a species, but analyses at higher taxonomical levels are necessary to understand and predict the independent rise of pathogens in a genus. We have sampled, sequenced, and assessed the diversity of genomes of validly named and tentative species of the Acinetobacter genus, a clade including major nosocomial pathogens and biotechnologically important species. We inferred a robust global phylogeny and delimited several new putative species. The genus is very ancient and extremely diverse: Genomes of highly divergent species share more orthologs than certain strains within a species. We systematically characterized elements and mechanisms driving genome diversification, such as conjugative elements, insertion sequences, and natural transformation. We found many error-prone polymerases that may play a role in resistance to toxins, antibiotics, and in the generation of genetic variation. Surprisingly, temperate phages, poorly studied in Acinetobacter, were found to account for a significant fraction of most genomes. Accordingly, many genomes encode clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems with some of the largest CRISPR-arrays found so far in bacteria. Integrons are strongly overrepresented in Acinetobacter baumannii, which correlates with its frequent resistance to antibiotics. Our data suggest that A. baumannii arose from an ancient population bottleneck followed by population expansion under strong purifying selection. The outstanding diversification of the species occurred largely by horizontal transfer, including some allelic recombination, at specific hotspots preferentially located close to the replication terminus. Our work sets a quantitative basis to understand the diversification of Acinetobacter into emerging resistant and versatile pathogens.

  2. The Genomic Diversification of the Whole Acinetobacter Genus: Origins, Mechanisms, and Consequences

    PubMed Central

    Touchon, Marie; Cury, Jean; Yoon, Eun-Jeong; Krizova, Lenka; Cerqueira, Gustavo C.; Murphy, Cheryl; Feldgarden, Michael; Wortman, Jennifer; Clermont, Dominique; Lambert, Thierry; Grillot-Courvalin, Catherine; Nemec, Alexandr; Courvalin, Patrice; Rocha, Eduardo P.C.

    2014-01-01

    Bacterial genomics has greatly expanded our understanding of microdiversification patterns within a species, but analyses at higher taxonomical levels are necessary to understand and predict the independent rise of pathogens in a genus. We have sampled, sequenced, and assessed the diversity of genomes of validly named and tentative species of the Acinetobacter genus, a clade including major nosocomial pathogens and biotechnologically important species. We inferred a robust global phylogeny and delimited several new putative species. The genus is very ancient and extremely diverse: Genomes of highly divergent species share more orthologs than certain strains within a species. We systematically characterized elements and mechanisms driving genome diversification, such as conjugative elements, insertion sequences, and natural transformation. We found many error-prone polymerases that may play a role in resistance to toxins, antibiotics, and in the generation of genetic variation. Surprisingly, temperate phages, poorly studied in Acinetobacter, were found to account for a significant fraction of most genomes. Accordingly, many genomes encode clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems with some of the largest CRISPR-arrays found so far in bacteria. Integrons are strongly overrepresented in Acinetobacter baumannii, which correlates with its frequent resistance to antibiotics. Our data suggest that A. baumannii arose from an ancient population bottleneck followed by population expansion under strong purifying selection. The outstanding diversification of the species occurred largely by horizontal transfer, including some allelic recombination, at specific hotspots preferentially located close to the replication terminus. Our work sets a quantitative basis to understand the diversification of Acinetobacter into emerging resistant and versatile pathogens. PMID:25313016

  3. Complete Genome Sequence of the Multiresistant Acinetobacter baumannii Strain AbH12O-A2, Isolated during a Large Outbreak in Spain

    PubMed Central

    Merino, M.; Alvarez-Fraga, L.; Gómez, M. J.; Aransay, A. M.; Lavín, J. L.; Chaves, F.

    2014-01-01

    We report the complete genome sequence of Acinetobacter baumannii strain AbH12O-A2, isolated during a large outbreak in Spain. The genome has 3,875,775 bp and 3,526 coding sequences, with 39.4% G+C content. The availability of this genome will facilitate the study of the pathogenicity of the Acinetobacter species. PMID:25395646

  4. Identification of NDM-1 in a Putatively Novel Acinetobacter Species (“NB14”) Closely Related to Acinetobacter pittii

    PubMed Central

    Espinal, Paula; Mosqueda, Noraida; Telli, Murat; van der Reijden, Tanny; Rolo, Dora; Fernández-Orth, Dietmar; Dijkshoorn, Lenie; Vila, Jordi

    2015-01-01

    In this study, we describe the molecular characterization of a plasmid-located blaNDM-1 harbored by an Acinetobacter clinical isolate recovered from a patient in Turkey that putatively constitutes a novel Acinetobacter species, as shown by its distinct ARDRA (amplified 16S ribosomal DNA restriction analysis) profile and molecular sequencing techniques. blaNDM-1 was carried by a conjugative plasmid widespread among non-baumannii Acinetobacter isolates, suggesting its potential for dissemination before reaching more clinically relevant Acinetobacter species. PMID:26259796

  5. Draft Genome Sequences of Multidrug-Resistant Acinetobacter sp. Strains from Colombian Hospitals

    PubMed Central

    Falquet, Laurent; Reguero, María T.; Mantilla, José R.; Valenzuela, Emilia M.; González, Elsa; Cepeda, Alexandra; Escalante, Andrea

    2013-01-01

    The draft genome sequences of the strains Acinetobacter baumannii 107m, Acinetobacter nosocomialis 28F, and Acinetobacter pittii 42F, isolated from Colombian hospitals, are reported here. These isolates are causative of nosocomial infections and are classified as multidrug resistant, as they showed resistance to four different antibiotic groups. PMID:24285656

  6. Draft Genome Sequence of the Environmentally Isolated Acinetobacter pittii Strain IPK_TSA6.1

    PubMed Central

    Lee, Yunmi

    2016-01-01

    Acinetobacter pittii is an opportunistic pathogen frequently isolated from Acinetobacter infections other than those from Acinetobacter baumannii. Multidrug resistance in A. pittii, including resistance to carbapenems, has been increasingly reported worldwide. Here, we report the 4.14-Mbp draft genome sequence of A. pittii IPK_TSA6.1 that was isolated from a nonhospital setting. PMID:27688336

  7. Comparative genomic analysis of Acinetobacter oleivorans DR1 to determine strain-specific genomic regions and gentisate biodegradation.

    PubMed

    Jung, Jaejoon; Madsen, Eugene L; Jeon, Che Ok; Park, Woojun

    2011-10-01

    The comparative genomics of Acinetobacter oleivorans DR1 assayed with A. baylyi ADP1, A. calcoaceticus PHEA-2, and A. baumannii ATCC 17978 revealed that the incorporation of phage-related genomic regions and the absence of transposable elements have contributed to the large size (4.15 Mb) of the DR1 genome. A horizontally transferred genomic region and a higher proportion of transcriptional regulator- and signal peptide-coding genes were identified as characteristics of the DR1 genome. Incomplete glucose metabolism, metabolic pathways of aromatic compounds, biofilm formation, antibiotics and metal resistance, and natural competence genes were conserved in four compared genomes. Interestingly, only strain DR1 possesses gentisate 1,2-dioxygenase (nagI) and grows on gentisate, whereas other species cannot. Expression of the nagI gene was upregulated during gentisate utilization, and four downstream open reading frames (ORFs) were cotranscribed, supporting the notion that gentisate metabolism is a unique characteristic of strain DR1. The genomic analysis of strain DR1 provides additional insights into the function, ecology, and evolution of Acinetobacter species.

  8. Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium

    PubMed Central

    Barbe, Valérie; Vallenet, David; Fonknechten, Nuria; Kreimeyer, Annett; Oztas, Sophie; Labarre, Laurent; Cruveiller, Stéphane; Robert, Catherine; Duprat, Simone; Wincker, Patrick; Ornston, L. Nicholas; Weissenbach, Jean; Marlière, Philippe; Cohen, Georges N.; Médigue, Claudine

    2004-01-01

    Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized Pseudomonas aeruginosa and Pseudomonas putida. Unlike these bacteria, the Acinetobacter ADP1 is highly competent for natural transformation which affords extraordinary convenience for genetic manipulation. The circular chromosome of the Acinetobacter ADP1, presented here, encodes 3325 predicted coding sequences, of which 60% have been classified based on sequence similarity to other documented proteins. The close evolutionary proximity of Acinetobacter and Pseudomonas species, as judged by the sequences of their 16S RNA genes and by the highest level of bidirectional best hits, contrasts with the extensive divergence in the GC content of their DNA (40 versus 62%). The chromosomes also differ significantly in size, with the Acinetobacter ADP1 chromosome <60% of the length of the Pseudomonas counterparts. Genome analysis of the Acinetobacter ADP1 revealed genes for metabolic pathways involved in utilization of a large variety of compounds. Almost all of these genes, with orthologs that are scattered in other species, are located in five major ‘islands of catabolic diversity’, now an apparent ‘archipelago of catabolic diversity’, within one-quarter of the overall genome. Acinetobacter ADP1 displays many features of other aerobic soil bacteria with metabolism oriented toward the degradation of organic compounds found in their natural habitat. A distinguishing feature of this genome is the absence of a gene corresponding to pyruvate kinase, the enzyme that generally catalyzes the terminal step in conversion of carbohydrates to pyruvate for respiration by the citric acid cycle. This finding supports the view that the cycle itself is centrally geared to the catabolic capabilities of this exceptionally versatile organism. PMID:15514110

  9. Phylogenetic signal in phenotypic traits related to carbon source assimilation and chemical sensitivity in Acinetobacter species.

    PubMed

    Van Assche, Ado; Álvarez-Pérez, Sergio; de Breij, Anna; De Brabanter, Joseph; Willems, Kris A; Dijkshoorn, Lenie; Lievens, Bart

    2017-01-01

    A common belief is that the phylogeny of bacteria may reflect molecular functions and phenotypic characteristics, pointing towards phylogenetic conservatism of traits. Here, we tested this hypothesis for a large set of Acinetobacter strains. Members of the genus Acinetobacter are widespread in nature, demonstrate a high metabolic diversity and are resistant to several environmental stressors. Notably, some species are known to cause opportunistic human infections. A total of 133 strains belonging to 33 species with validly published names, two genomic species and species of an as-yet unknown taxonomic status were analyzed using the GENIII technology of Biolog, which allows high-throughput phenotyping. We estimated the strength and significance of the phylogenetic signal of each trait across phylogenetic reconstructions based on partial RNA polymerase subunit B (rpoB) and core genome sequences. Secondly, we tested whether phylogenetic distance was a good predictor of trait differentiation by Mantel test analysis. And finally, evolutionary model fitting was used to determine if the data for each phenotypic character was consistent with a phylogenetic or an essentially random model of trait distribution. Our data revealed that some key phenotypic traits related to substrate assimilation and chemical sensitivity are linked to the phylogenetic placement of Acinetobacter species. The strongest phylogenetic signals found were for utilization of different carbon sources such as some organic acids, amino acids and sugars, thus suggesting that in the diversification of Acinetobacter carbon source assimilation has had a relevant role. Future work should be aimed to clarify how such traits have shaped the remarkable ability of this bacterial group to dominate in a wide variety of habitats.

  10. Use of Comparative Genomics To Characterize the Diversity of Acinetobacter baumannii Surveillance Isolates in a Health Care Institution.

    PubMed

    Wallace, Lalena; Daugherty, Sean C; Nagaraj, Sushma; Johnson, J Kristie; Harris, Anthony D; Rasko, David A

    2016-10-01

    Despite the increasing prevalence of the nosocomial pathogen Acinetobacter baumannii, little is known about which genomic components contribute to clinical presentation of this important pathogen. Most whole-genome comparisons of A. baumannii have focused on specific genomic regions associated with phenotypes in a limited number of genomes. In this work, we describe the results of a whole-genome comparative analysis of 254 surveillance isolates of Acinetobacter species, 203 of which were A. baumannii, isolated from perianal swabs and sputum samples collected as part of an infection control active surveillance program at the University of Maryland Medical Center. The collection of surveillance isolates includes both carbapenem-susceptible and -resistant isolates. Based on the whole-genome phylogeny, the A. baumannii isolates collected belong to two major phylogenomic lineages. Results from multilocus sequence typing indicated that one of the major phylogenetic groups of A. baumannii was comprised solely of strains from the international clonal lineage 2. The genomic content of the A. baumannii isolates was examined using large-scale BLAST score ratio analysis to identify genes that are associated with carbapenem-susceptible and -resistant isolates, as well as genes potentially associated with the source of isolation. This analysis revealed a number of genes that were exclusive or at greater frequency in each of these classifications. This study is the most comprehensive genomic comparison of Acinetobacter isolates from a surveillance study to date and provides important information that will contribute to our understanding of the success of A. baumannii as a human pathogen.

  11. Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks

    PubMed Central

    Fitzpatrick, Margaret A.; Hauser, Alan R.

    2015-01-01

    Acinetobacter baumannii frequently causes nosocomial infections and outbreaks. Whole-genome sequencing (WGS) is a promising technique for strain typing and outbreak investigations. We compared the performance of conventional methods with WGS for strain typing clinical Acinetobacter isolates and analyzing a carbapenem-resistant A. baumannii (CRAB) outbreak. We performed two band-based typing techniques (pulsed-field gel electrophoresis and repetitive extragenic palindromic-PCR), multilocus sequence type (MLST) analysis, and WGS on 148 Acinetobacter calcoaceticus-A. baumannii complex bloodstream isolates collected from a single hospital from 2005 to 2012. Phylogenetic trees inferred from core-genome single nucleotide polymorphisms (SNPs) confirmed three Acinetobacter species within this collection. Four major A. baumannii clonal lineages (as defined by MLST) circulated during the study, three of which are globally distributed and one of which is novel. WGS indicated that a threshold of 2,500 core SNPs accurately distinguished A. baumannii isolates from different clonal lineages. The band-based techniques performed poorly in assigning isolates to clonal lineages and exhibited little agreement with sequence-based techniques. After applying WGS to a CRAB outbreak that occurred during the study, we identified a threshold of 2.5 core SNPs that distinguished nonoutbreak from outbreak strains. WGS was more discriminatory than the band-based techniques and was used to construct a more accurate transmission map that resolved many of the plausible transmission routes suggested by epidemiologic links. Our study demonstrates that WGS is superior to conventional techniques for A. baumannii strain typing and outbreak analysis. These findings support the incorporation of WGS into health care infection prevention efforts. PMID:26699703

  12. Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks.

    PubMed

    Fitzpatrick, Margaret A; Ozer, Egon A; Hauser, Alan R

    2016-03-01

    Acinetobacter baumannii frequently causes nosocomial infections and outbreaks. Whole-genome sequencing (WGS) is a promising technique for strain typing and outbreak investigations. We compared the performance of conventional methods with WGS for strain typing clinical Acinetobacter isolates and analyzing a carbapenem-resistant A. baumannii (CRAB) outbreak. We performed two band-based typing techniques (pulsed-field gel electrophoresis and repetitive extragenic palindromic-PCR), multilocus sequence type (MLST) analysis, and WGS on 148 Acinetobacter calcoaceticus-A. baumannii complex bloodstream isolates collected from a single hospital from 2005 to 2012. Phylogenetic trees inferred from core-genome single nucleotide polymorphisms (SNPs) confirmed three Acinetobacter species within this collection. Four major A. baumannii clonal lineages (as defined by MLST) circulated during the study, three of which are globally distributed and one of which is novel. WGS indicated that a threshold of 2,500 core SNPs accurately distinguished A. baumannii isolates from different clonal lineages. The band-based techniques performed poorly in assigning isolates to clonal lineages and exhibited little agreement with sequence-based techniques. After applying WGS to a CRAB outbreak that occurred during the study, we identified a threshold of 2.5 core SNPs that distinguished nonoutbreak from outbreak strains. WGS was more discriminatory than the band-based techniques and was used to construct a more accurate transmission map that resolved many of the plausible transmission routes suggested by epidemiologic links. Our study demonstrates that WGS is superior to conventional techniques for A. baumannii strain typing and outbreak analysis. These findings support the incorporation of WGS into health care infection prevention efforts.

  13. Genome Sequence of an Acinetobacter baumannii Strain Carrying Three Acquired Carbapenemase Genes

    PubMed Central

    Oinuma, Ken-Ichi; Suzuki, Masato; Sato, Kanako; Nakaie, Kiyotaka; Niki, Makoto; Takizawa, Etsuko; Niki, Mamiko; Shibayama, Keigo; Yamada, Koichi; Kakeya, Hiroshi

    2016-01-01

    The emergence of multiple-carbapenemase-producing Acinetobacter strains has been a serious concern during the past decade. Here, we report the draft genome sequence of an Acinetobacter baumannii strain isolated from a Japanese patient with three acquired carbapenemase genes: blaNDM-1, blaTMB-1, and blaOXA-58. PMID:27856588

  14. Draft genome sequence of Acinetobacter pittii ST643 shared by cystic fibrosis patients

    PubMed Central

    Rocha, Géssica A; Ferreira, Alex G; Lima, Danielle F; Leão, Robson S; Carvalho-Assef, Ana Paula D; Folescu, Tânia W; Albano, Rodolpho M; Marques, Elizabeth A

    2016-01-01

    Acinetobacter pittii has emerged as an important hospital pathogen that is associated with outbreaks and drug resistance. In cystic fibrosis (CF) patients, the detection of Acinetobacter spp. is rare; however, we isolated the A. pittii sequence type ST643 in several Brazilian CF patients treated in the same centre. The current study describes the draft genome of A. pittii ST643. PMID:27653362

  15. Complete Genome Sequence of an Acinetobacter Strain Harboring the NDM-1 Gene.

    PubMed

    Sun, Yang; Song, Yang; Song, Hongbin; Liu, Jun; Wang, Pengzhi; Qiu, Shaofu; Chen, Shuo; Zhu, Lingwei; Ji, Xue; Wang, Zhongqiang; Liu, Nan; Xia, Liliang; Chen, Weijun; Feng, Shuzhang

    2013-04-18

    The NDM-1 gene is a significant public health concern. Acinetobacter is one of the most prevalent opportunistic pathogens causing recent nosocomial infections with NDM-1, and drug-resistant strains pose serious threats to public health worldwide. Herein, we present the genomic sequence of Acinetobacter calcoaceticus subsp. anitratus XM1570, a multidrug-resistant isolate that carries the blaNDM-1 gene.

  16. Complete Genome Sequence of Acinetobacter sp. Strain NCu2D-2 Isolated from a Mouse

    PubMed Central

    Blaschke, Ulrike

    2017-01-01

    ABSTRACT Whole-genome sequencing of Acinetobacter sp. strain NCu2D-2, isolated from the trachea of a mouse, revealed the presence of a plasmid of 309,964 bp with little overall similarity to known plasmids and enriched in insertion sequences (ISs) closely related to IS elements known from the nosocomial pathogen Acinetobacter baumannii. PMID:28126932

  17. Comparative genomic analysis of novel Acinetobacter symbionts: A combined systems biology and genomics approach

    PubMed Central

    Gupta, Vipin; Haider, Shazia; Sood, Utkarsh; Gilbert, Jack A.; Ramjee, Meenakshi; Forbes, Ken; Singh, Yogendra; Lopes, Bruno S.; Lal, Rup

    2016-01-01

    The increasing trend of antibiotic resistance in Acinetobacter drastically limits the range of therapeutic agents required to treat multidrug resistant (MDR) infections. This study focused on analysis of novel Acinetobacter strains using a genomics and systems biology approach. Here we used a network theory method for pathogenic and non-pathogenic Acinetobacter spp. to identify the key regulatory proteins (hubs) in each strain. We identified nine key regulatory proteins, guaA, guaB, rpsB, rpsI, rpsL, rpsE, rpsC, rplM and trmD, which have functional roles as hubs in a hierarchical scale-free fractal protein-protein interaction network. Two key hubs (guaA and guaB) were important for insect-associated strains, and comparative analysis identified guaA as more important than guaB due to its role in effective module regulation. rpsI played a significant role in all the novel strains, while rplM was unique to sheep-associated strains. rpsM, rpsB and rpsI were involved in the regulation of overall network topology across all Acinetobacter strains analyzed in this study. Future analysis will investigate whether these hubs are useful as drug targets for treating Acinetobacter infections. PMID:27378055

  18. Reliability of phenotypic tests for identification of Acinetobacter species.

    PubMed Central

    Gerner-Smidt, P; Tjernberg, I; Ursing, J

    1991-01-01

    A numerical approach was used for identification of 198 Acinetobacter strains assigned to DNA groups according to the classification of Tjernberg and Ursing (I. Tjernberg and J. Ursing, APMIS 97:595-605, 1989). The matrix used was constructed from data published by Bouvet and Grimont (P.J.M. Bouvet and P.A.D. Grimont, Int. J. Syst. Bacteriol. 36:228-240, 1986) and Bouvet and Jeanjean (P.J.M. Bouvet and S. Jeanjean, Res. Microbiol. 140:291-299, 1989). The tests chosen were those of the simplified identification scheme for Acinetobacter species devised by Bouvet and Grimont (P.J.M. Bouvet and P.A.D. Grimont, Ann. Inst. Pasteur/Microbiol. 138:569-578, 1987), namely, growth at 37, 41, and 44 degrees C, oxidation of glucose, gelatin hydrolysis, and assimilation of 14 carbon sources. Of the strains tested, 181 represented 12 DNA groups in the matrix; at a probability level of greater than or equal to 0.95, 78% of them were correctly identified, 2.2% were misidentified, and 19.8% were not identified. Seventeen strains represented two DNA groups not included in the matrix; nine of them were incorrectly assigned to a DNA group by these phenotypic tests. Because of problems of separating strains belonging to DNA groups 1, 2, 3, and 13 by using the phenotypic tests proposed by Bouvet and Grimont (Ann. Inst. Pasteur/Microbiol.), we suggest that these groups should be referred to as the Acinetobacter calcoaceticus-A. baumannii complex. PMID:2007635

  19. Comparative Genome Sequence Analysis of Multidrug-Resistant Acinetobacter baumannii▿ †

    PubMed Central

    Adams, Mark D.; Goglin, Karrie; Molyneaux, Neil; Hujer, Kristine M.; Lavender, Heather; Jamison, Jennifer J.; MacDonald, Ian J.; Martin, Kristienna M.; Russo, Thomas; Campagnari, Anthony A.; Hujer, Andrea M.; Bonomo, Robert A.; Gill, Steven R.

    2008-01-01

    The recent emergence of multidrug resistance (MDR) in Acinetobacter baumannii has raised concern in health care settings worldwide. In order to understand the repertoire of resistance determinants and their organization and origins, we compared the genome sequences of three MDR and three drug-susceptible A. baumannii isolates. The entire MDR phenotype can be explained by the acquisition of discrete resistance determinants distributed throughout the genome. A comparison of closely related MDR and drug-susceptible isolates suggests that drug efflux may be a less significant contributor to resistance to certain classes of antibiotics than inactivation enzymes are. A resistance island with a variable composition of resistance determinants interspersed with transposons, integrons, and other mobile genetic elements is a significant but not universal contributor to the MDR phenotype. Four hundred seventy-five genes are shared among all six clinical isolates but absent from the related environmental species Acinetobacter baylyi ADP1. These genes are enriched for transcription factors and transporters and suggest physiological features of A. baumannii that are related to adaptation for growth in association with humans. PMID:18931120

  20. Species identification within Acinetobacter calcoaceticus-baumannii complex using MALDI-TOF MS.

    PubMed

    Toh, Benjamin E W; Paterson, David L; Kamolvit, Witchuda; Zowawi, Hosam; Kvaskoff, David; Sidjabat, Hanna; Wailan, Alexander; Peleg, Anton Y; Huber, Charlotte A

    2015-11-01

    Acinetobacter baumannii, one of the more clinically relevant species in the Acinetobacter genus is well known to be multi-drug resistant and associated with bacteremia, urinary tract infection, pneumonia, wound infection and meningitis. However, it cannot be differentiated from closely related species such as Acinetobacter calcoaceticus, Acinetobacter pittii and Acinetobacter nosocomialis by most phenotypic tests and can only be differentiated by specific, time consuming genotypic tests with very limited use in clinical microbiological laboratories. As a result, these species are grouped into the A. calcoaceticus-A. baumannii (Acb) complex. Herein we investigated the mass spectra of 73 Acinetobacter spp., representing ten different species, using an AB SCIEX 5800 MALDI-TOF MS to differentiate members of the Acinetobacter genus, including the species of the Acb complex. RpoB gene sequencing, 16S rRNA sequencing, and gyrB multiplex PCR were also evaluated as orthogonal methods to identify the organisms used in this study. We found that whilst 16S rRNA and rpoB gene sequencing could not differentiate A. pittii or A. calcoaceticus, they can be differentiated using gyrB multiplex PCR and MALDI-TOF MS. All ten Acinetobacter species investigated could be differentiated by their MALDI-TOF mass spectra.

  1. Pathogenic Acinetobacter Species have a Functional Type I Secretion System and Contact-Dependent Inhibition Systems.

    PubMed

    Harding, Christian M; Pulido, Marina R; Di Venanzio, Gisela; Kinsella, Rachel L; Webb, Andrew I; Scott, Nichollas E; Pachón, Jerónimo; Feldman, Mario F

    2017-04-03

    Pathogenic Acinetobacter species, including A. baumannii and A. nosocomialis, are opportunistic human pathogens of increasing relevance worldwide. Although their mechanisms of drug resistance are well studied, the virulence factors that govern Acinetobacter pathogenesis are incompletely characterized. Here we define the complete secretome of A. nosocomialis strain M2 in minimal media and demonstrate that pathogenic Acinetobacter species produce both a functional type I secretion system (T1SS) and a contact dependent inhibition (CDI) system. Using bioinformatics, quantitative proteomics, and mutational analyses we show that Acinetobacter uses its T1SS for exporting two putative T1SS effectors, an RTX-Serralysin-like toxin and the biofilm associated protein (Bap). Moreover, we found that mutation of any component of the T1SS system abrogated type VI secretion activity under nutrient-limited conditions, indicating a previously unrecognized crosstalk between these two systems. We also demonstrate that the Acinetobacter T1SS is required for biofilm formation. Lastly, we show that both A. nosocomialis and A. baumannii produce functioning CDI systems that mediate growth inhibition of sister cells lacking the cognate immunity protein. The Acinetobacter CDI systems are widely distributed across pathogenic Acinetobacter species, with many A. baumannii isolates harboring two distinct CDI systems. Collectively, these data demonstrate the power of differential, quantitative proteomics approaches to study secreted proteins, define the role of previously uncharacterized protein export systems, and observe crosstalk between secretion systems in the pathobiology of medically relevant Acinetobacter The data are available via ProteomeXchange with identifier PXD005881.

  2. Complete Genome Sequence and Methylome Analysis of Acinetobacter calcoaceticus 65

    PubMed Central

    Fomenkov, Alexey; Vincze, Tamas; Degtyarev, Sergey K.

    2017-01-01

    ABSTRACT Acinetobacter calcoaceticus 65 is the original source strain for the restriction enzyme Acc65I. Its complete sequence and full methylome were determined using single-molecule real-time (SMRT) sequencing. PMID:28336599

  3. Improvement of MALDI-TOF MS profiling for the differentiation of species within the Acinetobacter calcoaceticus-Acinetobacter baumannii complex.

    PubMed

    Šedo, Ondrej; Nemec, Alexandr; Křížová, Lenka; Kačalová, Magdaléna; Zdráhal, Zbyněk

    2013-12-01

    MALDI-TOF MS is currently becoming the method of choice for rapid identification of bacterial species in routine diagnostics. Yet, this method suffers from the inability to differentiate reliably between some closely related bacterial species including those of the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex, namely A. baumannii and Acinetobacter nosocomialis. In the present study, we evaluated a protocol which was different from that used in the Bruker Daltonics identification system (MALDI BioTyper) to improve species identification using a taxonomically precisely defined set of 105 strains representing the four validly named species of the ACB complex. The novel protocol is based on the change in matrix composition from alpha-cyano-4-hydroxycinnamic acid (saturated solution in water:acetonitrile:trifluoroacetic acid, 47.5:50:2.5, v/v) to ferulic acid (12.5mgml(-1) solution in water:acetonitrile:formic acid 50:33:17, v/v), while the other steps of sample processing remain unchanged. Compared to the standard protocol, the novel one extended the range of detected compounds towards higher molecular weight, produced signals with better mass resolution, and allowed the detection of species-specific signals. As a result, differentiation of A. nosocomialis and A. baumannii strains by cluster analysis was improved and 13 A. nosocomialis strains, assigned erroneously or ambiguously by using the standard protocol, were correctly identified.

  4. Draft Genome Sequences of Acinetobacter baumannii Isolates from Wounded Military Personnel.

    PubMed

    Arivett, Brock A; Ream, Dave C; Fiester, Steven E; Kidane, Destaalem; Actis, Luis A

    2016-08-25

    Acinetobacter baumannii is a Gram-negative bacterium capable of causing hospital-acquired infections that has been grouped with Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species as ESKAPE pathogens because of their extensive drug resistance phenotypes and increasing risk to human health. Twenty-four multidrug-resistant A. baumannii strains isolated from wounded military personnel were sequenced and annotated.

  5. Acinetobacter Species Infections among Navy and Marine Corps Beneficiaries: 2014 Annual Report

    DTIC Science & Technology

    2015-07-20

    Acinetobacter Species Infections among Navy and Marine Corps Beneficiaries: 2014 Annual Report NMCPHC-EDC-TR-371-2015 By Paul...TITLE AND SUBTITLE 5a. CONTRACT NUMBER Acinetobacter Species Infections among Navy and Marine Corps Beneficiaries: 2014 Annual Report 5b. GRANT...ORGANIZATION NAME(SI AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT Navy and Marine Corps Public Health Center NUMBER EpiData Center Department

  6. Characterisation and genome sequence of the lytic Acinetobacter baumannii bacteriophage vB_AbaS_Loki.

    PubMed

    Turner, Dann; Wand, Matthew E; Briers, Yves; Lavigne, Rob; Sutton, J Mark; Reynolds, Darren M

    2017-01-01

    Acinetobacter baumannii has emerged as an important nosocomial pathogen in healthcare and community settings. While over 100 of Acinetobacter phages have been described in the literature, relatively few have been sequenced. This work describes the characterisation and genome annotation of a new lytic Acinetobacter siphovirus, vB_AbaS_Loki, isolated from activated sewage sludge. Sequencing revealed that Loki encapsulates a 41,308 bp genome, encoding 51 predicted open reading frames. Loki is most closely related to Acinetobacter phage IME_AB3 and more distantly related to Burkholderia phage KL1, Paracoccus phage vB_PmaS_IMEP1 and Pseudomonas phages vB_Pae_Kakheti25, vB_PaeS_SCH_Ab26 and PA73. Loki is characterised by a narrow host range, among the 40 Acinetobacter isolates tested, productive infection was only observed for the propagating host, A. baumannii ATCC 17978. Plaque formation was found to be dependent upon the presence of Ca2+ ions and adsorption to host cells was abolished upon incubation with a mutant of ATCC 17978 encoding a premature stop codon in lpxA. The complete genome sequence of vB_AbaS_Loki was deposited in the European Nucleotide Archive (ENA) under the accession number LN890663.

  7. Characterisation and genome sequence of the lytic Acinetobacter baumannii bacteriophage vB_AbaS_Loki

    PubMed Central

    Wand, Matthew E.; Briers, Yves; Lavigne, Rob; Sutton, J. Mark; Reynolds, Darren M.

    2017-01-01

    Acinetobacter baumannii has emerged as an important nosocomial pathogen in healthcare and community settings. While over 100 of Acinetobacter phages have been described in the literature, relatively few have been sequenced. This work describes the characterisation and genome annotation of a new lytic Acinetobacter siphovirus, vB_AbaS_Loki, isolated from activated sewage sludge. Sequencing revealed that Loki encapsulates a 41,308 bp genome, encoding 51 predicted open reading frames. Loki is most closely related to Acinetobacter phage IME_AB3 and more distantly related to Burkholderia phage KL1, Paracoccus phage vB_PmaS_IMEP1 and Pseudomonas phages vB_Pae_Kakheti25, vB_PaeS_SCH_Ab26 and PA73. Loki is characterised by a narrow host range, among the 40 Acinetobacter isolates tested, productive infection was only observed for the propagating host, A. baumannii ATCC 17978. Plaque formation was found to be dependent upon the presence of Ca2+ ions and adsorption to host cells was abolished upon incubation with a mutant of ATCC 17978 encoding a premature stop codon in lpxA. The complete genome sequence of vB_AbaS_Loki was deposited in the European Nucleotide Archive (ENA) under the accession number LN890663. PMID:28207864

  8. Genomic definition of species

    SciTech Connect

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  9. Draft Genome Sequence of a Multidrug-Resistant Acinetobacter baumannii Strain from Chile.

    PubMed

    Opazo, Andrés; Lopes, Bruno S; García, Patricia; Domínguez Yévenes, Mariana; Lima, Celia; Bello-Toledo, Helia; González-Rocha, Gerardo; Amyes, Sebastian G B

    2015-07-02

    Acinetobacter baumannii strain Ab5 was isolated in the year 2007 in Chile, being one of the first multidrug-resistant (MDR) cases reported in the country. Here, we present the very first draft genome sequence of an MDR Chilean strain, which shows the presence of diverse resistance and acquired virulence genes.

  10. Draft Genome Sequence of a Multidrug-Resistant Acinetobacter baumannii Strain from Chile

    PubMed Central

    Lopes, Bruno S.; García, Patricia; Domínguez Yévenes, Mariana; Lima, Celia; Bello-Toledo, Helia; González-Rocha, Gerardo; Amyes, Sebastian G. B.

    2015-01-01

    Acinetobacter baumannii strain Ab5 was isolated in the year 2007 in Chile, being one of the first multidrug-resistant (MDR) cases reported in the country. Here, we present the very first draft genome sequence of an MDR Chilean strain, which shows the presence of diverse resistance and acquired virulence genes. PMID:26139713

  11. Draft Genome Sequences of Clinical Isolates of Multidrug-Resistant Acinetobacter baumannii

    PubMed Central

    Erickson, Keesha E.; Madinger, Nancy E.

    2017-01-01

    ABSTRACT We report here the draft genome sequences of two clinically isolated Acinetobacter baumannii strains. These samples were obtained from patients at the University of Colorado Hospital in 2007 and 2013 and encode an estimated 20 and 13 resistance genes, respectively. PMID:28153899

  12. Whole-Genome Sequencing Elucidates Epidemiology of Nosocomial Clusters of Acinetobacter baumannii

    PubMed Central

    Willems, Stefanie; Kampmeier, Stefanie; Bletz, Stefan; Kossow, Annelene; Köck, Robin; Kipp, Frank

    2016-01-01

    We characterized two epidemiologically similar Acinetobacter baumannii clusters from two separate intensive care units (ICU) using core genome multilocus sequence typing. Clonal spread was confirmed in ICU-1 (12 of 14 isolates shared genotypes); in ICU-2, all genotypes (13 isolates) were diverse, thus excluding transmissions and enabling adequate infection control measures. PMID:27358465

  13. Complete Genome Sequence of Lytic Bacteriophage LZ35 Infecting Acinetobacter baumannii Isolates

    PubMed Central

    Guo, Zhonghe; Huang, Honglan; Wu, Xiaolin; Hao, Yuchong

    2016-01-01

    Acinetobacter baumannii is a Gram-negative opportunistic pathogen that is frequently associated with nosocomial infections. Bacteriophages infecting A. baumannii can be used as effective agents to control these infections. Here, we announce the complete genome sequence of the lytic bacteriophage LZ35 infecting A. baumannii isolates. PMID:27856573

  14. Acinetobacter Species Infections Among Navy and Marine Corps Beneficiaries: 2013 Annual Report

    DTIC Science & Technology

    2014-11-19

    the propagation of Acinetobacter, which flourishes in warm , humid environments . 3,5-7 DON and DOD rates peaked during the summer months (June-August...locations of the MCRDs. Another contributing factor to the high Marine recruit prevalence could be related to the unique environmental conditions...Acinetobacter Species Infections among Navy and Marine Corps Beneficiaries: 2013 Annual Report NMCPHC-EDC-TR-168-2014 By Paul Meddaugh and

  15. Draft Genome Sequence of the Biofilm-Hyperproducing Acinetobacter baumannii Clinical Strain MAR002

    PubMed Central

    Álvarez-Fraga, Laura; López, María; Merino, María; Rumbo-Feal, Soraya; Tomás, María

    2015-01-01

    We report the draft genome sequence of Acinetobacter baumannii strain MAR002, a biofilm-hyperproducing clinical strain isolated during the study CP/09/0033 (GEIH/REIPI-Ab2010, Spain). The genome of A. baumannii MAR002 has an approximate length of 3,717,929 bp and 3,300 protein-coding sequences, with a C+G content of 39.09%. PMID:26205868

  16. Draft Genome Sequence of Ammonia-Producing Acinetobacter sp. Strain MCC2139 from Dairy Effluent

    PubMed Central

    Chatterjee, Debasmita; Thakur, Ashoke Ranjan

    2013-01-01

    We report the draft genome sequence of an ammonia-producing, esculin-hydrolyzing, catalase-positive, gram-negative bacterium, Acinetobacter sp. strain MCC2139. This bacterium, isolated from dairy sludge and with optimum growth at 37°C, has a genome size of 2,967,280 bp with a G+C content of 42.3%. PMID:23814111

  17. Antibiotic susceptibility of Acinetobacter species in intensive care unit in Montenegro.

    PubMed

    Mijovic, Gordana; Pejakov, Ljubica; Vujosevic, Danijela

    2016-08-01

    The global increase in multidrug resistance of Acinetobacter has created widespread problems in the treatment of patients in intensive care units (ICUs). The aim of this study was to assess the current level of antimicrobial susceptibility of Acinetobacter species in ICU of Clinical Centre of Montenegro and determine their epidemiology. Antibiotic susceptibility was tested in 70 isolates of Acinetobacter collected from non-repeating samples taken from 40 patients. The first nine isolates were genotyped by repetitive sequence-based PCR (rep-PCR). Tigecycline was found to be the most active antimicrobial agent with 80.6% of susceptibility. All the isolates were multidrug resistant with fully resistance to cefalosporinas, piperacillin and piperacillin/tazobactam. More than half of them (58.5%) were probably extensively resistant. Seven out of nine examined strains were clonally related by rep-PCR. Our results showed extremely high rate of multidrug resistance (MDR) of Acinetobacter isolates and high percentage of its clonally spreading.

  18. Genomic sequencing of a strain of Acinetobacter baumannii and potential mechanisms to antibiotics resistance.

    PubMed

    Zhao, Lei; Li, Hongru; Zhu, Ziwen; Wakefield, Mark R; Fang, Yujiang; Ye, Ying

    2017-02-09

    Acinetobacter baumannii has been becoming a great challenge to clinicians due to their resistance to almost all available antibiotics. In this study, we sequenced the genome from a multiple antibiotics resistant Acinetobacter baumannii stain which was named A. baumannii-1isolated from China by SMRT sequencing technology to explore its potential mechanisms to antibiotic resistance. We found that several mechanisms might contribute to the antibiotic resistance of Acinetobacter baumannii. Specifically, we found that SNP in genes associated with nucleotide excision repair and ABC transporter might contribute to its resistance to multiple antibiotics; we also found that specific genes associated with bacterial DNA integration and recombination, DNA-mediated transposition and response to antibiotics might contribute to its resistance to multiple antibiotics; Furthermore, specific genes associated with penicillin and cephalosporin biosynthetic pathway and specific genes associated with CHDL and MBL β-lactamase genes might contribute to its resistance to multiple antibiotics. Thus, the detailed mechanisms by which Acinetobacter baumannii show extensive resistance to multiple antibiotics are very complicated. Such a study might be helpful to develop new strategies to control Acinetobacter baumannii infection.

  19. Antimicrobial susceptibility profile of Acinetobacter species isolated from blood cultures in two Japanese university hospitals.

    PubMed

    Kishii, Kozue; Kikuchi, Ken; Yoshida, Atsushi; Okuzumi, Katsuko; Uetera, Yushi; Yasuhara, Hiroshi; Moriya, Kyoji

    2014-02-01

    Carbapenem-resistant Acinetobacter baumannii has rapidly spread worldwide. This study investigated antibiotic susceptibility and genotypic resistance of 123 consecutive blood culture isolates of Acinetobacter species collected between 2003 and 2011 in two Japanese hospitals. The isolates were assigned to 13 species. Carbapenem resistance was detected in four isolates. Only one A. baumannii isolate had blaOXA-23 together with ISAba1; the remaining three isolates had IMP-1 metallo-β-lactamase. Quinolone resistance was detected in five isolates that had point mutations in the quinolone resistance-determining region. The predominance of various non-A. baumannii species and low prevalence of carbapenem resistance among blood culture isolates of Acinetobacter species in two Japanese hospitals were confirmed.

  20. Variation in the OC Locus of Acinetobacter baumannii Genomes Predicts Extensive Structural Diversity in the Lipooligosaccharide

    PubMed Central

    Kenyon, Johanna J.; Nigro, Steven J.; Hall, Ruth M.

    2014-01-01

    Lipooligosaccharide (LOS) is a complex surface structure that is linked to many pathogenic properties of Acinetobacter baumannii. In A. baumannii, the genes responsible for the synthesis of the outer core (OC) component of the LOS are located between ilvE and aspS. The content of the OC locus is usually variable within a species, and examination of 6 complete and 227 draft A. baumannii genome sequences available in GenBank non-redundant and Whole Genome Shotgun databases revealed nine distinct new types, OCL4-OCL12, in addition to the three known ones. The twelve gene clusters fell into two distinct groups, designated Group A and Group B, based on similarities in the genes present. OCL6 (Group B) was unique in that it included genes for the synthesis of L-Rhamnosep. Genetic exchange of the different configurations between strains has occurred as some OC forms were found in several different sequence types (STs). OCL1 (Group A) was the most widely distributed being present in 18 STs, and OCL6 was found in 16 STs. Variation within clones was also observed, with more than one OC locus type found in the two globally disseminated clones, GC1 and GC2, that include the majority of multiply antibiotic resistant isolates. OCL1 was the most abundant gene cluster in both GC1 and GC2 genomes but GC1 isolates also carried OCL2, OCL3 or OCL5, and OCL3 was also present in GC2. As replacement of the OC locus in the major global clones indicates the presence of sub-lineages, a PCR typing scheme was developed to rapidly distinguish Group A and Group B types, and to distinguish the specific forms found in GC1 and GC2 isolates. PMID:25247305

  1. Acinetobacter species as model microorganisms in environmental microbiology: current state and perspectives.

    PubMed

    Jung, Jaejoon; Park, Woojun

    2015-03-01

    Acinetobacter occupies an important position in nature because of its ubiquitous presence in diverse environments such as soils, fresh water, oceans, sediments, and contaminated sites. Versatile metabolic characteristics allow species of this genus to catabolize a wide range of natural compounds, implying active participation in the nutrient cycle in the ecosystem. On the other hand, multi-drug-resistant Acinetobacter baumannii causing nosocomial infections with high mortality has been raising serious concerns in medicine. Due to the ecological and clinical importance of the genus, Acinetobacter was proposed as a model microorganism for environmental microbiological studies, pathogenicity tests, and industrial production of chemicals. For these reasons, Acinetobacter has attracted significant attention in scientific and biotechnological fields, but only limited research areas such as natural transformation and aromatic compound degradation have been intensively investigated, while important physiological characteristics including quorum sensing, motility, and stress response have been neglected. The aim of this review is to summarize the recent achievements in Acinetobacter research with a special focus on strain DR1 and to compare the similarities and differences between species or other genera. Research areas that require more attention in future research are also suggested.

  2. Biofilm formation at the solid-liquid and air-liquid interfaces by Acinetobacter species

    PubMed Central

    2011-01-01

    Background The members of the genus Acinetobacter are Gram-negative cocobacilli that are frequently found in the environment but also in the hospital setting where they have been associated with outbreaks of nosocomial infections. Among them, Acinetobacter baumannii has emerged as the most common pathogenic species involved in hospital-acquired infections. One reason for this emergence may be its persistence in the hospital wards, in particular in the intensive care unit; this persistence could be partially explained by the capacity of these microorganisms to form biofilm. Therefore, our main objective was to study the prevalence of the two main types of biofilm formed by the most relevant Acinetobacter species, comparing biofilm formation between the different species. Findings Biofilm formation at the air-liquid and solid-liquid interfaces was investigated in different Acinetobacter spp. and it appeared to be generally more important at 25°C than at 37°C. The biofilm formation at the solid-liquid interface by the members of the ACB-complex was at least 3 times higher than the other species (80-91% versus 5-24%). In addition, only the isolates belonging to this complex were able to form biofilm at the air-liquid interface; between 9% and 36% of the tested isolates formed this type of pellicle. Finally, within the ACB-complex, the biofilm formed at the air-liquid interface was almost 4 times higher for A. baumannii and Acinetobacter G13TU than for Acinetobacter G3 (36%, 27% & 9% respectively). Conclusions Overall, this study has shown the capacity of the Acinetobacter spp to form two different types of biofilm: solid-liquid and air-liquid interfaces. This ability was generally higher at 25°C which might contribute to their persistence in the inanimate hospital environment. Our work has also demonstrated for the first time the ability of the members of the ACB-complex to form biofilm at the air-liquid interface, a feature that was not observed in other

  3. Genomics of Bacillus Species

    NASA Astrophysics Data System (ADS)

    Økstad, Ole Andreas; Kolstø, Anne-Brit

    Members of the genus Bacillus are rod-shaped spore-forming bacteria belonging to the Firmicutes, the low G+C gram-positive bacteria. The Bacillus genus was first described and classified by Ferdinand Cohn in Cohn (1872), and Bacillus subtilis was defined as the type species (Soule, 1932). Several Bacilli may be linked to opportunistic infections. However, pathogenicity among Bacillus spp. is mainly a feature of bacteria belonging to the Bacillus cereus group, including B. cereus, Bacillus anthracis, and Bacillus thuringiensis. Here we review the genomics of B. cereus group bacteria in relation to their roles as etiological agents of two food poisoning syndromes (emetic and diarrhoeal).

  4. Genomic and functional analysis of the type VI secretion system in Acinetobacter.

    PubMed

    Weber, Brent S; Miyata, Sarah T; Iwashkiw, Jeremy A; Mortensen, Brittany L; Skaar, Eric P; Pukatzki, Stefan; Feldman, Mario F

    2013-01-01

    The genus Acinetobacter is comprised of a diverse group of species, several of which have raised interest due to potential applications in bioremediation and agricultural purposes. In this work, we show that many species within the genus Acinetobacter possess the genetic requirements to assemble a functional type VI secretion system (T6SS). This secretion system is widespread among Gram negative bacteria, and can be used for toxicity against other bacteria and eukaryotic cells. The most studied species within this genus is A. baumannii, an emerging nosocomial pathogen that has become a significant threat to healthcare systems worldwide. The ability of A. baumannii to develop multidrug resistance has severely reduced treatment options, and strains resistant to most clinically useful antibiotics are frequently being isolated. Despite the widespread dissemination of A. baumannii, little is known about the virulence factors this bacterium utilizes to cause infection. We determined that the T6SS is conserved and syntenic among A. baumannii strains, although expression and secretion of the hallmark protein Hcp varies between strains, and is dependent on TssM, a known structural protein required for T6SS function. Unlike other bacteria, A. baumannii ATCC 17978 does not appear to use its T6SS to kill Escherichia coli or other Acinetobacter species. Deletion of tssM does not affect virulence in several infection models, including mice, and did not alter biofilm formation. These results suggest that the T6SS fulfils an important but as-yet-unidentified role in the various lifestyles of the Acinetobacter spp.

  5. Unravelling the genome of long chain N-acylhomoserine lactone-producing Acinetobacter sp. strain GG2 and identification of its quorum sensing synthase gene

    PubMed Central

    How, Kah Yan; Hong, Kar-Wai; Sam, Choon-Kook; Koh, Chong-Lek; Yin, Wai-Fong; Chan, Kok-Gan

    2015-01-01

    Myriad proteobacteria use N-acyl homoserine lactone (AHL) molecules as quorum sensing (QS) signals to regulate different physiological functions, including virulence, antibiotic production, and biofilm formation. Many of these proteobacteria possess LuxI/LuxR system as the QS mechanism. Recently, we reported the 3.89 Mb genome of Acinetobacter sp. strain GG2. In this work, the genome of this long chain AHL-producing bacterium was unravelled which led to the molecular characterization of luxI homologue, designated as aciI. This 552 bp gene was cloned and overexpressed in Escherichia coli BL21(DE3). The purified protein was ∼20.5 kDa and is highly similar to several autoinducer proteins of LuxI family among Acinetobacter species. To verify the AHL synthesis activity of this protein, high-resolution liquid chromatography–mass spectrometry analysis revealed the production of 3-oxo-dodecanoyl-homoserine lactone and 3-hydroxy-dodecanoyl-homoserine lactone from induced E. coli harboring the recombinant AciI. Our data show for the first time, the cloning and characterization of the luxI homologue from Acinetobacter sp. strain GG2, and confirmation of its AHLs production. These data are of great significance as the annotated genome of strain GG2 has provided a valuable insight in the study of autoinducer molecules and its roles in QS mechanism of the bacterium. PMID:25926817

  6. Using Vitek MALDI-TOF mass spectrometry to identify species belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii complex: a relevant alternative to molecular biology?

    PubMed

    Pailhoriès, Hélène; Daure, Sophie; Eveillard, Matthieu; Joly-Guillou, Marie-Laure; Kempf, Marie

    2015-10-01

    Acinetobacter baumannii belongs to the Acinetobacter calcoaceticus-baumannii complex (Acb) containing 2 other pathogenic species: Acinetobacter pittii and Acinetobacter nosocomialis. Identification of these bacteria remains problematic despite the use of matrix-assisted laser ionization time-of-flight mass spectrometry (MALDI-TOF MS). Here, we enriched the SARAMIS™ database of the Vitek MS® plus mass spectrometer to improve the identification of species of the Acb complex. For each species, we incremented reference spectra. Then, a SuperSpectrum was created based on the selection of 40 specific masses. In a second step, we validated reference spectra and SuperSpectra with 100 isolates identified by rpoB gene sequencing. All the isolates were correctly identified by MALDI-TOF MS with the database we created as compared to the identifications obtained by rpoB sequencing. Our database enabled rapid and reliable identification of the pathogen species belonging to the Acb complex. Identification by MALDI-TOF MS with our database is a good alternative to molecular biology.

  7. Resources for Genetic and Genomic Analysis of Emerging Pathogen Acinetobacter baumannii

    PubMed Central

    Ramage, Elizabeth; Weiss, Eli J.; Radey, Matthew; Hayden, Hillary S.; Held, Kiara G.; Huse, Holly K.; Zurawski, Daniel V.; Brittnacher, Mitchell J.; Manoil, Colin

    2015-01-01

    ABSTRACT Acinetobacter baumannii is a Gram-negative bacterial pathogen notorious for causing serious nosocomial infections that resist antibiotic therapy. Research to identify factors responsible for the pathogen's success has been limited by the resources available for genome-scale experimental studies. This report describes the development of several such resources for A. baumannii strain AB5075, a recently characterized wound isolate that is multidrug resistant and displays robust virulence in animal models. We report the completion and annotation of the genome sequence, the construction of a comprehensive ordered transposon mutant library, the extension of high-coverage transposon mutant pool sequencing (Tn-seq) to the strain, and the identification of the genes essential for growth on nutrient-rich agar. These resources should facilitate large-scale genetic analysis of virulence, resistance, and other clinically relevant traits that make A. baumannii a formidable public health threat. IMPORTANCE Acinetobacter baumannii is one of six bacterial pathogens primarily responsible for antibiotic-resistant infections that have become the scourge of health care facilities worldwide. Eliminating such infections requires a deeper understanding of the factors that enable the pathogen to persist in hospital environments, establish infections, and resist antibiotics. We present a set of resources that should accelerate genome-scale genetic characterization of these traits for a reference isolate of A. baumannii that is highly virulent and representative of current outbreak strains. PMID:25845845

  8. [Acinetobacter spp].

    PubMed

    Matsunaga, Naohisa

    2012-02-01

    Acinetobacter species are aerobic, glucose non-fermenting gram-negative rods, and ubiquitous in the environment. Acinetobacter spp. can survive for months on dry surfaces. Acinetobacter spp. have been grown from skin, pharynx, sputum, urine and feces. The most common Acinetobacter infection is pneumonia. According to Japan Nosocomial Infection Surveillance, 0.34% of the Acinetobacter spp. was multidrug-resistant in 2010. In Japan, Acinetobacter spp. whose imipenem MICs were > or = 16 microg/mL, amikacin > or = 32 microg/mL, and ciprofloxacin > or = 4 microg/mL were defined as multidrug-resistant Acinetobacter species (MDRA) in 2011 in the amended Infectious Diseases Control Law. Break-point Checkerboard Plate can help to infer an effective combination antimicrobial therapy. A selective medium for the isolation of MDRA is a great tool for active surveillance cultures. Treatment options for MDRA infections in Japan are very limited, because colistin, polymyxin B, or tigecycline is not approved. Keys to control MDRA are high levels of compliance with standard and contact precautions, appropriate cleaning and disinfection of the environment, and judicious antimicrobial use.

  9. Prevalence, genomic and metabolic profiles of Acinetobacter and Asaia associated with field-caught Aedes albopictus from Madagascar.

    PubMed

    Minard, Guillaume; Tran, Florence Hélène; Raharimalala, Fara Nantenaina; Hellard, Eléonore; Ravelonandro, Pierre; Mavingui, Patrick; Valiente Moro, Claire

    2013-01-01

    The presence of cultivable bacteria Acinetobacter and Asaia was recently demonstrated in the mosquito vector Aedes albopictus. However, it is not known how prevalent these bacteria are in field populations. Here, the presence of these bacteria in Ae. albopictus populations from Madagascar was diagnosed by amplification of 16S rRNA gene fragments. Both genera were detected at relatively high frequencies, 46% for Asaia and 74% for Acinetobacter. The prevalence of Acinetobacter correlated significantly with mosquito gender, and the prevalence of Asaia with the interaction between mosquito gender and the sampling site. For each bacterial genus, more male than female mosquitoes were infected. Using pulse field gel electrophoresis, no significant difference in genome size was found between Acinetobacter isolates from mosquitoes compared with free-living Acinetobacter. However, a great diversity was observed in plasmid numbers (from 1 to 12) and sizes (from < 8 to 690 kb). Mosquito isolates utilized fewer substrates than free-living isolates, but some substrates known as blood or plant components were specifically utilized by mosquito isolates. Therefore it is likely that a specific subpopulation of Acinetobacter is selected by Ae. albopictus. Overall, this study emphasizes the need to gain a global view on the bacterial partners in mosquito vectors.

  10. Antimicrobial susceptibility pattern in nosocomial infections caused by Acinetobacter species in Asir Region, Saudi Arabia.

    PubMed

    Abdalla, Nazar M; Osman, Amani A; Haimour, Waleed O; Sarhan, Mohammed A A; Mohammed, Mohammed N; Zyad, Eyhab M; Al-Ghtani, Abdalla M

    2013-03-15

    This study aimed at evaluating the sensitivity of antibiotics towards nosocomial infections caused by Acinetobacter species. The study took place during the period Dec. 2011- Dec. 2012 at Assir Central Hospital in collaboration with the department of microbiology, college of medicine, King Khalid University, Abha. A prospective study involving 150 patients presented with nosocomial infections due to Acinetobacter species detected by bacteriological tests; direct microscopy, culture in blood agar media, fermentation test in MacConkey media and MIC (minimum inhibitory concentration) for antibiotics sensitivity using Muller Hinton media and Chemical test using API 20. A 150 nosocomial infections in this study showed gram-negative coccobacilli, non motile, glucose-negative fermentor and oxidase negative. All isolates showed 100% sensitivity to: Imipramine, Meropenem, Colistin. From the rest of tested antibiotics the higher resistant ones were; Nitrofurantoin 87% and Cefoxitin 85%. The least resistant antibiotics; Imipenem 3% and Ticarcillin 7%. While variable resistance in the rest of tested antimicrobials. A 47 patients (31.3%) have used antibiotics prior to this study. The high rate of usage occurred in elder patients. The frequency of Acinetobacter calcoaceticus baumannii complex multi-drugs resistance ABCMDR is rising including almost all commonly used antibiotics. Only few antibiotics exert 100% sensitivity towards these bacteria.

  11. Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1

    PubMed Central

    Hamidian, Mohammad; Hawkey, Jane

    2015-01-01

    Multiply antibiotic-resistant Acinetobacter baumannii isolate D36 was recovered in Australia in 2008 and belongs to a distinct lineage of global clone 1 (GC1). Here, we present the complete 4.13 Mbp genome sequence (chromosome plus 4 plasmids), generated via long read sequencing (PacBio). PMID:26679588

  12. Draft Genome Sequences of Seven Multidrug-Resistant Acinetobacter baumannii Strains, Isolated from Respiratory Samples in Spain

    PubMed Central

    Labrador-Herrera, Gema; Álvarez, Rocío; López-Rojas, Rafael; Smani, Younes; Cebrero-Cangueiro, Tania; Rueda, Antonio; Pérez Florido, Javier; Pachón-Ibáñez, María Eugenia

    2016-01-01

    The draft genome sequences of seven multidrug-resistant Acinetobacter baumannii clinical strains belonging to sequence types ST-208 and ST-218 are reported in this study. They were isolated from tracheobronchial aspirate of mechanically ventilated adult patients admitted to the intensive care unit of a Spanish tertiary hospital during 2010 to 2011. PMID:27034482

  13. Complete Genome Sequence of a Multidrug-Resistant Acinetobacter baumannii Isolate Obtained from a Mexican Hospital (Sequence Type 422)

    PubMed Central

    Castro-Jaimes, Semiramis; Salgado-Camargo, Abraham David; Graña-Miraglia, Lucía; Lozano, Luis; Bocanegra-Ibarias, Paola; Volkow-Fernández, Patricia; Silva-Sanchez, Jesus; Castillo-Ramírez, Santiago

    2016-01-01

    Acinetobacter baumannii has emerged as a dangerous nosocomial pathogen, particularly for severely ill patients in intensive care units and patients with hematologic malignancies. Here, we present the complete genome sequence of a multidrug-resistant A. baumannii isolate, recovered from a Mexican hospital and classified as sequence type 422 according to the multilocus sequence typing Pasteur scheme. PMID:27340065

  14. Genome Sequence of vB_AbaS_TRS1, a Viable Prophage Isolated from Acinetobacter baumannii Strain A118

    PubMed Central

    Turner, Dann; Wand, Matthew E.; Sutton, J. Mark; Centron, Daniela; Kropinski, Andrew M.

    2016-01-01

    A novel temperate phage, vB_AbaS_TRS1, was isolated from cultures of Acinetobacter baumannii strain A118 that had been exposed to mitomycin C. Phage TRS1 belongs to the Siphoviridae family of bacteriophages and encapsulates a 40,749-bp genome encoding 70 coding sequences and a single tRNA. PMID:27738026

  15. Genome Sequence of vB_AbaS_TRS1, a Viable Prophage Isolated from Acinetobacter baumannii Strain A118.

    PubMed

    Turner, Dann; Wand, Matthew E; Sutton, J Mark; Centron, Daniela; Kropinski, Andrew M; Reynolds, Darren M

    2016-10-13

    A novel temperate phage, vB_AbaS_TRS1, was isolated from cultures of Acinetobacter baumannii strain A118 that had been exposed to mitomycin C. Phage TRS1 belongs to the Siphoviridae family of bacteriophages and encapsulates a 40,749-bp genome encoding 70 coding sequences and a single tRNA.

  16. Whole-genome sequence analysis of the naturally competent Acinetobacter baumannii clinical isolate A118.

    PubMed

    Traglia, German M; Chua, Katherina; Centrón, Daniela; Tolmasky, Marcelo E; Ramírez, María Soledad

    2014-08-26

    Recent studies have demonstrated a high genomic plasticity in Acinetobacter baumannii, which may explain its high capacity to acquire multiple antibiotic resistance determinants and to survive in the hospital environment. Acinetobacter baumannii strain A118 (Ab A118) was isolated in the year 1995 from a blood culture of an intensive care unit patient. As this particular strain showed some peculiar characteristic such as being naturally competent and susceptible to numerous antibiotics, we performed whole-genome comparison (WGC) studies to gain insights into the nature and extent of the genomic differences. The Ab A118 genome is approximately 3,824 kb long with a 38.4% GC content and contains 3,520 coding sequences. WGC studies showed that the Ab A118 genome has 98% average nucleotide identity with that of A. baumannii ATCC 17978, and 96% average nucleotide identity with that of strains AYE and ACICU. At least 12 inversions, 275 insertions, and 626 deletions were identified when the Ab A118 genome was compared with those of strains ATCC 17978, AYE, and ACICU using MAUVE WGC. Multiple gene order arrangements were observed among the analyzed strains. MAUVE WGC analysis identified 19 conserved segments, known as locally colinear blocks. The number of single nucleotide polymorphisms found when comparing the Ab A118 genome with that of strains ATCC 17978, AYE, and ACICU was 43,784 (1.1496%), 44,130 (1.158%), and 43,914 (1.153%), respectively. Genes comEA, pilQ, pilD, pilF, comL, pilA, comEC, pilI, pilH, pilO, pilN, pilY1(comC), pilE, pilR, and comM, potentially involved in natural competence were found in the Ab A118 genome. In particular, unlike in most strains where comM is interrupted by an insertion of a resistance island (AbaR), in strain Ab A118 it is uninterrupted.

  17. Whole-Genome Sequence Analysis of the Naturally Competent Acinetobacter baumannii Clinical Isolate A118

    PubMed Central

    Traglia, German M.; Chua, Katherina; Centrón, Daniela; Tolmasky, Marcelo E.; Ramírez, María Soledad

    2014-01-01

    Recent studies have demonstrated a high genomic plasticity in Acinetobacter baumannii, which may explain its high capacity to acquire multiple antibiotic resistance determinants and to survive in the hospital environment. Acinetobacter baumannii strain A118 (Ab A118) was isolated in the year 1995 from a blood culture of an intensive care unit patient. As this particular strain showed some peculiar characteristic such as being naturally competent and susceptible to numerous antibiotics, we performed whole-genome comparison (WGC) studies to gain insights into the nature and extent of the genomic differences. The Ab A118 genome is approximately 3,824 kb long with a 38.4% GC content and contains 3,520 coding sequences. WGC studies showed that the Ab A118 genome has 98% average nucleotide identity with that of A. baumannii ATCC 17978, and 96% average nucleotide identity with that of strains AYE and ACICU. At least 12 inversions, 275 insertions, and 626 deletions were identified when the Ab A118 genome was compared with those of strains ATCC 17978, AYE, and ACICU using MAUVE WGC. Multiple gene order arrangements were observed among the analyzed strains. MAUVE WGC analysis identified 19 conserved segments, known as locally colinear blocks. The number of single nucleotide polymorphisms found when comparing the Ab A118 genome with that of strains ATCC 17978, AYE, and ACICU was 43,784 (1.1496%), 44,130 (1.158%), and 43,914 (1.153%), respectively. Genes comEA, pilQ, pilD, pilF, comL, pilA, comEC, pilI, pilH, pilO, pilN, pilY1(comC), pilE, pilR, and comM, potentially involved in natural competence were found in the Ab A118 genome. In particular, unlike in most strains where comM is interrupted by an insertion of a resistance island (AbaR), in strain Ab A118 it is uninterrupted. PMID:25164683

  18. Genomics of Salmonella Species

    NASA Astrophysics Data System (ADS)

    Canals, Rocio; McClelland, Michael; Santiviago, Carlos A.; Andrews-Polymenis, Helene

    Progress in the study of Salmonella survival, colonization, and virulence has increased rapidly with the advent of complete genome sequencing and higher capacity assays for transcriptomic and proteomic analysis. Although many of these techniques have yet to be used to directly assay Salmonella growth on foods, these assays are currently in use to determine Salmonella factors necessary for growth in animal models including livestock animals and in in vitro conditions that mimic many different environments. As sequencing of the Salmonella genome and microarray analysis have revolutionized genomics and transcriptomics of salmonellae over the last decade, so are new high-throughput sequencing technologies currently accelerating the pace of our studies and allowing us to approach complex problems that were not previously experimentally tractable.

  19. Whole-Genome Sequence of a Colombian Acinetobacter baumannii Strain, a Coproducer of OXA-72 and OXA-255-Like Carbapenemases

    PubMed Central

    Saavedra, Sandra Yamile; Prada-Cardozo, Diego; Pérez-Cardona, Hermes; Hidalgo, Andrea Melissa; González, María Nilse; Reguero, María T.; Valenzuela de Silva, Emilia M.; Mantilla, José R.; Falquet, Laurent; Barreto-Hernández, Emiliano; Duarte, Carolina

    2017-01-01

    ABSTRACT Colombian Acinetobacter baumannii strain ST920 was isolated from the sputum of a 68-year-old male patient. This isolate possessed blaOXA-72 and blaOXA-255-like genes. The assembled genome contained 4,104,098 pb and 38.79% G+C content. This is the first case reported of the coproduction (blaOXA-72 and blaOXA-255-like) of carbapenem-hydrolyzing class D β-lactamases (CHDLs) in Acinetobacter baumannii. PMID:28209815

  20. Molecular Methods for Identification of Acinetobacter Species by Partial Sequencing of the rpoB and 16S rRNA Genes

    PubMed Central

    Khosravi, Azar Dokht; Shahraki, Abdolrazagh Hashemi; Heidarieh, Parvin; Sheikhi, Nasrin

    2015-01-01

    Background Acinetobacter spp. is a diverse group of Gram-negative bacteria which are ubiquitous in soil and water, and an important cause of nosocomial infections. The purpose of this study was to identify a collection of Acinetobacter spp. clinical isolates accurately and to investigate their antibiotic susceptibility patterns. Materials and Methods A total of 197 non-duplicate clinical isolates of Acinetobacter spp. isolates identified using conventional biochemical tests. The molecular technique of PCR-RFLP and sequence analysis of rpoB and 16S rRNA genes was applied for species identification. Antimicrobial susceptibility test was performed with a disk diffusion assay. Results Based on 16S rRNA and rpoB genes analysis separately, most of clinical isolates can be identified with high bootstrap values. However, the identity of the isolate 555T was uncertain due to high similarity of A. grimontii and A. junii. Identification by concatenation of 16S rRNA and rpoB confirmed the identity of clinical isolates of Acenitobacer to species level confidently. Accordingly, the isolate 555T assigned as A. grimontii due to 100% similarity to A. grimontii. Moreover, this isolate showed 98.64% to A. junii. Besides, the identity of the isolates 218T and 364T was confirmed as Genomic species 3 and A. calcoaceticus respectively. So, the majority of Acinetobacter spp. isolates, were identified as: A. baumannii (131 isolates, 66%), A. calcoaceticus (9 isolates, 4.5%), and A. genomosp 16 (8 isolates, 4%). The rest of identified species showed the lower frequencies. In susceptibility test, 105 isolates (53%), presented high antibiotic resistance of 90% to ceftriaxone, piperacillin, piperacillin tazobactam, amikacin, and 81% to ciprofloxacin. Conclusion Sequence analysis of the 16S rRNA and rpoB spacer simultaneously was able to do identification of Acinetobacter spp. to species level. A.baumannii was identified as the most prevalent species with high antibiotic resistance. Other

  1. Genome-wide recombination drives diversification of epidemic strains of Acinetobacter baumannii.

    PubMed

    Snitkin, Evan S; Zelazny, Adrian M; Montero, Clemente I; Stock, Frida; Mijares, Lilia; Murray, Patrick R; Segre, Julie A

    2011-08-16

    Acinetobacter baumannii is an emerging human pathogen and a significant cause of nosocomial infections among hospital patients worldwide. The enormous increase in multidrug resistance among hospital isolates and the recent emergence of pan-drug-resistant strains underscores the urgency to understand how A. baumannii evolves in hospital environments. To this end, we undertook a genomic study of a polyclonal outbreak of multidrug-resistant A. baumannii at the research-based National Institutes of Health Clinical Center. Comparing the complete genome sequences of the three dominant outbreak strain types enabled us to conclude that, despite all belonging to the same epidemic lineage, the three strains diverged before their arrival at the National Institutes of Health. The simultaneous presence of three divergent strains from this lineage supports its increasing prevalence in international hospitals and suggests an ongoing adaptation to the hospital environment. Further genomic comparisons uncovered that much of the diversification that occurred since the divergence of the three outbreak strains was mediated by homologous recombination across 20% of their genomes. Inspection of recombinant regions revealed that several regions were associated with either the loss or swapping out of genes encoding proteins that are exposed to the cell surface or that synthesize cell-surface molecules. Extending our analysis to a larger set of international clinical isolates revealed a previously unappreciated ability of A. baumannii to vary surface molecules through horizontal gene transfer, with subsequent intraspecies dissemination by homologous recombination. These findings have immediate implications in surveillance, prevention, and treatment of A. baumannii infections.

  2. Molecular detection of Acinetobacter species in lice and keds of domestic animals in Oromia Regional State, Ethiopia.

    PubMed

    Kumsa, Bersissa; Socolovschi, Cristina; Parola, Philippe; Rolain, Jean-Marc; Raoult, Didier

    2012-01-01

    This study was conducted to determine the presence of Acinetobacter and Rickettsia species DNA in lice and Melophagus ovinus (sheep ked) of animals from Oromia Regional State in Ethiopia. From September through November 2011, a total of 207 cattle, 85 sheep, 47 dogs and 16 cats were examined for ectoparasites. Results of morphological identification revealed several species of ectoparasites: Linognathus vituli (L. vituli), Bovicola bovis (B. bovis) and Solenopotes capillatus (S. capillatus) on cattle; B. ovis and Melophagus ovinus (M. ovinus) on sheep; and Heterodoxus spiniger (H. spiniger) on dogs. There was a significantly (p≤0.0001) higher prevalence of L. vituli observed in cattle than both S. capillatus and B. bovis. Molecular identification of lice using an 18S rRNA gene analysis confirms the identified lice species by morphological methods. We detected different Acinetobacter species among lice (11.1%) and keds (86.4%) including A. soli in L. vituli of cattle, A. lowffii in M. ovinus of sheep, A. pittii in H. spiniger of dogs, 1 new Acinetobacter spp. in M. ovinus and 2 new Acinetobacter spp. in H. spiniger of dogs using partial rpoB gene sequence analysis. There was a significantly higher prevalence of Acinetobacter spp. in keds than in lice (p≤0.00001). Higher percentage of Acinetobacter spp. DNA was detected in H. spiniger than in both B. ovis and L. vituli (p≤0.00001). Carbapenemase resistance encoding genes for blaOXA-23, blaOXA-24, blaOXA-58, blaNDM-1 and blaOXA-51 were not found in any lice and keds. These findings suggest that synanthropic animals and their ectoparasites might increase the risk of human exposure to zoonotic pathogens and could be a source for Acinetobacter spp. infections in humans. However, additional epidemiological data are required to determine whether ectoparasites of animals can act as environmental reservoirs and play a role in spreading these bacteria to both animal and human hosts.

  3. Molecular Detection of Acinetobacter Species in Lice and Keds of Domestic Animals in Oromia Regional State, Ethiopia

    PubMed Central

    Kumsa, Bersissa; Socolovschi, Cristina; Parola, Philippe; Rolain, Jean-Marc; Raoult, Didier

    2012-01-01

    This study was conducted to determine the presence of Acinetobacter and Rickettsia species DNA in lice and Melophagus ovinus (sheep ked) of animals from Oromia Regional State in Ethiopia. From September through November 2011, a total of 207 cattle, 85 sheep, 47 dogs and 16 cats were examined for ectoparasites. Results of morphological identification revealed several species of ectoparasites: Linognathus vituli (L. vituli), Bovicola bovis (B. bovis) and Solenopotes capillatus (S. capillatus) on cattle; B. ovis and Melophagus ovinus (M. ovinus) on sheep; and Heterodoxus spiniger (H. spiniger) on dogs. There was a significantly (p≤0.0001) higher prevalence of L. vituli observed in cattle than both S. capillatus and B. bovis. Molecular identification of lice using an 18S rRNA gene analysis confirms the identified lice species by morphological methods. We detected different Acinetobacter species among lice (11.1%) and keds (86.4%) including A. soli in L. vituli of cattle, A. lowffii in M. ovinus of sheep, A. pittii in H. spiniger of dogs, 1 new Acinetobacter spp. in M. ovinus and 2 new Acinetobacter spp. in H. spiniger of dogs using partial rpoB gene sequence analysis. There was a significantly higher prevalence of Acinetobacter spp. in keds than in lice (p≤0.00001). Higher percentage of Acinetobacter spp. DNA was detected in H. spiniger than in both B. ovis and L. vituli (p≤0.00001). Carbapenemase resistance encoding genes for blaOXA-23, blaOXA-24, blaOXA-58, blaNDM-1 and blaOXA-51 were not found in any lice and keds. These findings suggest that synanthropic animals and their ectoparasites might increase the risk of human exposure to zoonotic pathogens and could be a source for Acinetobacter spp. infections in humans. However, additional epidemiological data are required to determine whether ectoparasites of animals can act as environmental reservoirs and play a role in spreading these bacteria to both animal and human hosts. PMID:23285015

  4. The Complete Genome and Phenome of a Community-Acquired Acinetobacter baumannii

    PubMed Central

    Farrugia, Daniel N.; Elbourne, Liam D. H.; Hassan, Karl A.; Eijkelkamp, Bart A.; Tetu, Sasha G.; Brown, Melissa H.; Shah, Bhumika S.; Peleg, Anton Y.; Mabbutt, Bridget C.; Paulsen, Ian T.

    2013-01-01

    Many sequenced strains of Acinetobacter baumannii are established nosocomial pathogens capable of resistance to multiple antimicrobials. Community-acquired A. baumannii in contrast, comprise a minor proportion of all A. baumannii infections and are highly susceptible to antimicrobial treatment. However, these infections also present acute clinical manifestations associated with high reported rates of mortality. We report the complete 3.70 Mbp genome of A. baumannii D1279779, previously isolated from the bacteraemic infection of an Indigenous Australian; this strain represents the first community-acquired A. baumannii to be sequenced. Comparative analysis of currently published A. baumannii genomes identified twenty-four accessory gene clusters present in D1279779. These accessory elements were predicted to encode a range of functions including polysaccharide biosynthesis, type I DNA restriction-modification, and the metabolism of novel carbonaceous and nitrogenous compounds. Conversely, twenty genomic regions present in previously sequenced A. baumannii strains were absent in D1279779, including gene clusters involved in the catabolism of 4-hydroxybenzoate and glucarate, and the A. baumannii antibiotic resistance island, known to bestow resistance to multiple antimicrobials in nosocomial strains. Phenomic analysis utilising the Biolog Phenotype Microarray system indicated that A. baumannii D1279779 can utilise a broader range of carbon and nitrogen sources than international clone I and clone II nosocomial isolates. However, D1279779 was more sensitive to antimicrobial compounds, particularly beta-lactams, tetracyclines and sulphonamides. The combined genomic and phenomic analyses have provided insight into the features distinguishing A. baumannii isolated from community-acquired and nosocomial infections. PMID:23527001

  5. Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for species identification of Acinetobacter strains isolated from blood cultures.

    PubMed

    Kishii, K; Kikuchi, K; Matsuda, N; Yoshida, A; Okuzumi, K; Uetera, Y; Yasuhara, H; Moriya, K

    2014-05-01

    The clinical relevance of Acinetobacter species, other than A. baumannii, as human pathogens has not been sufficiently assessed owing to the insufficiency of simple phenotypic clinical diagnostic laboratory tests. Infections caused by these organisms have different impacts on clinical outcome and require different treatment and management approaches. It is therefore important to correctly identify Acinetobacter species. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been introduced to identify a wide range of microorganisms in clinical laboratories, but only a few studies have examined its utility for identifying Acinetobacter species, particularly those of the non-Acinetobacter baumannii complex. We therefore evaluated MALDI-TOF MS for identification of Acinetobacter species by comparing it with sequence analysis of rpoB using 123 isolates of Acinetobacter species from blood. Of the isolates examined, we identified 106/123 (86.2%) to species, and 16/123 (13.0%) could only be identified as acinetobacters. The identity of one isolate could not be established. Of the 106 species identified, 89/106 (84.0%) were confirmed by rpoB sequence analysis, and 17/106 (16.0%) were discordant. These data indicate correct identification of 89/123 (72.4%) isolates. Surprisingly, all blood culture isolates were identified as 13 species of Acinetobacter, and the incidence of Acinetobacter pittii was unexpectedly high (42/123; 34.1%) and exceeded that of A. baumannii (22/123; 17.9%). Although the present identification rate using MALDI-TOF MS is not acceptable for species-level identification of Acinetobacter, further expansion of the database should remedy this situation.

  6. A distinct alleles and genetic recombination of pmrCAB operon in species of Acinetobacter baumannii complex isolates.

    PubMed

    Kim, Dae Hun; Ko, Kwan Soo

    2015-07-01

    To investigate pmrCAB sequence divergence in 5 species of Acinetobacter baumannii complex, a total of 80 isolates from a Korean hospital were explored. We evaluated nucleotide and amino acid polymorphisms of pmrCAB operon, and phylogenetic trees were constructed for each gene of prmCAB operon. Colistin and polymyxin B susceptibility was determined for all isolates, and multilocus sequence typing was also performed for A. baumannii isolates. Our results showed that each species of A. baumannii complex has divergent pmrCAB operon sequences. We identified a distinct pmrCAB allele allied with Acinetobacter nosocomialis in gene trees. Different grouping in each gene tree suggests sporadic recombination or emergence of pmrCAB genes among Acinetobacter species. Sequence polymorphisms among Acinetobacter species might not be associated with colistin resistance. We revealed that a distinct pmrCAB allele may be widespread across the continents such as North America and Asia and that sporadic genetic recombination or emergence of pmrCAB genes might occur.

  7. Identification and characterisation of the putative phage-related endolysins through full genome sequence analysis in Acinetobacter baumannii ATCC 17978.

    PubMed

    Lai, Meng-Jiun; Soo, Po-Chi; Lin, Nien-Tsung; Hu, Anren; Chen, You-Jie; Chen, Li-Kuang; Chang, Kai-Chih

    2013-08-01

    Acinetobacter baumannii has recently emerged as a major cause of healthcare-associated infections owing to an increase in its antimicrobial resistance to virtually all available drugs. The ability of endolysins (lysozymes) to digest cell walls when applied exogenously to bacterial cells has enabled their use as novel antibacterials. In order to utilise endolysins as a therapeutic alternative to antibiotics, we surveyed the genome sequence of A. baumannii ATCC 17978 and successfully identified two phage-related endolysin genes, A1S_1600 and A1S_2016 (termed lysAB3 and lysAB4, respectively). Following cloning and expression/purification, various antibacterial activities of these two phage-related endolysins were determined in vitro. Zymographic assays showed that only purified LysAB3 could lyse the peptidoglycan of the A. baumannii cell wall. When applied exogenously, both LysAB3 and LysAB4 were active against most Acinetobacter spp. tested but had virtually no activity against other non-Acinetobacter spp. Scanning electron microscopy revealed that exposure to 100μg/mL LysAB3 and LysAB4 for up to 60min caused a remarkable modification of the cell shape of A. baumannii. These results indicate that the genes encoding phage-related endolysins can be readily isolated from the bacterial genome and have potential for the development of novel antimicrobial agents.

  8. Evolution of Carbapenem-Resistant Acinetobacter baumannii Revealed through Whole-Genome Sequencing and Comparative Genomic Analysis

    PubMed Central

    Li, Henan; Liu, Fei; Zhang, Yawei; Wang, Xiaojuan; Zhao, Chunjiang; Chen, Hongbin; Zhang, Feifei; Zhu, Baoli

    2014-01-01

    Acinetobacter baumannii is a globally important nosocomial pathogen characterized by an evolving multidrug resistance. A total of 35 representative clinical A. baumannii strains isolated from 13 hospitals in nine cities in China from 1999 to 2011, including 32 carbapenem-resistant and 3 carbapenem-susceptible A. baumannii strains, were selected for whole-genome sequencing and comparative genomic analysis. Phylogenetic analysis revealed that the earliest strain, strain 1999BJAB11, and two strains isolated in Zhejiang Province in 2004 were the founder strains of carbapenem-resistant A. baumannii. Ten types of AbaR resistance islands were identified, and a previously unreported AbaR island, which comprised a two-component response regulator, resistance-related proteins, and RND efflux system proteins, was identified in two strains isolated in Zhejiang in 2004. Multiple transposons or insertion sequences (ISs) existed in each strain, and these gradually tended to diversify with evolution. Some of these IS elements or transposons were the first to be reported, and most of them were mainly found in strains from two provinces. Genome feature analysis illustrated diversified resistance genes, surface polysaccharides, and a restriction-modification system, even in strains that were phylogenetically and epidemiologically very closely related. IS-mediated deletions were identified in the type VI secretion system region, the csuE region, and core lipooligosaccharide (LOS) loci. Recombination occurred in the heme utilization region, and intrinsic resistance genes (blaADC and blaOXA-51-like variants) and three novel blaOXA-51-like variants (blaOXA-424, blaOXA-425, and blaOXA-426) were identified. Our results could improve the understanding of the evolutionary processes that contribute to the emergence of carbapenem-resistant A. baumannii strains and help elucidate the molecular evolutionary mechanism in A. baumannii. PMID:25487793

  9. Distribution of carbapenem resistance determinants among epidemic and non-epidemic types of Acinetobacter species in Japan.

    PubMed

    Matsui, Mari; Suzuki, Satowa; Yamane, Kunikazu; Suzuki, Masato; Konda, Toshifumi; Arakawa, Yoshichika; Shibayama, Keigo

    2014-06-01

    We performed a comparative molecular analysis on three types of clinically isolated Acinetobacter spp.: epidemic sequence types (STs) of Acinetobacter baumannii (epidemic ST-AB), non-epidemic sequence types of A. baumannii (non-epidemic ST-AB) and non-baumannii Acinetobacter spp. A total of 87 isolates - 46 A. baumannii, 25 A. pittii and 16 A. nosocomialis - from 43 hospitals were analysed. Of these, 31 A. baumannii isolates were ST1 or ST2 according to the Pasteur Institute multilocus sequence typing scheme and were defined as epidemic ST-AB. The other 15 A. baumannii isolates were defined as non-epidemic ST-AB. The epidemic ST-AB isolates harboured the blaOXA-23-like gene or had an ISAba1 element upstream of blaOXA-51-like, or both, whereas non-epidemic ST-AB and non-baumannii Acinetobacter spp. isolates harboured blaOXA-58-like or metallo-β-lactamase genes, or both. The proportion of multidrug-resistant isolates was significantly higher in the epidemic ST-AB isolates (48 %) than that in the other types of Acinetobacter isolates (5 %) (P<0.05). In addition, epidemic ST-AB isolates exhibited a relatively higher proportion of fluoroquinolone resistance. We demonstrated that, in terms of genotypes and phenotypes of antimicrobial resistance, non-epidemic ST-AB isolates shared more similarity with non-baumannii Acinetobacter spp. isolates than with epidemic ST-AB isolates, regardless of bacterial species. In addition, this study revealed that, even in Japan, where IMP-type metallo-β-lactamase producers are endemic, epidemic ST-AB harbouring blaIMP have not yet emerged.

  10. A New Double Digestion Ligation Mediated Suppression PCR Method for Simultaneous Bacteria DNA-Typing and Confirmation of Species: An Acinetobacter sp. Model

    PubMed Central

    Stojowska, Karolina; Krawczyk, Beata

    2014-01-01

    We have designed a new ddLMS PCR (double digestion Ligation Mediated Suppression PCR) method based on restriction site polymorphism upstream from the specific target sequence for the simultaneous identification and differentiation of bacterial strains. The ddLMS PCR combines a simple PCR used for species or genus identification and the LM PCR strategy for strain differentiation. The bacterial identification is confirmed in the form of the PCR product(s), while the length of the PCR product makes it possible to differentiate between bacterial strains. If there is a single copy of the target sequence within genomic DNA, one specific PCR product is created (simplex ddLMS PCR), whereas for multiple copies of the gene the fingerprinting patterns can be obtained (multiplex ddLMS PCR). The described ddLMS PCR method is designed for rapid and specific strain differentiation in medical and microbiological studies. In comparison to other LM PCR it has substantial advantages: enables specific species' DNA-typing without the need for pure bacterial culture selection, is not sensitive to contamination with other cells or genomic DNA, and gives univocal “band-based” results, which are easy to interpret. The utility of ddLMS PCR was shown for Acinetobacter calcoaceticus-baumannii (Acb) complex, the genetically closely related and phenotypically similar species and also important nosocomial pathogens, for which currently, there are no recommended methods for screening, typing and identification. In this article two models are proposed: 3′ recA-ddLMS PCR-MaeII/RsaI for Acb complex interspecific typing and 5′ rrn-ddLMS PCR-HindIII/ApaI for Acinetobacter baumannii intraspecific typing. ddLMS PCR allows not only for DNA-typing but also for confirmation of species in one reaction. Also, practical guidelines for designing a diagnostic test based on ddLMS PCR for genotyping different species of bacteria are provided. PMID:25522278

  11. Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group.

    PubMed

    Iacono, Michele; Villa, Laura; Fortini, Daniela; Bordoni, Roberta; Imperi, Francesco; Bonnal, Raoul J P; Sicheritz-Ponten, Thomas; De Bellis, Gianluca; Visca, Paolo; Cassone, Antonio; Carattoli, Alessandra

    2008-07-01

    The whole-genome sequence of an epidemic, multidrug-resistant Acinetobacter baumannii strain (strain ACICU) belonging to the European clone II group and carrying the plasmid-mediated bla(OXA)(-)(58) carbapenem resistance gene was determined. The A. baumannii ACICU genome was compared with the genomes of A. baumannii ATCC 17978 and Acinetobacter baylyi ADP1, with the aim of identifying novel genes related to virulence and drug resistance. A. baumannii ACICU has a single chromosome of 3,904,116 bp (which is predicted to contain 3,758 genes) and two plasmids, pACICU1 and pACICU2, of 28,279 and 64,366 bp, respectively. Genome comparison showed 86.4% synteny with A. baumannii ATCC 17978 and 14.8% synteny with A. baylyi ADP1. A conspicuous number of transporters belonging to different superfamilies was predicted for A. baumannii ACICU. The relative number of transporters was much higher in ACICU than in ATCC 17978 and ADP1 (76.2, 57.2, and 62.5 transporters per Mb of genome, respectively). An antibiotic resistance island, AbaR2, was identified in ACICU and had plausibly evolved by reductive evolution from the AbaR1 island previously described in multiresistant strain A. baumannii AYE. Moreover, 36 putative alien islands (pAs) were detected in the ACICU genome; 24 of these had previously been described in the ATCC 17978 genome, 4 are proposed here for the first time and are present in both ATCC 17978 and ACICU, and 8 are unique to the ACICU genome. Fifteen of the pAs in the ACICU genome encode genes related to drug resistance, including membrane transporters and ex novo acquired resistance genes. These findings provide novel insight into the genetic basis of A. baumannii resistance.

  12. Draft Genome Sequence of Klebsiella pneumoniae Carbapenemase-Producing Acinetobacter baumannii Strain M3AC9-7, Isolated from Puerto Rico

    PubMed Central

    Martínez, Teresa; Ropelewski, Alexander J.; González-Mendez, Ricardo; Vázquez, Guillermo J.

    2015-01-01

    We report the draft genome of a multidrug resistant, Klebsiella pneumoniae carbapenemase (KPC)-producing Acinetobacter baumannii strain M3AC9-7 that belongs to the novel sequence type, ST250. The draft genome consists of a total length of 4.09 Mbp and a G+C content of 38.95%. PMID:25858845

  13. Draft Genome Sequence of the Mercury-Resistant Bacterium Acinetobacter idrijaensis Strain MII, Isolated from a Mine-Impacted Area, Idrija, Slovenia

    PubMed Central

    Caballero Pérez, Juan; Cruz Medina, Julio Alfonso; Molina Vera, Carlos; Salas Rosas, Luz María; Limpens Gutiérrez, Citlalli; García Salinas, Isaac; Hernández Ramírez, Miriam Rebeca; Soto Alonso, Gerardo; Cruz Hernández, Andrés; Saldaña Gutiérrez, Carlos; Romero Gómez, Sergio; Pastrana Martínez, Xóchitl; Álvarez Hidalgo, Erika; Gosar, Mateja; Dizdarevič, Tatjana

    2014-01-01

    We report here the first draft assembly for the genome of Acinetobacter idrijaensis strain MII, isolated from the Idrija mercury mine area (Slovenia). This strain shows a strikingly high tolerance to mercury, and the genome sequence shows genes involved in the mechanisms for heavy metal tolerance pathways and multidrug efflux pumps. PMID:25395645

  14. Draft Genome Sequence of a Multidrug-Resistant Klebsiella pneumoniae Carbapenemase-Producing Acinetobacter baumannii Sequence Type 2 Isolate from Puerto Rico

    PubMed Central

    Martínez, Teresa; Ropelewski, Alexander J.; González-Mendez, Ricardo; Vázquez, Guillermo J.

    2016-01-01

    We report here the draft genome sequence of Acinetobacter baumannii strain M3AC14-8, sequence type 2 (ST2), carrying a chromosomally carried blaKPC-2 gene. The draft genome consists of a total length of 4.11 Mbp and a G+C content of 39.25%. PMID:27540056

  15. Genomic and proteomic evidences unravel the UV-resistome of the poly-extremophile Acinetobacter sp. Ver3

    PubMed Central

    Kurth, Daniel; Belfiore, Carolina; Gorriti, Marta F.; Cortez, Néstor; Farias, María E.; Albarracín, Virginia H.

    2015-01-01

    Ultraviolet radiation can damage biomolecules, with detrimental or even lethal effects for life. Even though lower wavelengths are filtered by the ozone layer, a significant amount of harmful UV-B and UV-A radiation reach Earth’s surface, particularly in high altitude environments. high-altitude Andean lakes (HAALs) are a group of disperse shallow lakes and salterns, located at the Dry Central Andes region in South America at altitudes above 3,000 m. As it is considered one of the highest UV-exposed environments, HAAL microbes constitute model systems to study UV-resistance mechanisms in environmental bacteria at various complexity levels. Herein, we present the genome sequence of Acinetobacter sp. Ver3, a gammaproteobacterium isolated from Lake Verde (4,400 m), together with further experimental evidence supporting the phenomenological observations regarding this bacterium ability to cope with increased UV-induced DNA damage. Comparison with the genomes of other Acinetobacter strains highlighted a number of unique genes, such as a novel cryptochrome. Proteomic profiling of UV-exposed cells identified up-regulated proteins such as a specific cytoplasmic catalase, a putative regulator, and proteins associated to amino acid and protein synthesis. Down-regulated proteins were related to several energy-generating pathways such as glycolysis, beta-oxidation of fatty acids, and electronic respiratory chain. To the best of our knowledge, this is the first report on a genome from a polyextremophilic Acinetobacter strain. From the genomic and proteomic data, an “UV-resistome” was defined, encompassing the genes that would support the outstanding UV-resistance of this strain. PMID:25954258

  16. Genomic and proteomic evidences unravel the UV-resistome of the poly-extremophile Acinetobacter sp. Ver3.

    PubMed

    Kurth, Daniel; Belfiore, Carolina; Gorriti, Marta F; Cortez, Néstor; Farias, María E; Albarracín, Virginia H

    2015-01-01

    Ultraviolet radiation can damage biomolecules, with detrimental or even lethal effects for life. Even though lower wavelengths are filtered by the ozone layer, a significant amount of harmful UV-B and UV-A radiation reach Earth's surface, particularly in high altitude environments. high-altitude Andean lakes (HAALs) are a group of disperse shallow lakes and salterns, located at the Dry Central Andes region in South America at altitudes above 3,000 m. As it is considered one of the highest UV-exposed environments, HAAL microbes constitute model systems to study UV-resistance mechanisms in environmental bacteria at various complexity levels. Herein, we present the genome sequence of Acinetobacter sp. Ver3, a gammaproteobacterium isolated from Lake Verde (4,400 m), together with further experimental evidence supporting the phenomenological observations regarding this bacterium ability to cope with increased UV-induced DNA damage. Comparison with the genomes of other Acinetobacter strains highlighted a number of unique genes, such as a novel cryptochrome. Proteomic profiling of UV-exposed cells identified up-regulated proteins such as a specific cytoplasmic catalase, a putative regulator, and proteins associated to amino acid and protein synthesis. Down-regulated proteins were related to several energy-generating pathways such as glycolysis, beta-oxidation of fatty acids, and electronic respiratory chain. To the best of our knowledge, this is the first report on a genome from a polyextremophilic Acinetobacter strain. From the genomic and proteomic data, an "UV-resistome" was defined, encompassing the genes that would support the outstanding UV-resistance of this strain.

  17. Update on Acinetobacter species: mechanisms of antimicrobial resistance and contemporary in vitro activity of minocycline and other treatment options.

    PubMed

    Castanheira, Mariana; Mendes, Rodrigo E; Jones, Ronald N

    2014-12-01

    Among Acinetobacter species, A. baumannii and other closely related species are commonly implicated in nosocomial infections. These organisms are usually multidrug resistant (MDR), and therapeutic options to treat A. baumannii infections are very limited. Clinicians have been resorting to older antimicrobial agents to treat infections caused by MDR A. baumannii, and some of these agents have documented toxicity and/or are not optimized for the infection type to be treated. Recent clinical experience supported by antimicrobial susceptibility data suggests that minocycline has greater activity than other tetracyclines and glycylcyclines against various MDR pathogens that have limited therapeutic options available, including Acinetobacter species. An intravenous formulation of minocycline has recently become available for clinical use, and in contrast to most older tetracyclines, minocycline has high activity against Acinetobacter species. In this report, we summarized some of the characteristics of the tetracycline class, and quantified the minocycline activity against contemporary (2007-2011) isolates and its potential therapeutic role against a collection of 5477 A. baumannii and other relevant gram-negative organisms when compared directly with tetracycline, doxycycline, and other broad-spectrum antimicrobial agents. Acinetobacter baumannii strains were highly resistant to all agents tested, with the exception of minocycline (79.1% susceptible) and colistin (98.8% susceptible). Minocycline (minimum inhibitory concentration that inhibits 50% and 90% of the isolates [MIC(50/90)]: 1/8 µg/mL) displayed greater activity than doxycycline (MIC(50/90): 2/>8 µg/mL) and tetracycline hydrochloride (HCL) (only 30.2% susceptible) against A. baumannii isolates, and was significantly more active than other tetracyclines against Burkholderia cepacia, Escherichia coli, Serratia marcescens, and Stenotrophomonas maltophilia isolates. In vitro susceptibility testing using

  18. The genome sequence of Acinetobacter baumannii isolated from a septicemic patient in a local hospital in Malaysia

    PubMed Central

    Izwan, I.; Teh, L.K.; Salleh, M.Z.

    2015-01-01

    Acinetobacter baumannii is a Gram negative, strictly aerobic clinical pathogen causing mostly nosocomial infections globally. The DNA of an isolate from the blood of a local septicemic patient was sequenced using the Illumina GA IIx. The draft genome generated is 4,178,008 bp with a G + C content of 42%. From the annotation results, 47 resistance determinants including 16 multidrug resistance (MDR) genes were identified. The data may be accessed via the GenBank WGS master accession number APWV00000000. PMID:26697353

  19. Worldwide dissemination of acquired carbapenem-hydrolysing class D β-lactamases in Acinetobacter spp. other than Acinetobacter baumannii.

    PubMed

    Zander, Esther; Fernández-González, Ana; Schleicher, Xenia; Dammhayn, Cathrin; Kamolvit, Witchuda; Seifert, Harald; Higgins, Paul G

    2014-04-01

    The aim of this study was to identify acquired OXA-type carbapenemases in Acinetobacter spp. other than Acinetobacter baumannii. From a total of 453 carbapenem-susceptible and -resistant Acinetobacter isolates collected worldwide, 23 were positive for blaOXA genes by multiplex PCR. These isolates were identified as Acinetobacter pittii (n=18), Acinetobacter nosocomialis (n=2), Acinetobacter junii (n=1) and Acinetobacter genomic species 14TU/13BJ (n=2). The blaOXA genes and associated insertion sequence (IS) elements were sequenced by primer walking. In 11 of these isolates, sequencing of the PCR products revealed that they were false-positive for blaOXA. The remaining 12 isolates, originating from Europe, Asia, South America, North America and South Africa, harboured OXA-23 (n=4), OXA-58 (n=5), OXA-40-like (n=1) and OXA-143-like (n=1); one A. pittii isolate harboured both OXA-23 and OXA-58. IS elements were associated with blaOXA in 10 isolates. OXA multiplex PCR showed a high degree of false-positive results (47.8%), indicating that detection of blaOXA in non-baumanniiAcinetobacter spp. should be confirmed using additional methods.

  20. Microbial species delineation using whole genome sequences

    SciTech Connect

    Kyrpides, Nikos; Mukherjee, Supratim; Ivanova, Natalia; Mavrommatics, Kostas; Pati, Amrita; Konstantinidis, Konstantinos

    2014-10-20

    Species assignments in prokaryotes use a manual, poly-phasic approach utilizing both phenotypic traits and sequence information of phylogenetic marker genes. With thousands of genomes being sequenced every year, an automated, uniform and scalable approach exploiting the rich genomic information in whole genome sequences is desired, at least for the initial assignment of species to an organism. We have evaluated pairwise genome-wide Average Nucleotide Identity (gANI) values and alignment fractions (AFs) for nearly 13,000 genomes using our fast implementation of the computation, identifying robust and widely applicable hard cut-offs for species assignments based on AF and gANI. Using these cutoffs, we generated stable species-level clusters of organisms, which enabled the identification of several species mis-assignments and facilitated the assignment of species for organisms without species definitions.

  1. Genomic definition of species. Revision 2

    SciTech Connect

    Crkvenjakov, R.; Drmanac, R.

    1993-03-01

    A genome is the sum total of the DNA sequences in the cells of an individual organism. The common usage that species possess genomes comes naturally to biochemists, who have shown that all protein and nucleic acid molecules are at the same time species- and individual-specific, with minor individual variations being superimposed on a consensus sequence that is constant for a species. By extension, this property is attributed to the common features of DNA in the chromosomes of members of a given species and is called species genome. Our proposal for the definition of a biological species is as follows: A species comprises a group of actual and potential biological organisms built according to a unique genome program that is recorded, and at least in part expressed, in the structures of their genomic nucleic acid molecule(s), having intragroup sequence differences which can be fully interconverted in the process of organismal reproduction.

  2. Acinetobacter seifertii sp. nov., a member of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex isolated from human clinical specimens.

    PubMed

    Nemec, Alexandr; Krizova, Lenka; Maixnerova, Martina; Sedo, Ondrej; Brisse, Sylvain; Higgins, Paul G

    2015-03-01

    This study aimed to define the taxonomic status of a phenetically distinct group of 16 strains that corresponds to Acinetobacter genomic species 'close to 13TU', a provisional genomic species of the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex recognized by Gerner-Smidt and Tjernberg in 1993. These strains have been isolated in different countries since the early 1990s and were mostly recovered from human clinical specimens. They were compared with 45 reference strains representing the known taxa of the ACB complex using taxonomic methods relevant to the genus Acinetobacter. Based on sequence analysis of the concatenated partial sequences (2976 bp) of seven housekeeping genes, the 16 strains formed a tight and well-supported cluster (intracluster sequence identity of ≥98.4 %) that was clearly separated from the other members of the ACB complex (≤94.7 %). The species status of the group was supported by average nucleotide identity values of ≤91.7 % between the whole genome sequence of representative strain NIPH 973(T) (NCBI accession no. APOO00000000) and those of the other species. In addition, whole-cell matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) MS analyses indicated the distinctness of the group at the protein level. Metabolic and physiological tests revealed several typical features of the group, although they did not allow its reliable differentiation from the other members of the ACB complex. We conclude that the 16 strains represent a distinct novel species, for which we propose the name Acinetobacter seifertii sp. nov. The type strain is NIPH 973(T) ( = CIP 110471(T) = CCUG 34785(T) = CCM 8535(T)).

  3. Draft Genome Sequence of Acinetobacter bereziniae HPC229, a Carbapenem-Resistant Clinical Strain from Argentina Harboring blaNDM-1

    PubMed Central

    Brovedan, Marco; Marchiaro, Patricia M.; Morán-Barrio, Jorgelina; Revale, Santiago; Cameranesi, Marcela; Brambilla, Luciano; Viale, Alejandro M.

    2016-01-01

    We report here the draft genome sequence of an NDM-1-producing Acinetobacter bereziniae clinical strain, HPC229. This strain harbors both plasmid and chromosomal resistance determinants toward different β-lactams and aminoglycosides as well as several types of multidrug efflux pumps, most likely representing an adaptation strategy for survival under different environments. PMID:26966220

  4. Genomic Evolution of Two Acinetobacter baumannii Clinical Strains from ST-2 Clones Isolated in 2000 and 2010 (ST-2_clon_2000 and ST-2_clon_2010).

    PubMed

    López, M; Rueda, A; Florido, J P; Blasco, L; Gato, E; Fernández-García, L; Martínez-Martínez, L; Fernández-Cuenca, F; Pachón, J; Cisneros, J M; Garnacho-Montero, J; Vila, J; Rodríguez-Baño, J; Pascual, A; Bou, G; Tomás, M

    2016-10-20

    Acinetobacter baumannii is a successful nosocomial pathogen due to its ability to persist in hospital environments by acquiring mobile elements such as transposons, plasmids, and phages. In this study, we compared two genomes of A. baumannii clinical strains isolated in 2000 (ST-2_clon_2000) and 2010 (ST-2_clon_2010) from GenBank project PRJNA308422.

  5. Genomic Evolution of Two Acinetobacter baumannii Clinical Strains from ST-2 Clones Isolated in 2000 and 2010 (ST-2_clon_2000 and ST-2_clon_2010)

    PubMed Central

    López, M.; Rueda, A.; Florido, J. P.; Blasco, L.; Gato, E.; Fernández-García, L.; Martínez-Martínez, L.; Fernández-Cuenca, F.; Pachón, J.; Cisneros, J. M.; Garnacho-Montero, J.; Vila, J.; Rodríguez-Baño, J.; Pascual, A.; Bou, G.

    2016-01-01

    Acinetobacter baumannii is a successful nosocomial pathogen due to its ability to persist in hospital environments by acquiring mobile elements such as transposons, plasmids, and phages. In this study, we compared two genomes of A. baumannii clinical strains isolated in 2000 (ST-2_clon_2000) and 2010 (ST-2_clon_2010) from GenBank project PRJNA308422. PMID:27795287

  6. Draft Genome Sequence of the Plant Growth–Promoting Rhizobacterium Acinetobacter radioresistens Strain SA188 Isolated from the Desert Plant Indigofera argentea

    PubMed Central

    Lafi, Feras F.; Alam, Intikhab; Bisseling, Ton; Geurts, Rene; Bajic, Vladimir B.

    2017-01-01

    ABSTRACT Acinetobacter radioresistens strain SA188 is a plant endophytic bacterium, isolated from root nodules of the desert plants Indigofera spp., collected in Jizan, Saudi Arabia. Here, we report the 3.2-Mb draft genome sequence of strain SA188, highlighting characteristic pathways for plant growth–promoting activity and environmental adaptation. PMID:28254978

  7. Complete Genome Sequence of the Clinical Strain Acinetobacter baumannii R2090 Carrying the Chromosomally Encoded Metallo-β-Lactamase Gene blaNDM-1

    PubMed Central

    Krahn, Thomas; Wibberg, Daniel; Maus, Irena; Winkler, Anika; Nordmann, Patrice; Pühler, Alfred; Poirel, Laurent

    2015-01-01

    Acinetobacter baumannii is an emerging human pathogen causing nosocomial and community-acquired infections. Here, we present the complete genome sequence of the clinical A. baumannii strain R2090 carrying the metallo-β-lactamase gene blaNDM-1 in its chromosome within the transposon Tn125. PMID:26358593

  8. Draft Genome Sequence of Acinetobacter bereziniae HPC229, a Carbapenem-Resistant Clinical Strain from Argentina Harboring blaNDM-1.

    PubMed

    Brovedan, Marco; Marchiaro, Patricia M; Morán-Barrio, Jorgelina; Revale, Santiago; Cameranesi, Marcela; Brambilla, Luciano; Viale, Alejandro M; Limansky, Adriana S

    2016-03-10

    We report here the draft genome sequence of an NDM-1-producing Acinetobacter bereziniae clinical strain, HPC229. This strain harbors both plasmid and chromosomal resistance determinants toward different β-lactams and aminoglycosides as well as several types of multidrug efflux pumps, most likely representing an adaptation strategy for survival under different environments.

  9. Genomic definition of species. Revision 1

    SciTech Connect

    Crkvenjakov, R.; Dramanac, R.

    1992-06-01

    A genome is the sum total of the DNA sequences in the cells of an individual organism. The common usage that species possess genomes comes naturally to biochemists, who have shown that all protein and nucleic acid molecules are at the same time species and individual-specific, with minor individual variations being superimposed on a consensus sequence that is constant for a species. By extension, this property is attributed to the common features of DNA in the chromosomes of members of a given species and is called (species) genome. The definition of species based on chromosomes, genes, or genome common to its member organisms has been implied or mentioned in passing numerous times. Some population biologists think that members of species have similar ``homeostatic genotypes,`` which are to a degree resistant to mutation or environmental change in the production of a basic phenotype.

  10. Pillows, an unexpected source of Acinetobacter.

    PubMed

    Weernink, A; Severin, W P; Tjernberg, I; Dijkshoorn, L

    1995-03-01

    From 1989 until 1992 an increase in the number of isolations of Acinetobacter was observed in a community hospital in The Netherlands. The organisms were spread throughout the hospital and a common source was suspected. Feather pillows were found to harbour high numbers of acinetobacters. Replacement with synthetic pillows and correction of the laundry procedure resulted in a significant reduction of Acinetobacter isolations. A number of isolates from patients and from pillows were indistinguishable using biotyping, antibiogram typing and cell envelope protein typing. By the use of DNA-DNA hybridization most isolates were identified to A. baumannii and the unnamed closely related genomic species 13. A number of isolates, mostly from pillows, were identified as A. radioresistens. The outcome of cultivation, intervention and typing suggests that the feather pillows played an important role in the outbreak.

  11. Genomics, environmental genomics and the issue of microbial species.

    PubMed

    Ward, D M; Cohan, F M; Bhaya, D; Heidelberg, J F; Kühl, M; Grossman, A

    2008-02-01

    A microbial species concept is crucial for interpreting the variation detected by genomics and environmental genomics among cultivated microorganisms and within natural microbial populations. Comparative genomic analyses of prokaryotic species as they are presently described and named have led to the provocative idea that prokaryotes may not form species as we think about them for plants and animals. There are good reasons to doubt whether presently recognized prokaryotic species are truly species. To achieve a better understanding of microbial species, we believe it is necessary to (i) re-evaluate traditional approaches in light of evolutionary and ecological theory, (ii) consider that different microbial species may have evolved in different ways and (iii) integrate genomic, metagenomic and genome-wide expression approaches with ecological and evolutionary theory. Here, we outline how we are using genomic methods to (i) identify ecologically distinct populations (ecotypes) predicted by theory to be species-like fundamental units of microbial communities, and (ii) test their species-like character through in situ distribution and gene expression studies. By comparing metagenomic sequences obtained from well-studied hot spring cyanobacterial mats with genomic sequences of two cultivated cyanobacterial ecotypes, closely related to predominant native populations, we can conduct in situ population genetics studies that identify putative ecotypes and functional genes that determine the ecotypes' ecological distinctness. If individuals within microbial communities are found to be grouped into ecologically distinct, species-like populations, knowing about such populations should guide us to a better understanding of how genomic variation is linked to community function.

  12. Unusual features of the sequences of copies of the 16S-23S rRNA internal transcribed spacer regions of Acinetobacter bereziniae, Acinetobacter guillouiae and Acinetobacter baylyi arise from horizontal gene transfer events.

    PubMed

    Maslunka, Christopher; Gürtler, Volker; Seviour, Robert

    2015-02-01

    The highly variable nature of the internal transcribed spacer region (ITS) has been claimed to represent an ideal target for designing species-specific probes/primers capable of differentiating between closely related Acinetobacter species. However, several Acinetobacter species contain multiple ITS copies of variable lengths, and these include Acinetobacter bereziniae, Acinetobacter guillouiae and Acinetobacter baylyi. This study shows these length variations result from inter-genomic insertion/deletion events (indels) involving horizontal transfer of ITS fragments of other Acinetobacter species and possibly unrelated bacteria, as shown previously by us. In some instances, indel incorporation results in the loss of probe target sites in the recipient cell ITS. In other cases, some indel sequences contain target sites for probes designed from a single ITS sequence to target other Acinetobacter species. Hence, these can generate false positives. The largest of the indels that remove probe sites is 683 bp (labelled bay/i1-0), and it derives from the horizontal transfer of a complete ITS between A. bereziniae BCRC15423(T) and A. baylyi strain ADP1. As a consequence, ITS sequencing or fingerprinting cannot be used to distinguish between the 683 bp ITS in these two strains.

  13. Acinetobacter Pneumonia: A Review

    PubMed Central

    Hartzell, Joshua D.; Kim, Andrew S.; Kortepeter, Mark G.; Moran, Kimberly A.

    2007-01-01

    Acinetobacter species are becoming a major cause of nosocomial infections, including hospital-acquired and ventilator-associated pneumonia. Acinetobacter species have become increasingly resistant to antibiotics over the past several years and currently present a significant challenge in treating these infections. Physicians now rely on older agents, such as polymyxins (colistin), for treatment. This paper reviews the epidemiology, treatment, and prevention of this emerging pathogen. PMID:18092011

  14. Enrichment of Acinetobacter spp. from food samples.

    PubMed

    Carvalheira, Ana; Ferreira, Vânia; Silva, Joana; Teixeira, Paula

    2016-05-01

    Relatively little is known about the role of foods in the chain of transmission of acinetobacters and the occurrence of different Acinetobacter spp. in foods. Currently, there is no standard procedure to recover acinetobacters from food in order to gain insight into the food-related ecology and epidemiology of acinetobacters. This study aimed to assess whether enrichment in Dijkshoorn enrichment medium followed by plating in CHROMagar™ Acinetobacter medium is a useful method for the isolation of Acinetobacter spp. from foods. Recovery of six Acinetobacter species from food spiked with these organisms was compared for two selective enrichment media (Baumann's enrichment and Dijkshoorn's enrichment). Significantly (p < 0.01) higher cell counts were obtained in Dijkshoorn's enrichment. Next, the Dijkshoorn's enrichment followed by direct plating on CHROMagar™ Acinetobacter was applied to detect Acinetobacter spp. in different foods. Fourteen different presumptive acinetobacters were recovered and assumed to represent nine different strains on the basis of REP-PCR typing. Eight of these strains were identified by rpoB gene analysis as belonging to the species Acinetobacter johnsonii, Acinetobacter calcoaceticus, Acinetobacter guillouiae and Acinetobacter gandensis. It was not possible to identify the species level of one strain which may suggests that it represents a distinct species.

  15. OryzaGenome: Genome Diversity Database of Wild Oryza Species.

    PubMed

    Ohyanagi, Hajime; Ebata, Toshinobu; Huang, Xuehui; Gong, Hao; Fujita, Masahiro; Mochizuki, Takako; Toyoda, Atsushi; Fujiyama, Asao; Kaminuma, Eli; Nakamura, Yasukazu; Feng, Qi; Wang, Zi-Xuan; Han, Bin; Kurata, Nori

    2016-01-01

    The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a text-based browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tab-delimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.

  16. Identification of antibiotic resistance genes in the multidrug-resistant Acinetobacter baumannii strain, MDR-SHH02, using whole-genome sequencing.

    PubMed

    Wang, Hualiang; Wang, Jinghua; Yu, Peijuan; Ge, Ping; Jiang, Yanqun; Xu, Rong; Chen, Rong; Liu, Xuejie

    2017-02-01

    This study aimed to investigate antibiotic resistance genes in the multidrug-resistant (MDR) Acinetobacter baumannii (A. baumanii) strain, MDR-SHH02, using whole‑genome sequencing (WGS). The antibiotic resistance of MDR-SHH02 isolated from a patient with breast cancer to 19 types of antibiotics was determined using the Kirby‑Bauer method. WGS of MDR-SHH02 was then performed. Following quality control and transcriptome assembly, functional annotation of genes was conducted, and the phylogenetic tree of MDR-SHH02, along with another 5 A. baumanii species and 2 Acinetobacter species, was constructed using PHYLIP 3.695 and FigTree v1.4.2. Furthermore, pathogenicity islands (PAIs) were predicted by the pathogenicity island database. Potential antibiotic resistance genes in MDR-SHH02 were predicted based on the information in the Antibiotic Resistance Genes Database (ARDB). MDR-SHH02 was found to be resistant to all of the tested antibiotics. The total draft genome length of MDR-SHH02 was 4,003,808 bp. There were 74.25% of coding sequences to be annotated into 21 of the Clusters of Orthologous Groups (COGs) of protein terms, such as 'transcription' and 'amino acid transport and metabolism'. Furthermore, there were 45 PAIs homologous to the sequence MDRSHH02000806. Additionally, a total of 12 gene sequences in MDR-SHH02 were highly similar to the sequences of antibiotic resistance genes in ARDB, including genes encoding aminoglycoside‑modifying enzymes [e.g., aac(3)-Ia, ant(2'')‑Ia, aph33ib and aph(3')-Ia], β-lactamase genes (bl2b_tem and bl2b_tem1), sulfonamide-resistant dihydropteroate synthase genes (sul1 and sul2), catb3 and tetb. These results suggest that numerous genes mediate resistance to various antibiotics in MDR-SHH02, and provide a clinical guidance for the personalized therapy of A. baumannii-infected patients.

  17. Identification of antibiotic resistance genes in the multidrug-resistant Acinetobacter baumannii strain, MDR-SHH02, using whole-genome sequencing

    PubMed Central

    Wang, Hualiang; Wang, Jinghua; Yu, Peijuan; Ge, Ping; Jiang, Yanqun; Xu, Rong; Chen, Rong; Liu, Xuejie

    2017-01-01

    This study aimed to investigate antibiotic resistance genes in the multidrug-resistant (MDR) Acinetobacter baumannii (A. baumanii) strain, MDR-SHH02, using whole-genome sequencing (WGS). The antibiotic resistance of MDR-SHH02 isolated from a patient with breast cancer to 19 types of antibiotics was determined using the Kirby-Bauer method. WGS of MDR-SHH02 was then performed. Following quality control and transcriptome assembly, functional annotation of genes was conducted, and the phylogenetic tree of MDR-SHH02, along with another 5 A. baumanii species and 2 Acinetobacter species, was constructed using PHYLIP 3.695 and FigTree v1.4.2. Furthermore, pathogenicity islands (PAIs) were predicted by the pathogenicity island database. Potential antibiotic resistance genes in MDR-SHH02 were predicted based on the information in the Antibiotic Resistance Genes Database (ARDB). MDR-SHH02 was found to be resistant to all of the tested antibiotics. The total draft genome length of MDR-SHH02 was 4,003,808 bp. There were 74.25% of coding sequences to be annotated into 21 of the Clusters of Orthologous Groups (COGs) of protein terms, such as 'transcription' and 'amino acid transport and metabolism'. Furthermore, there were 45 PAIs homologous to the sequence MDRSHH02000806. Additionally, a total of 12 gene sequences in MDR-SHH02 were highly similar to the sequences of antibiotic resistance genes in ARDB, including genes encoding aminoglycoside-modifying enzymes [e.g., aac(3)-Ia, ant(2″)-Ia, aph33ib and aph(3′)-Ia], β-lactamase genes (bl2b_tem and bl2b_tem1), sulfonamide-resistant dihydropteroate synthase genes (sul1 and sul2), catb3 and tetb. These results suggest that numerous genes mediate resistance to various antibiotics in MDR-SHH02, and provide a clinical guidance for the personalized therapy of A. baumannii-infected patients. PMID:28035408

  18. Genome size differences in Hyalella cryptic species.

    PubMed

    Vergilino, Roland; Dionne, Kaven; Nozais, Christian; Dufresne, France; Belzile, Claude

    2012-02-01

    The Hyalella azteca (Saussure) complex includes numerous amphipod cryptic species in freshwater habitats in America as revealed by DNA barcoding surveys. Two ecomorphs (small and large) have evolved numerous times in this complex. Few phenotypic criteria have been found to differentiate between the numerous species of this complex. The present study aims to explore genome size differences between some species of the H. azteca complex co-occurring in a Canadian boreal lake using flow cytometry. Nuclear DNA content was estimated for 50 individuals belonging to six COI haplotypes corresponding to four provisional species of the H. azteca complex. Species from the large ecomorph had C-values significantly larger than species from the small ecomorph, whereas slight differences were found among species of the small ecomorph. These differences in genome sizes might be linked to ecological and physiological differences among species of the H. azteca complex.

  19. Spreading of AbaR-type genomic islands in multidrug resistance Acinetobacter baumannii strains belonging to different clonal complexes.

    PubMed

    Ramírez, María Soledad; Vilacoba, Elisabet; Stietz, María Silvina; Merkier, Andrea Karina; Jeric, Paola; Limansky, Adriana S; Márquez, Carolina; Bello, Helia; Catalano, Mariana; Centrón, Daniela

    2013-07-01

    In order to determine the occurrence of AbaR-type genomic island in multidrug resistant Acinetobacter baumannii (MDRAb) strains circulating in Argentina, Uruguay, and Chile, we studied 51 MDRAb isolates recovered from several hospitals over 30 years. AbaR-type genomic resistance islands were found in 36 MDRAb isolates since 1986 till now. MLST technique allowed us to identify the presence of four different Clonal Complexes (109, 104, 119, 113) among the positive AbaR-type island positive strains. This is the first description of AbaR-type islands in the CC104 and CC113 that are the most widespread Clonal Complexes in Argentina. In addition, PCR mapping exposed different arrays to those previously described, evidencing the plasticity of this island. Our results evidence a widespread distribution of the AbaR-type genomic islands along the time in the MDRAb population, including the epidemic global clone 1 (GC1) as well as different clonal complexes to those already described in the literature.

  20. Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity

    PubMed Central

    2011-01-01

    Background Acinetobacter baumannii has recently emerged as a significant global pathogen, with a surprisingly rapid acquisition of antibiotic resistance and spread within hospitals and health care institutions. This study examines the genomic content of three A. baumannii strains isolated from distinct body sites. Isolates from blood, peri-anal, and wound sources were examined in an attempt to identify genetic features that could be correlated to each isolation source. Results Pulsed-field gel electrophoresis, multi-locus sequence typing and antibiotic resistance profiles demonstrated genotypic and phenotypic variation. Each isolate was sequenced to high-quality draft status, which allowed for comparative genomic analyses with existing A. baumannii genomes. A high resolution, whole genome alignment method detailed the phylogenetic relationships of sequenced A. baumannii and found no correlation between phylogeny and body site of isolation. This method identified genomic regions unique to both those isolates found on the surface of the skin or in wounds, termed colonization isolates, and those identified from body fluids, termed invasive isolates; these regions may play a role in the pathogenesis and spread of this important pathogen. A PCR-based screen of 74 A. baumanii isolates demonstrated that these unique genes are not exclusive to either phenotype or isolation source; however, a conserved genomic region exclusive to all sequenced A. baumannii was identified and verified. Conclusions The results of the comparative genome analysis and PCR assay show that A. baumannii is a diverse and genomically variable pathogen that appears to have the potential to cause a range of human disease regardless of the isolation source. PMID:21639920

  1. Multidrug-resistant Acinetobacter meningitis in children

    PubMed Central

    Shah, Ira; Kapdi, Muznah

    2016-01-01

    Acinetobacter species have emerged as one of the most troublesome pathogens for healthcare institutions globally. In more recent times, nosocomial infections involving the central nervous system, skin and soft tissue, and bone have emerged as highly problematic. Acinetobacter species infection is common in intensive care units; however, Acinetobacter baumannii meningitis is rarely reported. Here, we report two cases of Acinetobacter baumannii meningitis which was multidrug resistance and ultimately required the carbapenem group of drugs for the treatment.

  2. Genomics of Pathogenic Vibrio Species

    NASA Astrophysics Data System (ADS)

    Dziejman, Michelle; Yildiz, Fitnat H.

    Members of the heterotrophic bacterial family Vibrionaceae are native inhabitants of aquatic environments worldwide, constituting a diverse and abundant component of marine microbial organisms. Over 60 species of the genus Vibrio have been identified (Thompson et al., 2004) and their phenotypic heterogeneity is well documented. The ecology of the genus remains less well understood, however, despite reports that vibrios are the dominant microorganisms inhabiting the superficial water layer and colonizing the chitinous exoskeleton of zooplankton (e.g., copepods, Thompson et al., 2004). Although some species were originally isolated from seawater as free living organisms, most were isolated in association with marine life such as bivalves, fish, eels, or shrimp.

  3. Characterization of hydrogen peroxide-resistant Acinetobacter species isolated during the Mars Phoenix spacecraft assembly.

    PubMed

    Derecho, I; McCoy, K B; Vaishampayan, P; Venkateswaran, K; Mogul, R

    2014-10-01

    The microbiological inventory of spacecraft and the associated assembly facility surfaces represent the primary pool of forward contaminants that may impact the integrity of life-detection missions. Herein, we report on the characterization of several strains of hydrogen peroxide-resistant Acinetobacter, which were isolated during the Mars Phoenix lander assembly. All Phoenix-associated Acinetobacter strains possessed very high catalase specific activities, and the specific strain, A. gyllenbergii 2P01AA, displayed a survival against hydrogen peroxide (no loss in 100 mM H2O2 for 1 h) that is perhaps the highest known among Gram-negative and non-spore-forming bacteria. Proteomic characterizations reveal a survival mechanism inclusive of proteins coupled to peroxide degradation (catalase and alkyl hydroperoxide reductase), energy/redox management (dihydrolipoamide dehydrogenase), protein synthesis/folding (EF-G, EF-Ts, peptidyl-tRNA hydrolase, DnaK), membrane functions (OmpA-like protein and ABC transporter-related protein), and nucleotide metabolism (HIT family hydrolase). Together, these survivability and biochemical parameters support the hypothesis that oxidative tolerance and the related biochemical features are the measurable phenotypes or outcomes for microbial survival in the spacecraft assembly facilities, where the low-humidity (desiccation) and clean (low-nutrient) conditions may serve as selective pressures. Hence, the spacecraft-associated Acinetobacter, due to the conferred oxidative tolerances, may ultimately hinder efforts to reduce spacecraft bioburden when using chemical sterilants, thus suggesting that non-spore-forming bacteria may need to be included in the bioburden accounting for future life-detection missions.

  4. Dynamics of genome change among Legionella species

    PubMed Central

    Joseph, Sandeep J.; Cox, Daniel; Wolff, Bernard; Morrison, Shatavia S.; Kozak-Muiznieks, Natalia A.; Frace, Michael; Didelot, Xavier; Castillo-Ramirez, Santiago; Winchell, Jonas; Read, Timothy D.; Dean, Deborah

    2016-01-01

    Legionella species inhabit freshwater and soil ecosystems where they parasitize protozoa. L. pneumonphila (LP) serogroup-1 (Lp1) is the major cause of Legionnaires’ Disease (LD), a life-threatening pulmonary infection that can spread systemically. The increased global frequency of LD caused by Lp and non-Lp species underscores the need to expand our knowledge of evolutionary forces underlying disease pathogenesis. Whole genome analyses of 43 strains, including all known Lp serogroups 1–17 and 17 emergent LD-causing Legionella species (of which 33 were sequenced in this study) in addition to 10 publicly available genomes, resolved the strains into four phylogenetic clades along host virulence demarcations. Clade-specific genes were distinct for genetic exchange and signal-transduction, indicating adaptation to specific cellular and/or environmental niches. CRISPR spacer comparisons hinted at larger pools of accessory DNA sequences in Lp than predicted by the pan-genome analyses. While recombination within Lp was frequent and has been reported previously, population structure analysis identified surprisingly few DNA admixture events between species. In summary, diverse Legionella LD–causing species share a conserved core-genome, are genetically isolated from each other, and selectively acquire genes with potential for enhanced virulence. PMID:27633769

  5. Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1

    PubMed Central

    Kenyon, Johanna J.; Hamidian, Mohammad; Schultz, Mark B.; Pickard, Derek J.; Dougan, Gordon

    2016-01-01

    The majority of Acinetobacter baumannii isolates that are multiply, extensively and pan-antibiotic resistant belong to two globally disseminated clones, GC1 and GC2, that were first noticed in the 1970s. Here, we investigated microevolution and phylodynamics within GC1 via analysis of 45 whole-genome sequences, including 23 sequenced for this study. The most recent common ancestor of GC1 arose around 1960 and later diverged into two phylogenetically distinct lineages. In the 1970s, the main lineage acquired the AbaR resistance island, conferring resistance to older antibiotics, via a horizontal gene transfer event. We estimate a mutation rate of ∼5 SNPs genome− 1 year− 1 and detected extensive recombination within GC1 genomes, introducing nucleotide diversity into the population at >20 times the substitution rate (the ratio of SNPs introduced by recombination compared with mutation was 22). The recombination events were non-randomly distributed in the genome and created significant diversity within loci encoding outer surface molecules (including the capsular polysaccharide, the outer core lipooligosaccharide and the outer membrane protein CarO), and spread antimicrobial resistance-conferring mutations affecting the gyrA and parC genes and insertion sequence insertions activating the ampC gene. Both GC1 lineages accumulated resistance to newer antibiotics through various genetic mechanisms, including the acquisition of plasmids and transposons or mutations in chromosomal genes. Our data show that GC1 has diversified into multiple successful extensively antibiotic-resistant subclones that differ in their surface structures. This has important implications for all avenues of control, including epidemiological tracking, antimicrobial therapy and vaccination. PMID:28348844

  6. Acinetobacter bohemicus sp. nov. widespread in natural soil and water ecosystems in the Czech Republic.

    PubMed

    Krizova, Lenka; Maixnerova, Martina; Sedo, Ondrej; Nemec, Alexandr

    2014-10-01

    We investigated the taxonomic status of a phenetically unique group of 25 Acinetobacter strains which were isolated from multiple soil and water samples collected in natural ecosystems in the Czech Republic. Based on the comparative sequence analyses of the rpoB, gyrB, and 16S rRNA genes, the strains formed a coherent and well separated branch within the genus Acinetobacter. The genomic uniqueness of the group at the species level was supported by the low average nucleotide identity values (≤77.37%) between the whole genome sequences of strain ANC 3994(T) (NCBI accession no. APOH00000000) and the representatives of the known Acinetobacter species. Moreover, all 25 strains created a tight cluster clearly separated from all hitherto described species based on whole-cell protein profiling by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and shared a unique combination of metabolic and physiological properties. The capacity to assimilate l-histidine and the inability to grow at 35°C differentiated them from their phenotypically closest neighbor, Acinetobacter johnsonii. We conclude that the 25 strains represent a novel Acinetobacter species, for which the name Acinetobacter bohemicus sp. nov. is proposed. The type strain of A. bohemicus is ANC 3994(T) (=CIP 110496(T)=CCUG 63842(T)=CCM 8462(T)).

  7. A Genomic Redefinition of Pseudomonas avellanae species

    PubMed Central

    Scortichini, Marco; Marcelletti, Simone; Ferrante, Patrizia; Firrao, Giuseppe

    2013-01-01

    The circumscription of bacterial species is a complex task. So far, DNA-DNA hybridization (DDH), 16S rRNA gene sequencing, and multiocus sequence typing analysis (MLSA) are currently the preferred techniques for their genetic determination. However, the average nucleotide identity (ANI) analysis of conserved and shared genes between two bacterial strains based on the pair-wise genome comparisons, with support of the tetranucleotide frequency correlation coefficients (TETRA) value, has recently been proposed as a reliable substitute for DDH. The species demarcation boundary has been set to a value of 95-96% of the ANI identity, with further confirmation through the assessment of the corresponding TETRA value. In this study, we performed a genome-wide MLSA of 14 phytopathogenic pseudomonads genomes, and assessed the ANI and TETRA values of 27 genomes, representing seven out of the nine genomospecies of Pseudomonas spp. sensu Gardan et alii, and their phylogenetic relationships using maximum likelihood and Bayesian approaches. The results demonstrate the existence of a well demarcated genomic cluster that includes strains classified as P. avellanae, P. syringae pv. theae, P. s. pv. actinidiae and one P. s. pv. morsprunorum strain all belonging to the single species P. avellanae. In addition, when compared with P. avellanae, five strains of P. s. pv. tomato, including the model strain DC3000, and one P. s. pv. lachrymans strain, appear as very closely related to P. avellanae, with ANI values of nearly 96% as confirmed by the TETRA analysis. Conversely, one representative strain, previously classified as P. avellanae and isolated in central Italy, is a genuine member of the P. syringae species complex and can be defined as P. s. pv. avellanae. Currently. The core and pan genomes of P. avellanae species consist of 3,995 and 5,410 putative protein-coding genes, respectively. PMID:24086635

  8. Antimicrobial susceptibility profiling and genomic diversity of Acinetobacter baumannii isolates: A study in western Iran

    PubMed Central

    Mohajeri, Parviz; Farahani, Abbas; Feizabadi, Mohammad Mehdi; Ketabi, Hosnieh; Abiri, Ramin; Najafi, Farid

    2013-01-01

    Background and Objective Acinetobacter baumannii is an aerobic non-motile Gram-negative bacterial pathogen that is resistant to most antibiotics. Carbapenems are the most common antibiotics for the treatment of infections caused by this pathogen. Mechanisms of antibiotic-resistance in A. baumannii are mainly mediated by efflux pumps-lactamases. The aim of this study was to determine antibiotic susceptibility, the possibility of existence of OXAs genes and fingerprinting by Pulsed-Field Gel Electrophoresis (PFGE) among clinical isolates of Acinetobacter collected from Kermanshah hospitals. Materials and Methods One hundred and four isolates were collected from patients attending Imam Reza, Taleghani and Imam Khomeini hospitals of Kermanshah (Iran). Isolates were identified by biochemical tests and API 20NE kit. The susceptibility to different antibiotics was assessed with Kirby-Bauer disk diffusion method. PCR was performed for detection of bla OXA-23, bla OXA-24, bla OXA-51 and bla OXA-58 beta-lactamase genes. Clonal relatedness was estimated by PFGE (with the restriction enzyme Apa I) and DNA patterns were analyzed by Gel compare II 6.5 software. Results All isolates showed high-level of resistance to imipenem, meropenem as well as to other antimicrobial agents, while no resistance to polymyxin B, colistin, tigecylcine and minocycline was observed. The bla OXA-23like and bla OXA-24 like were found among 77.9% and 19.2% of the isolates, respectively. All isolates were positive for bla OXA-51, but none produced any amplicon for bla OXA-58. PFGE genotype analysis suggested the existence of eight clones among the 104 strains [A (n = 35), B (n = 29), C (n = 19), D (n = 10), E (n = 4), F (n = 3), G (n = 3), H (n = 1)]. Clone A was the dominant clone in hospital settings particularly infection wards so that the isolates in this group, compared to the other clones, showed higher levels of resistance to antibiotics. Conclusion The bla OXA-51-like and bla OXA-23like were

  9. Draft Genome Sequences of Acinetobacter baumannii Strains Harboring the blaNDM-1 Gene Isolated in Lebanon from Civilians Wounded during the Syrian Civil War.

    PubMed

    Tokajian, Sima; Eisen, Jonathan A; Jospin, Guillaume; Hamze, Monzer; Rafei, Rayane; Salloum, Tamara; Ibrahim, Joe; Coil, David A

    2016-01-28

    We present here the draft genome sequences of multidrug-resistant blaNDM-1-positive Acinetobacter baumannii strains ACMH-6200 and ACMH-6201, isolated in north Lebanon from civilians wounded during the Syrian civil war. The draft genomes were contained in 217 contigs for ACMH-6200 and 83 contigs for ACMH-6201, including a combined 3,997,237 bases for ACMH-6200 and 3,983,110 bases for ACMH-6201, with 39% and 38.9% G+C content, respectively.

  10. Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

    PubMed Central

    Lassalle, Florent; Campillo, Tony; Vial, Ludovic; Baude, Jessica; Costechareyre, Denis; Chapulliot, David; Shams, Malek; Abrouk, Danis; Lavire, Céline; Oger-Desfeux, Christine; Hommais, Florence; Guéguen, Laurent; Daubin, Vincent; Muller, Daniel; Nesme, Xavier

    2011-01-01

    The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome—one on the circular chromosome and six on the linear chromosome—suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species. PMID:21795751

  11. Multidrug Resistant Acinetobacter

    PubMed Central

    Manchanda, Vikas; Sanchaita, Sinha; Singh, NP

    2010-01-01

    Emergence and spread of Acinetobacter species, resistant to most of the available antimicrobial agents, is an area of great concern. It is now being frequently associated with healthcare associated infections. Literature was searched at PUBMED, Google Scholar, and Cochrane Library, using the terms ‘Acinetobacter Resistance, multidrug resistant (MDR), Antimicrobial Therapy, Outbreak, Colistin, Tigecycline, AmpC enzymes, and carbapenemases in various combinations. The terms such as MDR, Extensively Drug Resistant (XDR), and Pan Drug Resistant (PDR) have been used in published literature with varied definitions, leading to confusion in the correlation of data from various studies. In this review various mechanisms of resistance in the Acinetobacter species have been discussed. The review also probes upon the current therapeutic options, including combination therapies available to treat infections due to resistant Acinetobacter species in adults as well as children. There is an urgent need to enforce infection control measures and antimicrobial stewardship programs to prevent the further spread of these resistant Acinetobacter species and to delay the emergence of increased resistance in the bacteria. PMID:20927292

  12. Investigations on the genomic diversity of OXA from isolated Acinetobacter baumannii.

    PubMed

    Ma, Z; Zhou, L Q; Wang, H; Luo, L P

    2015-11-23

    We distinguished the four OXA-type carbapenemase subgroup alleles present in 120 strains of Acinetobacter baumannii by using polymerase chain reaction (PCR) and investigated the distributions of the OXA subgroups in clinically isolated samples. Amplification of the OXA genes blaOXA-23, blaOXA-24, blaOXA-51, and blaOXA-58 was performed by multiplex PCR. Antibiotics susceptibility test was conducted for determine the sensitivity of the A. baumannii to clinical common used antibiotics by Kirby-Bauer method. Results revealed that 46 (51.69%) of the samples were positive for only the blaOXA51 gene and 41 (46.07%) were positive for both the blaOXA51 and blaOXA58 genes in the 89 isolates of A. baumannii. Among these, 45 were carbapenem-resistant and 44 carbapenem-sensitive. Strains containing either blaOXA51 or blaOXA58 showed resistance or sensitivity to carbapenems, respectively. A. baumannii isolated from intensive care units showed significantly higher resistance rate to Cefepime, Piperacillin-tazobactam, Amikacin, Ceftazidime, Cefotaxime, Sulfamethoxazole-trimethoprim, and Gentamicin than those isolated from other departments (P < 0.05). In conclusion, we found that the presence of blaOXA-51 and blaOXA-58 appears to convey a mechanism of resistance or sensitivity to carbapenems, respectively, in A. baumannii clinical isolates.

  13. Genome Sequence of a Clinical Strain of Acinetobacter baumannii Belonging to the ST79/PFGE-HUI-1 Clone Lacking the AdeABC (Resistance-Nodulation-Cell Division-Type) Efflux Pump

    PubMed Central

    López, M.; Álvarez-Fraga, L.; Gato, E.; Blasco, L.; Poza, M.; Fernández-García, L.; Bou, G.

    2016-01-01

    Increased expression of chromosomal genes for resistance-nodulation-cell division-type efflux systems plays a major role in the multidrug resistance of Acinetobacter baumannii. Little is known about the genetic characteristics of clinical strains of Acinetobacter baumannii lacking the AdeABC pump. In this study, we sequenced the genome of clinical strain Ab421 GEIH-2010 (belonging to clone ST79/PFGE-HUI-1 from the GEIH-REIPI Ab. 2010 project) which lacks this efflux pump. PMID:27609928

  14. Genome Sequence of a Clinical Strain of Acinetobacter baumannii Belonging to the ST79/PFGE-HUI-1 Clone Lacking the AdeABC (Resistance-Nodulation-Cell Division-Type) Efflux Pump.

    PubMed

    López, M; Álvarez-Fraga, L; Gato, E; Blasco, L; Poza, M; Fernández-García, L; Bou, G; Tomás, M

    2016-09-08

    Increased expression of chromosomal genes for resistance-nodulation-cell division-type efflux systems plays a major role in the multidrug resistance of Acinetobacter baumannii Little is known about the genetic characteristics of clinical strains of Acinetobacter baumannii lacking the AdeABC pump. In this study, we sequenced the genome of clinical strain Ab421 GEIH-2010 (belonging to clone ST79/PFGE-HUI-1 from the GEIH-REIPI Ab. 2010 project) which lacks this efflux pump.

  15. Resistance of Permafrost and Modern Acinetobacter lwoffii Strains to Heavy Metals and Arsenic Revealed by Genome Analysis.

    PubMed

    Mindlin, Sofia; Petrenko, Anatolii; Kurakov, Anton; Beletsky, Alexey; Mardanov, Andrey; Petrova, Mayya

    2016-01-01

    We performed whole-genome sequencing of five permafrost strains of Acinetobacter lwoffii (frozen for 15-3000 thousand years) and analyzed their resistance genes found in plasmids and chromosomes. Four strains contained multiple plasmids (8-12), which varied significantly in size (from 4,135 to 287,630 bp) and genetic structure; the fifth strain contained only two plasmids. All large plasmids and some medium-size and small plasmids contained genes encoding resistance to various heavy metals, including mercury, cobalt, zinc, cadmium, copper, chromium, and arsenic compounds. Most resistance genes found in the ancient strains of A. lwoffii had their closely related counterparts in modern clinical A. lwoffii strains that were also located on plasmids. The vast majority of the chromosomal resistance determinants did not possess complete sets of the resistance genes or contained truncated genes. Comparative analysis of various A. lwoffii and of A. baumannii strains discovered a number of differences between them: (i) chromosome sizes in A. baumannii exceeded those in A. lwoffii by about 20%; (ii) on the contrary, the number of plasmids in A. lwoffii and their total size were much higher than those in A. baumannii; (iii) heavy metal resistance genes in the environmental A. lwoffii strains surpassed those in A. baumannii strains in the number and diversity and were predominantly located on plasmids. Possible reasons for these differences are discussed.

  16. Resistance of Permafrost and Modern Acinetobacter lwoffii Strains to Heavy Metals and Arsenic Revealed by Genome Analysis

    PubMed Central

    Kurakov, Anton; Beletsky, Alexey; Mardanov, Andrey

    2016-01-01

    We performed whole-genome sequencing of five permafrost strains of Acinetobacter lwoffii (frozen for 15–3000 thousand years) and analyzed their resistance genes found in plasmids and chromosomes. Four strains contained multiple plasmids (8–12), which varied significantly in size (from 4,135 to 287,630 bp) and genetic structure; the fifth strain contained only two plasmids. All large plasmids and some medium-size and small plasmids contained genes encoding resistance to various heavy metals, including mercury, cobalt, zinc, cadmium, copper, chromium, and arsenic compounds. Most resistance genes found in the ancient strains of A. lwoffii had their closely related counterparts in modern clinical A. lwoffii strains that were also located on plasmids. The vast majority of the chromosomal resistance determinants did not possess complete sets of the resistance genes or contained truncated genes. Comparative analysis of various A. lwoffii and of A. baumannii strains discovered a number of differences between them: (i) chromosome sizes in A. baumannii exceeded those in A. lwoffii by about 20%; (ii) on the contrary, the number of plasmids in A. lwoffii and their total size were much higher than those in A. baumannii; (iii) heavy metal resistance genes in the environmental A. lwoffii strains surpassed those in A. baumannii strains in the number and diversity and were predominantly located on plasmids. Possible reasons for these differences are discussed. PMID:27795957

  17. A new subclass of intrinsic aminoglycoside nucleotidyltransferases, ANT(3")-II, is horizontally transferred among Acinetobacter spp. by homologous recombination

    PubMed Central

    Zhang, Gang; Leclercq, Sébastien Olivier; Tian, Jingjing; Wang, Chao; Ai, Guomin; Liu, Shuangjiang

    2017-01-01

    The emergence and spread of antibiotic resistance among Acinetobacter spp. have been investigated extensively. Most studies focused on the multiple antibiotic resistance genes located on plasmids or genomic resistance islands. On the other hand, the mechanisms controlling intrinsic resistance are still not well understood. In this study, we identified the novel subclass of aminoglycoside nucleotidyltransferase ANT(3")-II in Acinetobacter spp., which comprised numerous variants distributed among three main clades. All members of this subclass can inactivate streptomycin and spectinomycin. The three ant(3")-II genes, encoding for the three ANT(3")-II clades, are widely distributed in the genus Acinetobacter and always located in the same conserved genomic region. According to their prevalence, these genes are intrinsic in Acinetobacter baumannii, Acinetobacter pittii, and Acinetobacter gyllenbergii. We also demonstrated that the ant(3")-II genes are located in a homologous recombination hotspot and were recurrently transferred among Acinetobacter species. In conclusion, our findings demonstrated a novel mechanism of natural resistance in Acinetobacter spp., identified a novel subclass of aminoglycoside nucleotidyltransferase and provided new insight into the evolutionary history of intrinsic resistance genes. PMID:28152054

  18. Genomic and systems evolution in Vibrionaceae species

    PubMed Central

    Gu, Jianying; Neary, Jennifer; Cai, Hong; Moshfeghian, Audrey; Rodriguez, Stephen A; Lilburn, Timothy G; Wang, Yufeng

    2009-01-01

    Background The steadily increasing number of prokaryotic genomes has accelerated the study of genome evolution; in particular, the availability of sets of genomes from closely related bacteria has facilitated the exploration of the mechanisms underlying genome plasticity. The family Vibrionaceae is found in the Gammaproteobacteria and is abundant in aquatic environments. Taxa from the family Vibrionaceae are diversified in their life styles; some species are free living, others are symbiotic, and others are human pathogens. This diversity makes this family a useful set of model organisms for studying bacterial evolution. This evolution is driven by several forces, among them gene duplication and lateral gene transfer, which are believed to provide raw material for functional redundancy and novelty. The resultant gene copy increase in one genome is then detected as lineage-specific expansion (LSE). Results Here we present the results of a detailed comparison of the genomes of eleven Vibrionaceae strains that have distinct life styles and distinct phenotypes. The core genome shared by all eleven strains is composed of 1,882 genes, which make up about 31%–50% of the genome repertoire. We further investigated the distribution and features of genes that have been specifically expanded in one unique lineage of the eleven strains. Abundant duplicate genes have been identified in the eleven Vibrionaceae strains, with 1–11% of the whole genomes composed lineage specific radiations. These LSEs occurred in two distinct patterns: the first type yields one or more copies of a single gene; we call this a single gene expansion. The second pattern has a high evolutionary impact, as the expansion involves two or more gene copies in a block, with the duplicated block located next to the original block (a contiguous block expansion) or at some distance from the original block (a discontiguous block expansion). We showed that LSEs involve genes that are tied to defense and

  19. Whole-Genome Pyrosequencing of an Epidemic Multidrug-Resistant Acinetobacter baumannii Strain Belonging to the European Clone II Group ▿ †

    PubMed Central

    Iacono, Michele; Villa, Laura; Fortini, Daniela; Bordoni, Roberta; Imperi, Francesco; Bonnal, Raoul J. P.; Sicheritz-Ponten, Thomas; De Bellis, Gianluca; Visca, Paolo; Cassone, Antonio; Carattoli, Alessandra

    2008-01-01

    The whole-genome sequence of an epidemic, multidrug-resistant Acinetobacter baumannii strain (strain ACICU) belonging to the European clone II group and carrying the plasmid-mediated blaOXA-58 carbapenem resistance gene was determined. The A. baumannii ACICU genome was compared with the genomes of A. baumannii ATCC 17978 and Acinetobacter baylyi ADP1, with the aim of identifying novel genes related to virulence and drug resistance. A. baumannii ACICU has a single chromosome of 3,904,116 bp (which is predicted to contain 3,758 genes) and two plasmids, pACICU1 and pACICU2, of 28,279 and 64,366 bp, respectively. Genome comparison showed 86.4% synteny with A. baumannii ATCC 17978 and 14.8% synteny with A. baylyi ADP1. A conspicuous number of transporters belonging to different superfamilies was predicted for A. baumannii ACICU. The relative number of transporters was much higher in ACICU than in ATCC 17978 and ADP1 (76.2, 57.2, and 62.5 transporters per Mb of genome, respectively). An antibiotic resistance island, AbaR2, was identified in ACICU and had plausibly evolved by reductive evolution from the AbaR1 island previously described in multiresistant strain A. baumannii AYE. Moreover, 36 putative alien islands (pAs) were detected in the ACICU genome; 24 of these had previously been described in the ATCC 17978 genome, 4 are proposed here for the first time and are present in both ATCC 17978 and ACICU, and 8 are unique to the ACICU genome. Fifteen of the pAs in the ACICU genome encode genes related to drug resistance, including membrane transporters and ex novo acquired resistance genes. These findings provide novel insight into the genetic basis of A. baumannii resistance. PMID:18411315

  20. Origins of species: acquired genomes and individuality

    NASA Technical Reports Server (NTRS)

    Margulis, L.

    1993-01-01

    Entire genomes with their accompanying protein synthetic systems are transferred throughout the biosphere primarily as bacteria and protists which become symbionts as they irreversibly integrate into pre-existing organisms to form more complex individuals. Individualization is stabilized by simultaneous transmission of once-separate heterologous genetic systems. The origin of new species is hypothesized to correlate with the acquisition, integration and subsequent inheritance of such acquired microbial genomes. These processes were recognized by Mereschkovsky ("Symbiogenesis" in Russian, 1909) and by Wallin ("Symbionticism", see p. 181, this issue).

  1. Location of the fracture faces within the cell envelope of Acinetobacter species strain MJT-F5-5.

    PubMed

    Sleytr, U B; Thornley, M J; Glauert, A M

    1974-05-01

    The cell wall of the gram-negative bacterium Acinetobacter species strain MJT/F5/5 shows in thin section an external "additional" layer, an outer membrane, an intermediate layer, and a dense layer. Negatively stained preparations showed that the additional layer is composed of hexagonally arranged subunits. In glycerol-treated preparations, freeze-etching revealed that the cell walls consist of four layers, with the main plane of fracture between layers cw 2 and cw 3. The surface of [Formula: see text] 2 consisted of densely packed particles, whereas [Formula: see text] 3 appeared to be fibrillar. In cell envelopes treated with lysozyme by various methods, the removal of the dense layer has detached the outer membrane and additional layer from the underlying layers, as shown in thin sections. When freeze-etched in the absence of glycerol, these detached outer membranes with additional layers fractured to reveal both the faces [Formula: see text] 2 and [Formula: see text] 3 with their characteristic surface structures, and, in addition, both the external and internal etched surfaces were revealed. This experiment provided conclusive evidence that the main fracture plane in the cell wall lies within the interior of the outer membrane. This and other evidence showed that the corresponding layers in thin sections and freeze-etched preparations are: the additional layer, cw 1; the outer membrane, cw (2 + 3); and the intermediate and dense layers together from cw 4. Because of similarities in structure between this Acinetobacter and other gram-negative bacteria, it seemed probable that the interior of the outer membrane is the plane most liable to fracture in the cell walls of most gram-negative bacteria.

  2. Comparative Genomics of Two ST 195 Carbapenem-Resistant Acinetobacter baumannii with Different Susceptibility to Polymyxin Revealed Underlying Resistance Mechanism

    PubMed Central

    Lean, Soo-Sum; Yeo, Chew Chieng; Suhaili, Zarizal; Thong, Kwai-Lin

    2016-01-01

    Acinetobacter baumannii is a Gram-negative nosocomial pathogen of importance due to its uncanny ability to acquire resistance to most antimicrobials. These include carbapenems, which are the drugs of choice for treating A. baumannii infections, and polymyxins, the drugs of last resort. Whole genome sequencing was performed on two clinical carbapenem-resistant A. baumannii AC29 and AC30 strains which had an indistinguishable ApaI pulsotype but different susceptibilities to polymyxin. Both genomes consisted of an approximately 3.8 Mbp circular chromosome each and several plasmids. AC29 (susceptible to polymyxin) and AC30 (resistant to polymyxin) belonged to the ST195 lineage and are phylogenetically clustered under the International Clone II (IC-II) group. An AbaR4-type resistance island (RI) interrupted the comM gene in the chromosomes of both strains and contained the blaOXA−23 carbapenemase gene and determinants for tetracycline and streptomycin resistance. AC29 harbored another copy of blaOXA−23 in a large (~74 kb) conjugative plasmid, pAC29b, but this gene was absent in a similar plasmid (pAC30c) found in AC30. A 7 kb Tn1548::armA RI which encodes determinants for aminoglycoside and macrolide resistance, is chromosomally-located in AC29 but found in a 16 kb plasmid in AC30, pAC30b. Analysis of known determinants for polymyxin resistance in AC30 showed mutations in the pmrA gene encoding the response regulator of the two-component pmrAB signal transduction system as well as in the lpxD, lpxC, and lpsB genes that encode enzymes involved in the biosynthesis of lipopolysaccharide (LPS). Experimental evidence indicated that impairment of LPS along with overexpression of pmrAB may have contributed to the development of polymyxin resistance in AC30. Cloning of a novel variant of the blaAmpC gene from AC29 and AC30, and its subsequent expression in E. coli also indicated its likely function as an extended-spectrum cephalosporinase. PMID:26779129

  3. Mapping whole genome shotgun sequence and variant calling in mammalian species without their reference genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomics research in mammals has produced reference genome sequences that are essential for identifying variation associated with disease. High quality reference genome sequences are now available for humans, model species, and economically important agricultural animals. Comparisons between these s...

  4. Complete genome sequence of hypervirulent and outbreak-associated Acinetobacter baumannii strain LAC-4: epidemiology, resistance genetic determinants and potential virulence factors

    PubMed Central

    Ou, Hong-Yu; Kuang, Shan N.; He, Xinyi; Molgora, Brenda M.; Ewing, Peter J.; Deng, Zixin; Osby, Melanie; Chen, Wangxue; Xu, H. Howard

    2015-01-01

    Acinetobacter baumannii is an important human pathogen due to its multi-drug resistance. In this study, the genome of an ST10 outbreak A. baumannii isolate LAC-4 was completely sequenced to better understand its epidemiology, antibiotic resistance genetic determinants and potential virulence factors. Compared with 20 other complete genomes of A. baumannii, LAC-4 genome harbors at least 12 copies of five distinct insertion sequences. It contains 12 and 14 copies of two novel IS elements, ISAba25 and ISAba26, respectively. Additionally, three novel composite transposons were identified: Tn6250, Tn6251 and Tn6252, two of which contain resistance genes. The antibiotic resistance genetic determinants on the LAC-4 genome correlate well with observed antimicrobial susceptibility patterns. Moreover, twelve genomic islands (GI) were identified in LAC-4 genome. Among them, the 33.4-kb GI12 contains a large number of genes which constitute the K (capsule) locus. LAC-4 harbors several unique putative virulence factor loci. Furthermore, LAC-4 and all 19 other outbreak isolates were found to harbor a heme oxygenase gene (hemO)-containing gene cluster. The sequencing of the first complete genome of an ST10 A. baumannii clinical strain should accelerate our understanding of the epidemiology, mechanisms of resistance and virulence of A. baumannii. PMID:25728466

  5. Structure of a short-chain dehydrogenase/reductase (SDR) within a genomic island from a clinical strain of Acinetobacter baumannii.

    PubMed

    Shah, Bhumika S; Tetu, Sasha G; Harrop, Stephen J; Paulsen, Ian T; Mabbutt, Bridget C

    2014-10-01

    Over 15% of the genome of an Australian clinical isolate of Acinetobacter baumannii occurs within genomic islands. An uncharacterized protein encoded within one island feature common to this and other International Clone II strains has been studied by X-ray crystallography. The 2.4 Å resolution structure of SDR-WM99c reveals it to be a new member of the classical short-chain dehydrogenase/reductase (SDR) superfamily. The enzyme contains a nucleotide-binding domain and, like many other SDRs, is tetrameric in form. The active site contains a catalytic tetrad (Asn117, Ser146, Tyr159 and Lys163) and water molecules occupying the presumed NADP cofactor-binding pocket. An adjacent cleft is capped by a relatively mobile helical subdomain, which is well positioned to control substrate access.

  6. Acinetobacter infection--an emerging threat to human health.

    PubMed

    Visca, Paolo; Seifert, Harald; Towner, Kevin J

    2011-12-01

    The genus Acinetobacter comprises a complex and heterogeneous group of bacteria, many of which are capable of causing a range of opportunistic, often catheter-related, infections in humans. However, Acinetobacter baumannii, as well as its close relatives belonging to genomic species 3 ("Acinetobacter pittii") and 13TU ("Acinetobacter nosocomialis"), are important nosocomial pathogens, often associated with epidemic outbreaks of infection, that are only rarely found outside of a clinical setting. These organisms are frequently pandrug-resistant and are capable of causing substantial morbidity and mortality in patients with severe underlying disease, both in the hospital and in the community. Several epidemic clonal lineages of A. baumannii have disseminated worldwide and seem to have a selective advantage over non-epidemic strains. The reasons for the success of these epidemic lineages remain to be elucidated, but could be related to the potential of these organisms to achieve very dynamic reorganization and rapid evolution of their genome, including the acquisition and expression of additional antibiotic resistance determinants, under fluctuating environmental and selective conditions.

  7. GENOMIC APPROACHES FOR CROSS-SPECIES EXTRAPOLATION IN TOXICOLOGY

    EPA Science Inventory

    The latest tools for investigating stress in organisms, genomic technologies provide great insight into how different organisms respond to environmental conditions. However, their usefulness needs testing, verification, and codification. Genomic Approaches for Cross-Species Extra...

  8. Draft Genome Sequence of Acinetobacter oleivorans PF1, a Diesel-Degrading and Plant-Growth-Promoting Endophytic Strain Isolated from Poplar Trees Growing on a Diesel-Contaminated Plume

    PubMed Central

    Gkorezis, Panagiotis; Rineau, Francois; Van Hamme, Jonathan; Daghio, Matteo; Thijs, Sofie; Weyens, Nele

    2015-01-01

    We report the 3.7-Mb draft genome of Acinetobacter oleivorans strain PF1, a hydrocarbonoclastic Gram-negative bacterium in the class Gammaproteobacteria, isolated from poplar trees growing on a diesel-contaminated plume at the Ford Motor Company site in Genk, Belgium. Strain PF1 is a potent plant-growth promoter, useful for diesel fuel phytoremediation applications. PMID:25657268

  9. Distribution and molecular profiling of class 1 integrons in MDR Acinetobacter baumannii isolates and whole genome-based analysis of antibiotic resistance mechanisms in a representative strain.

    PubMed

    Zhu, Yuying; Yi, Yong; Liu, Fei; Lv, Na; Yang, Xi; Li, Jing; Hu, Yongfei; Zhu, Baoli

    2014-11-01

    The class 1 integron is an important driver of the nosocomial dissemination of multidrug-resistant (MDR) bacteria, such as Acinetobacters. In this study, we characterized the gene cassette arrays of class 1 integrons in Acinetobacter baumannii, where the detailed structure of these integrons for 38 clinical strains was analyzed. The results showed that there are three types of gene cassette arrays that are carried by different class 1 integrons, among them the aac(6')-IId-catB8-aadA1 array was the most prevalent. For detailed analysis of the integron structure, whole genome sequencing was carried out on strain AB16, and it was found that a single integron on its chromosome has a partial Tn21 transposon in its 5' flanking region and two complete copies of the insertion element IS26 in both the 5' and 3' flanking regions, indicating that the integron could be acquired by horizontal gene transfer. Furthermore, there is one resistance island AbaR22, one bla gene containing a transposon, four intrinsic resistant genes and one efflux pump that together confer six types of antibiotic resistance.

  10. Genomics and the origin of species.

    PubMed

    Seehausen, Ole; Butlin, Roger K; Keller, Irene; Wagner, Catherine E; Boughman, Janette W; Hohenlohe, Paul A; Peichel, Catherine L; Saetre, Glenn-Peter; Bank, Claudia; Brännström, Ake; Brelsford, Alan; Clarkson, Chris S; Eroukhmanoff, Fabrice; Feder, Jeffrey L; Fischer, Martin C; Foote, Andrew D; Franchini, Paolo; Jiggins, Chris D; Jones, Felicity C; Lindholm, Anna K; Lucek, Kay; Maan, Martine E; Marques, David A; Martin, Simon H; Matthews, Blake; Meier, Joana I; Möst, Markus; Nachman, Michael W; Nonaka, Etsuko; Rennison, Diana J; Schwarzer, Julia; Watson, Eric T; Westram, Anja M; Widmer, Alex

    2014-03-01

    Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.

  11. Rapid identification of Acinetobacter baumannii, Acinetobacter nosocomialis and Acinetobacter pittii with a multiplex PCR assay.

    PubMed

    Chen, Te-Li; Lee, Yi-Tzu; Kuo, Shu-Chen; Yang, Su-Pen; Fung, Chang-Phone; Lee, Shou-Dong

    2014-09-01

    Acinetobacter baumannii, Acinetobacter nosocomialis and Acinetobacter pittii are clinically relevant members of the Acinetobacter calcoaceticus-A. baumannii (Acb) complex and important nosocomial pathogens. These three species are genetically closely related and phenotypically similar; however, they differ in their epidemiology, antibiotic resistance and pathogenicity. In this study, we investigated the use of a multiplex PCR-based assay designed to detect internal fragments of the 16S-23S rRNA intergenic region and the gyrB and recA genes. The assay was capable of differentiating A. baumannii, A. nosocomialis and A. pittii in a reliable manner. In 23 different reference strains and 89 clinical isolates of Acinetobacter species, the assay accurately identified clinically relevant Acb complex species except those 'between 1 and 3' or 'close to 13TU'. None of the non-Acb complex species was misidentified. In an analysis of 1034 positive blood cultures, the assay had a sensitivity of 92.4 % and specificity of 98.2 % for Acb complex identification. Our results show that a single multiplex PCR assay can reliably differentiate clinically relevant Acb complex species. Thus, this method may be used to better understand the clinical differences between infections caused by these species.

  12. THE PHYLOGENY AND GENOME OF TRICHINELLA SPECIES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In 2004, funding was received by Washington University’s Genome Sequencing Center through NHGRI, to completely sequence several nematode genomes as part of a holistic effort to advance our understanding of the human genome. Trichinella spiralis was among this group because of its strategic ...

  13. More Than Just Light: Clinical Relevance of Light Perception in the Nosocomial Pathogen Acinetobacter baumannii and Other Members of the Genus Acinetobacter.

    PubMed

    Ramírez, María Soledad; Müller, Gabriela Leticia; Pérez, Jorgelina Fernanda; Golic, Adrián Ezequiel; Mussi, María Alejandra

    2015-11-01

    A summary of the major findings concerning light modulation in Acinetobacter baumannii, which governs aspects related to the success of this microorganism as a nosocomial pathogen, is presented. Particularly, the evidence shows that light modulates the ability of the bacteria to persist in the environment, its virulence against eukaryotic hosts and even susceptibility to certain antibiotics. The light signal is sensed through different mechanisms, in some cases involving specialized photoreceptors of the BLUF-type, whereas in others, directly by a photosensitizer molecule. We also provide new data concerning the genomic context of BLUF-domain containing proteins within the genus Acinetobacter, as well as further insights into the mechanism of light-mediated reduction in susceptibility to antibiotics. The overall information points toward light being a crucial stimulus in the lifestyle of members of the genus Acinetobacter as well as in other clinically relevant species, such as members of the ESKAPE group, playing therefore an important role in the clinical settings.

  14. Structure of a short-chain dehydrogenase/reductase (SDR) within a genomic island from a clinical strain of Acinetobacter baumannii

    SciTech Connect

    Shah, Bhumika S. Tetu, Sasha G.; Harrop, Stephen J.; Paulsen, Ian T.; Mabbutt, Bridget C.

    2014-09-25

    The structure of a short-chain dehydrogenase encoded within genomic islands of A. baumannii strains has been solved to 2.4 Å resolution. This classical SDR incorporates a flexible helical subdomain. The NADP-binding site and catalytic side chains are identified. Over 15% of the genome of an Australian clinical isolate of Acinetobacter baumannii occurs within genomic islands. An uncharacterized protein encoded within one island feature common to this and other International Clone II strains has been studied by X-ray crystallography. The 2.4 Å resolution structure of SDR-WM99c reveals it to be a new member of the classical short-chain dehydrogenase/reductase (SDR) superfamily. The enzyme contains a nucleotide-binding domain and, like many other SDRs, is tetrameric in form. The active site contains a catalytic tetrad (Asn117, Ser146, Tyr159 and Lys163) and water molecules occupying the presumed NADP cofactor-binding pocket. An adjacent cleft is capped by a relatively mobile helical subdomain, which is well positioned to control substrate access.

  15. The genome of the mesopolyploid crop species Brassica rapa.

    PubMed

    Wang, Xiaowu; Wang, Hanzhong; Wang, Jun; Sun, Rifei; Wu, Jian; Liu, Shengyi; Bai, Yinqi; Mun, Jeong-Hwan; Bancroft, Ian; Cheng, Feng; Huang, Sanwen; Li, Xixiang; Hua, Wei; Wang, Junyi; Wang, Xiyin; Freeling, Michael; Pires, J Chris; Paterson, Andrew H; Chalhoub, Boulos; Wang, Bo; Hayward, Alice; Sharpe, Andrew G; Park, Beom-Seok; Weisshaar, Bernd; Liu, Binghang; Li, Bo; Liu, Bo; Tong, Chaobo; Song, Chi; Duran, Christopher; Peng, Chunfang; Geng, Chunyu; Koh, Chushin; Lin, Chuyu; Edwards, David; Mu, Desheng; Shen, Di; Soumpourou, Eleni; Li, Fei; Fraser, Fiona; Conant, Gavin; Lassalle, Gilles; King, Graham J; Bonnema, Guusje; Tang, Haibao; Wang, Haiping; Belcram, Harry; Zhou, Heling; Hirakawa, Hideki; Abe, Hiroshi; Guo, Hui; Wang, Hui; Jin, Huizhe; Parkin, Isobel A P; Batley, Jacqueline; Kim, Jeong-Sun; Just, Jérémy; Li, Jianwen; Xu, Jiaohui; Deng, Jie; Kim, Jin A; Li, Jingping; Yu, Jingyin; Meng, Jinling; Wang, Jinpeng; Min, Jiumeng; Poulain, Julie; Wang, Jun; Hatakeyama, Katsunori; Wu, Kui; Wang, Li; Fang, Lu; Trick, Martin; Links, Matthew G; Zhao, Meixia; Jin, Mina; Ramchiary, Nirala; Drou, Nizar; Berkman, Paul J; Cai, Qingle; Huang, Quanfei; Li, Ruiqiang; Tabata, Satoshi; Cheng, Shifeng; Zhang, Shu; Zhang, Shujiang; Huang, Shunmou; Sato, Shusei; Sun, Silong; Kwon, Soo-Jin; Choi, Su-Ryun; Lee, Tae-Ho; Fan, Wei; Zhao, Xiang; Tan, Xu; Xu, Xun; Wang, Yan; Qiu, Yang; Yin, Ye; Li, Yingrui; Du, Yongchen; Liao, Yongcui; Lim, Yongpyo; Narusaka, Yoshihiro; Wang, Yupeng; Wang, Zhenyi; Li, Zhenyu; Wang, Zhiwen; Xiong, Zhiyong; Zhang, Zhonghua

    2011-08-28

    We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.

  16. Draft Genome Sequence of Acinetobacter sp. Strain BMW17, a Cellulolytic and Plant Growth-Promoting Bacterium Isolated from the Rhizospheric Region of Phragmites karka of Chilika Lake, India.

    PubMed

    Mishra, Samir R; Ray, Lopamudra; Panda, Ananta Narayan; Sahu, Neha; Xess, Sonal S; Jadhao, Sudhir; Suar, Mrutyunjay; Adhya, Tapan Kumar; Rastogi, Gurdeep; Pattnaik, Ajit Kumar; Raina, Vishakha

    2016-06-30

    We report the 3.16 Mb draft genome of Acinetobacter sp. strain BMW17, a Gram-negative bacterium in the class of Gammaproteobacteria, isolated from the rhizospheric region of Phragmites karka, an invasive weed in Chilika Lake, Odisha, India. The strain BMW17(T) is capable of degrading cellulose and is also an efficient plant growth promoter that can be useful for various phytoremedial and commercial applications.

  17. Draft Genome Sequence of Acinetobacter sp. Strain BMW17, a Cellulolytic and Plant Growth-Promoting Bacterium Isolated from the Rhizospheric Region of Phragmites karka of Chilika Lake, India

    PubMed Central

    Mishra, Samir R.; Ray, Lopamudra; Panda, Ananta Narayan; Sahu, Neha; Xess, Sonal S.; Jadhao, Sudhir; Suar, Mrutyunjay; Adhya, Tapan Kumar; Rastogi, Gurdeep; Pattnaik, Ajit Kumar

    2016-01-01

    We report the 3.16 Mb draft genome of Acinetobacter sp. strain BMW17, a Gram-negative bacterium in the class of Gammaproteobacteria, isolated from the rhizospheric region of Phragmites karka, an invasive weed in Chilika Lake, Odisha, India. The strain BMW17T is capable of degrading cellulose and is also an efficient plant growth promoter that can be useful for various phytoremedial and commercial applications. PMID:27365343

  18. Staring at the cold sun: blue light regulation is distributed within the genus Acinetobacter.

    PubMed

    Golic, Adrián; Vaneechoutte, Mario; Nemec, Alexandr; Viale, Alejandro M; Actis, Luis A; Mussi, María Alejandra

    2013-01-01

    We previously showed that the opportunistic nosocomial pathogen Acinetobacter baumannii is able to sense and respond to light via BlsA, a BLUF (Blue-Light-sensing Using FAD)-domain photoreceptor protein. Here, we extend our previous studies showing that light regulation is not restricted to A. baumannii, but rather widespread within the genus Acinetobacter. First, we found that blue light modulates motility and biofilm formation in many species of the genus, including members of the Acinetobacter calcoaceticus-A. baumannii complex. In many of these species blue light acts as a key factor guiding the decision between motility or sessility at 24°C, whereas in A. baumannii, light inhibits both motility and biofilm formation. We also show that light regulation of motility occurred not only at 24°C but also at 37°C in non-A. baumannii species, contrasting the situation of A. baumannii which only shows photoregulation at 24°C. Second, we show that Acinetobacter baylyi (strain ADP1) BLUF-photoreceptors can functionally replace in vivo the A. baumannii 17978 BlsA protein and that the pathways leading to biofilm formation are inversely regulated at 24°C between these two microorganisms. Finally, we found the presence of predicted genes coding BLUF-containing proteins in all Acinetobacter sequenced genomes, even though the copy number is variable among them. Phylogenetic analysis suggests a common origin for all BLUF domains present in members of this genus, and could distinguish well-differentiated clusters that group together BLUF homologs from different species, a situation particularly clear for members of the ACB complex. Despite a role played by these BLUF domain-containing proteins in the photoregulation observed in the members of the genus Acinetobacter is a likely scenario given our findings in A. baumannii and A. baylyi, further research will contribute to confirm this possibility.

  19. Rapid species identification and epidemiological analysis of carbapenem-resistant Acinetobacter spp. by a PCR-based open reading frame typing method.

    PubMed

    Yamada, Yuki; Endo, Kentaro; Sawase, Kaori; Anetai, Marie; Narita, Kazuya; Hatakeyama, Yuji; Ishifuji, Katsunori; Kurota, Makiko; Suwabe, Akira

    2016-09-01

    The spread of carbapenem-resistant Acinetobacter spp. has become a global problem. In this study, 18 carbapenem-resistant Acinetobacter calcoaceticus-baumannii (ACB) complexes, identified using a conventional biochemical method at our hospital during 2004-2013, were studied for species identification and epidemiological analyses. Species identification was performed using matrix-assisted laser desorption ionization-time-of-flight MS, a partial sequence analysis of rpoB and a PCR-based ORF typing (POT) method. The POT method can not only identify the species of ACB complexes but also simultaneously determine the international epidemic clones and the genetic identities of Acinetobacterbaumannii in several hours. Carbapenem resistance gene detection by PCR, molecular epidemiological analysis by PFGE and Pasteur Institute multilocus sequence typing (MLST) analysis were performed. All three methods identified 18 isolates as A. baumannii (n=10), Acinetobacterpittii (n=4) and Acinetobacternosocomialis (n=4). A metallo-β-lactamase gene in all strains of A. pittii and A. nosocomialis and an ISAba1 gene in the upstream of the blaOXA-51-like gene in eight strains of A. baumannii were detected, respectively, as carbapenemase-related genes. Results from PFGE demonstrated that nine strains of A. baumannii were closely related genetically. Results of MLST analysis showed that A. baumannii are classifiable to sequence type 2. These results were consistent with those obtained using the POT method. This POT method can easily and rapidly identify the international epidemic clones and the identities of A. baumannii. It can be a useful tool for infection control.

  20. Acinetobacter sp. strain Ths, a novel psychrotolerant and alkalitolerant bacterium that utilizes hydrocarbon.

    PubMed

    Yamahira, Keiko; Hirota, Kikue; Nakajima, Kenji; Morita, Naoki; Nodasaka, Yoshinobu; Yumoto, Isao

    2008-09-01

    A novel psychrotolerant, alkalitolerant bacterium, strain Ths, was isolated from a soil sample immersed in hot spring water containing hydrocarbons and grown on a chemically defined medium containing n-tetradecane as the sole carbon source. The isolate grew at 0 degrees C but not at temperatures higher than 45 degrees C; its optimum growth temperature was 27 degrees C. It grew in the pH range of 7-9. The strain utilized C(13)-C(30) n-alkane and fluorene at pH 9 and 4 degrees C. To our knowledge, this is the first report on the bacterium that utilizes a wide range of hydrocarbons at a high pH and a low temperature. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Ths is closely related to genomic species 6 ATCC 17979 (99.1% similarity), genomic species BJ13/TU14 ATCC 17905 (97.8% similarity), genomic species 9 ATCC 9957 (97.6% similarity) belonging to the genus Acinetobacter and to Acinetobacter calcoaceticus JCM 6842(T) (97.5% similarity). DNA-DNA hybridization revealed that the isolate has 62, 25, 18 and 19% relatedness, respectively, to genomic species 6 ATCC 17979, genomic species BJ13/TU14 ATCC 17905, genomic species 9 ATCC 9957 and A. calcoaceticus, respectively.

  1. Alternative splicing in teleost fish genomes: same-species and cross-species analysis and comparisons.

    PubMed

    Lu, Jianguo; Peatman, Eric; Wang, Wenqi; Yang, Qing; Abernathy, Jason; Wang, Shaolin; Kucuktas, Huseyin; Liu, Zhanjiang

    2010-06-01

    Alternative splicing (AS) is a mechanism by which the coding diversity of the genome can be greatly increased. Rates of AS are known to vary according to the complexity of eukaryotic species potentially explaining the tremendous phenotypic diversity among species with similar numbers of coding genes. Little is known, however, about the nature or rate of AS in teleost fish. Here, we report the characteristics of AS in teleost fish and classification and frequency of five canonical AS types. We conducted both same-species and cross-species analysis utilizing the Genome Mapping and Alignment Program (GMAP) and an AS pipeline (ASpipe) to study AS in four genome-enabled species (Danio rerio, Oryzias latipes, Gasterosteus aculeatus, and Takifugu rubripes) and one species lacking a complete genome sequence, Ictalurus punctatus. AS frequency was lowest in the highly duplicated genome of zebrafish (17% of mapped genes). The compact genome of the pufferfish showed the highest occurrence of AS (approximately 43% of mapped genes). An inverse correlation between AS frequency and genome size was consistent across all analyzed species. Cross-species comparisons utilizing zebrafish as the reference genome allowed the identification of additional putative AS genes not revealed by zebrafish transcripts. Approximately, 50% of AS genes identified by same-species comparisons were shared among two or more species. A searchable website, the Teleost Alternative Splicing Database, was created to allow easy identification and visualization of AS transcripts in the studied teleost genomes. Our results and associated database should further our understanding of alternative splicing as an important functional and evolutionary mechanism in the genomes of teleost fish.

  2. Characterization of Plasmids in Extensively Drug-Resistant Acinetobacter Strains Isolated in India and Pakistan

    PubMed Central

    Carvalho, Maria J.; Toleman, Mark A.; White, P. Lewis; Connor, Thomas R.; Mushtaq, Ammara; Weeks, Janis L.; Kumarasamy, Karthikeyan K.; Raven, Katherine E.; Török, M. Estée; Peacock, Sharon J.; Howe, Robin A.; Walsh, Timothy R.

    2014-01-01

    The blaNDM-1 gene is associated with extensive drug resistance in Gram-negative bacteria. This probably spread to Enterobacteriaceae from Acinetobacter spp., and we characterized plasmids associated with blaNDM-1 in Acinetobacter spp. to gain insight into their role in this dissemination. Four clinical NDM-1-producing Acinetobacter species strains from India and Pakistan were investigated. A plasmid harboring blaNDM-1, pNDM-40-1, was characterized by whole-genome sequencing of Acinetobacter bereziniae CHI-40-1 and comparison with related plasmids. The presence of similar plasmids in strains from Pakistan was sought by PCR and sequencing of amplicons. Conjugation frequency was tested and stability of pNDM-40-1 investigated by real-time PCR of isolates passaged with and without antimicrobial selection pressure. A. bereziniae and Acinetobacter haemolyticus strains contained plasmids similar to the pNDM-BJ01-like plasmids identified in Acinetobacter spp. in China. The backbone of pNDM-40-1 was almost identical to that of pNDM-BJ01-like plasmids, but the transposon harboring blaNDM-1, Tn125, contained two short deletions. Escherichia coli and Acinetobacter pittii transconjugants were readily obtained. Transconjugants retained pNDM-40-1 after a 14-day passage experiment, although stability was greater with meropenem selection. Fragments of pNDM-BJ01-like plasmid backbones are found near blaNDM-1 in some genetic contexts from Enterobacteriaceae, suggesting that cross-genus transfer has occurred. pNDM-BJ01-like plasmids have been described in isolates originating from a wide geographical region in southern Asia. In vitro data on plasmid transfer and stability suggest that these plasmids could have contributed to the spread of blaNDM-1 into Enterobacteriaceae. PMID:25421466

  3. Characterization of plasmids in extensively drug-resistant acinetobacter strains isolated in India and Pakistan.

    PubMed

    Jones, Lim S; Carvalho, Maria J; Toleman, Mark A; White, P Lewis; Connor, Thomas R; Mushtaq, Ammara; Weeks, Janis L; Kumarasamy, Karthikeyan K; Raven, Katherine E; Török, M Estée; Peacock, Sharon J; Howe, Robin A; Walsh, Timothy R

    2015-02-01

    The blaNDM-1 gene is associated with extensive drug resistance in Gram-negative bacteria. This probably spread to Enterobacteriaceae from Acinetobacter spp., and we characterized plasmids associated with blaNDM-1 in Acinetobacter spp. to gain insight into their role in this dissemination. Four clinical NDM-1-producing Acinetobacter species strains from India and Pakistan were investigated. A plasmid harboring blaNDM-1, pNDM-40-1, was characterized by whole-genome sequencing of Acinetobacter bereziniae CHI-40-1 and comparison with related plasmids. The presence of similar plasmids in strains from Pakistan was sought by PCR and sequencing of amplicons. Conjugation frequency was tested and stability of pNDM-40-1 investigated by real-time PCR of isolates passaged with and without antimicrobial selection pressure. A. bereziniae and Acinetobacter haemolyticus strains contained plasmids similar to the pNDM-BJ01-like plasmids identified in Acinetobacter spp. in China. The backbone of pNDM-40-1 was almost identical to that of pNDM-BJ01-like plasmids, but the transposon harboring blaNDM-1, Tn125, contained two short deletions. Escherichia coli and Acinetobacter pittii transconjugants were readily obtained. Transconjugants retained pNDM-40-1 after a 14-day passage experiment, although stability was greater with meropenem selection. Fragments of pNDM-BJ01-like plasmid backbones are found near blaNDM-1 in some genetic contexts from Enterobacteriaceae, suggesting that cross-genus transfer has occurred. pNDM-BJ01-like plasmids have been described in isolates originating from a wide geographical region in southern Asia. In vitro data on plasmid transfer and stability suggest that these plasmids could have contributed to the spread of blaNDM-1 into Enterobacteriaceae.

  4. Population Genomic Analysis Reveals Highly Conserved Mitochondrial Genomes in the Yeast Species Lachancea thermotolerans

    PubMed Central

    Freel, Kelle C.; Friedrich, Anne; Hou, Jing; Schacherer, Joseph

    2014-01-01

    The increasing availability of mitochondrial (mt) sequence data from various yeasts provides a tool to study genomic evolution within and between different species. While the genomes from a range of lineages are available, there is a lack of information concerning intraspecific mtDNA diversity. Here, we analyzed the mt genomes of 50 strains from Lachancea thermotolerans, a protoploid yeast species that has been isolated from several locations (Europe, Asia, Australia, South Africa, and North / South America) and ecological sources (fruit, tree exudate, plant material, and grape and agave fermentations). Protein-coding genes from the mtDNA were used to construct a phylogeny, which reflected a similar, yet less resolved topology than the phylogenetic tree of 50 nuclear genes. In comparison to its sister species Lachancea kluyveri, L. thermotolerans has a smaller mt genome. This is due to shorter intergenic regions and fewer introns, of which the latter are only found in COX1. We revealed that L. kluyveri and L. thermotolerans share similar levels of intraspecific divergence concerning the nuclear genomes. However, L. thermotolerans has a more highly conserved mt genome with the coding regions characterized by low rates of nonsynonymous substitution. Thus, in the mt genomes of L. thermotolerans, stronger purifying selection and lower mutation rates potentially shape genome diversity in contract to what was found for L. kluyveri, demonstrating that the factors driving mt genome evolution are different even between closely related species. PMID:25212859

  5. Acinetobacter: an underrated foodborne pathogen?

    PubMed

    Amorim, Angelo Maximo Batista de; Nascimento, Janaína Dos Santos

    2017-02-28

    The increasing prevalence of foodborne diseases observed in developing countries has been linked to a rise in the consumption of raw foods. However, unlike the classical pathogens that are commonly implicated in foodborne illnesses, members of the genus Acinetobacter are rarely associated with diarrheal disease, probably because of the difficulty in isolating these Gram-negative bacteria from food sources. Nevertheless, several species of Acinetobacter, especially A. baumannii, possess many of the characteristics associated with successful pathogens and exhibit a prodigious ability to acquire the multiple-drug resistance (MDR) phenotype. In this mini-review, we summarize the epidemiological data relating to MDR Acinetobacter and consider evidence suggesting that contaminated dairy products, along with raw fruit and vegetables, constitute extra-hospital reservoirs of this underrated pathogen, and may represent an increased risk to immunocompromised individuals and young children in healthcare settings.

  6. Genomics of Extinct and Endangered Species (2011 JGI User Meeting)

    ScienceCinema

    Shuster, Stephen [Penn State University

    2016-07-12

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Stephen Shuster of Penn State University gives a presentation on "Genomics of Extinct and Endangered Species" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  7. Genomics of Extinct and Endangered Species (2011 JGI User Meeting)

    SciTech Connect

    Shuster, Stephen

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Stephen Shuster of Penn State University gives a presentation on "Genomics of Extinct and Endangered Species" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  8. Acinetobacter lactucae sp. nov., isolated from iceberg lettuce (Asteraceae: Lactuca sativa).

    PubMed

    Rooney, Alejandro P; Dunlap, Christopher A; Flor-Weiler, Lina B

    2016-09-01

    Strain NRRL B-41902T and three closely related strains were isolated from iceberg lettuce. The strain was found to consist of strictly aerobic, Gram-stain-negative rods that formed cocci in late stationary phase. 16S rRNA gene sequence analysis showed that strain NRRL B-41902T was most closely related to species within the genera Acinetobacter, and that a grouping of it and the three other closely related strains was most closely related to the type strain of Acinetobacter pittii, which was also confirmed through a phylogenomic analysis. Moreover, in silico DNA-DNA hybridization analysis revealed a substantial amount of genomic divergence (39.1 %) between strain NRRL B-41902T and the type strain of A. pittii, which is expected if the strains represent distinct species. Further phenotypic analysis revealed that strain NRRL B-41902T was able to utilize a combination of l-serine, citraconic acid and citramalic acid, which differentiated it from other, closely related Acinetobacter species. Therefore, strain NRRL B-41902T (=CCUG 68785T) is proposed as the type strain of a novel species, Acinetobacter lactucae sp. nov.

  9. Acinetobacter variabilis sp. nov. (formerly DNA group 15 sensu Tjernberg & Ursing), isolated from humans and animals.

    PubMed

    Krizova, Lenka; McGinnis, Jana; Maixnerova, Martina; Nemec, Matej; Poirel, Laurent; Mingle, Lisa; Sedo, Ondrej; Wolfgang, William; Nemec, Alexandr

    2015-03-01

    We aimed to define the taxonomic status of 16 strains which were phenetically congruent with Acinetobacter DNA group 15 described by Tjernberg & Ursing in 1989. The strains were isolated from a variety of human and animal specimens in geographically distant places over the last three decades. Taxonomic analysis was based on an Acinetobacter-targeted, genus-wide approach that included the comparative sequence analysis of housekeeping, protein-coding genes, whole-cell profiling based on matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), an array of in-house physiological and metabolic tests, and whole-genome comparative analysis. Based on analyses of the rpoB and gyrB genes, the 16 strains formed respective, strongly supported clusters clearly separated from the other species of the genus Acinetobacter. The distinctness of the group at the species level was indicated by average nucleotide identity values of ≤82 % between the whole genome sequences of two of the 16 strains (NIPH 2171(T) and NIPH 899) and those of the known species. In addition, the coherence of the group was also supported by MALDI-TOF MS. All 16 strains were non-haemolytic and non-gelatinase-producing, grown at 41 °C and utilized a rather limited number of carbon sources. Virtually every strain displayed a unique combination of metabolic and physiological features. We conclude that the 16 strains represent a distinct species of the genus Acinetobacter, for which the name Acinetobacter variabilis sp. nov. is proposed to reflect its marked phenotypic heterogeneity. The type strain is NIPH 2171(T) ( = CIP 110486(T) = CCUG 26390(T) = CCM 8555(T)).

  10. Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species

    PubMed Central

    Hirakawa, Hideki; Shirasawa, Kenta; Kosugi, Shunichi; Tashiro, Kosuke; Nakayama, Shinobu; Yamada, Manabu; Kohara, Mistuyo; Watanabe, Akiko; Kishida, Yoshie; Fujishiro, Tsunakazu; Tsuruoka, Hisano; Minami, Chiharu; Sasamoto, Shigemi; Kato, Midori; Nanri, Keiko; Komaki, Akiko; Yanagi, Tomohiro; Guoxin, Qin; Maeda, Fumi; Ishikawa, Masami; Kuhara, Satoru; Sato, Shusei; Tabata, Satoshi; Isobe, Sachiko N.

    2014-01-01

    Cultivated strawberry (Fragaria x ananassa) is octoploid and shows allogamous behaviour. The present study aims at dissecting this octoploid genome through comparison with its wild relatives, F. iinumae, F. nipponica, F. nubicola, and F. orientalis by de novo whole-genome sequencing on an Illumina and Roche 454 platforms. The total length of the assembled Illumina genome sequences obtained was 698 Mb for F. x ananassa, and ∼200 Mb each for the four wild species. Subsequently, a virtual reference genome termed FANhybrid_r1.2 was constructed by integrating the sequences of the four homoeologous subgenomes of F. x ananassa, from which heterozygous regions in the Roche 454 and Illumina genome sequences were eliminated. The total length of FANhybrid_r1.2 thus created was 173.2 Mb with the N50 length of 5137 bp. The Illumina-assembled genome sequences of F. x ananassa and the four wild species were then mapped onto the reference genome, along with the previously published F. vesca genome sequence to establish the subgenomic structure of F. x ananassa. The strategy adopted in this study has turned out to be successful in dissecting the genome of octoploid F. x ananassa and appears promising when applied to the analysis of other polyploid plant species. PMID:24282021

  11. Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species.

    PubMed

    Hirakawa, Hideki; Shirasawa, Kenta; Kosugi, Shunichi; Tashiro, Kosuke; Nakayama, Shinobu; Yamada, Manabu; Kohara, Mistuyo; Watanabe, Akiko; Kishida, Yoshie; Fujishiro, Tsunakazu; Tsuruoka, Hisano; Minami, Chiharu; Sasamoto, Shigemi; Kato, Midori; Nanri, Keiko; Komaki, Akiko; Yanagi, Tomohiro; Guoxin, Qin; Maeda, Fumi; Ishikawa, Masami; Kuhara, Satoru; Sato, Shusei; Tabata, Satoshi; Isobe, Sachiko N

    2014-01-01

    Cultivated strawberry (Fragaria x ananassa) is octoploid and shows allogamous behaviour. The present study aims at dissecting this octoploid genome through comparison with its wild relatives, F. iinumae, F. nipponica, F. nubicola, and F. orientalis by de novo whole-genome sequencing on an Illumina and Roche 454 platforms. The total length of the assembled Illumina genome sequences obtained was 698 Mb for F. x ananassa, and ∼200 Mb each for the four wild species. Subsequently, a virtual reference genome termed FANhybrid_r1.2 was constructed by integrating the sequences of the four homoeologous subgenomes of F. x ananassa, from which heterozygous regions in the Roche 454 and Illumina genome sequences were eliminated. The total length of FANhybrid_r1.2 thus created was 173.2 Mb with the N50 length of 5137 bp. The Illumina-assembled genome sequences of F. x ananassa and the four wild species were then mapped onto the reference genome, along with the previously published F. vesca genome sequence to establish the subgenomic structure of F. x ananassa. The strategy adopted in this study has turned out to be successful in dissecting the genome of octoploid F. x ananassa and appears promising when applied to the analysis of other polyploid plant species.

  12. Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing

    PubMed Central

    Staton, Margaret; Best, Teodora; Khodwekar, Sudhir; Owusu, Sandra; Xu, Tao; Xu, Yi; Jennings, Tara; Cronn, Richard; Arumuganathan, A. Kathiravetpilla; Coggeshall, Mark; Gailing, Oliver; Liang, Haiying; Romero-Severson, Jeanne; Schlarbaum, Scott; Carlson, John E.

    2015-01-01

    Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence. PMID:26698853

  13. Intra-species sequence comparisons for annotating genomes

    SciTech Connect

    Boffelli, Dario; Weer, Claire V.; Weng, Li; Lewis, Keith D.; Shoukry, Malak I.; Pachter, Lior; Keys, David N.; Rubin, Edward M.

    2004-07-15

    Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its high rate of allelic polymorphism and ease of genetic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intra-species sequence comparisons for genome annotation. A large number of C. intestinalis specimens were collected from four continents and a set of genomic intervals amplified, resequenced and analyzed to determine the mutation rates at each nucleotide in the sequence. We found that regions with low mutation rates efficiently demarcated functionally constrained sequences: these include a set of noncoding elements, which we showed in C intestinalis transgenic assays to act as tissue-specific enhancers, as well as the location of coding sequences. This illustrates that comparisons of multiple members of a species can be used for genome annotation, suggesting a path for the annotation of the sequenced genomes of organisms occupying uncharacterized phylogenetic branches of the animal kingdom and raises the possibility that the resequencing of a large number of Homo sapiens individuals might be used to annotate the human genome and identify sequences defining traits unique to our species. The sequence data from this study has been submitted to GenBank under accession nos. AY667278-AY667407.

  14. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

    PubMed Central

    Dasmahapatra, Kanchon K; Walters, James R.; Briscoe, Adriana D.; Davey, John W.; Whibley, Annabel; Nadeau, Nicola J.; Zimin, Aleksey V.; Hughes, Daniel S. T.; Ferguson, Laura C.; Martin, Simon H.; Salazar, Camilo; Lewis, James J.; Adler, Sebastian; Ahn, Seung-Joon; Baker, Dean A.; Baxter, Simon W.; Chamberlain, Nicola L.; Chauhan, Ritika; Counterman, Brian A.; Dalmay, Tamas; Gilbert, Lawrence E.; Gordon, Karl; Heckel, David G.; Hines, Heather M.; Hoff, Katharina J.; Holland, Peter W.H.; Jacquin-Joly, Emmanuelle; Jiggins, Francis M.; Jones, Robert T.; Kapan, Durrell D.; Kersey, Paul; Lamas, Gerardo; Lawson, Daniel; Mapleson, Daniel; Maroja, Luana S.; Martin, Arnaud; Moxon, Simon; Palmer, William J.; Papa, Riccardo; Papanicolaou, Alexie; Pauchet, Yannick; Ray, David A.; Rosser, Neil; Salzberg, Steven L.; Supple, Megan A.; Surridge, Alison; Tenger-Trolander, Ayse; Vogel, Heiko; Wilkinson, Paul A.; Wilson, Derek; Yorke, James A.; Yuan, Furong; Balmuth, Alexi L.; Eland, Cathlene; Gharbi, Karim; Thomson, Marian; Gibbs, Richard A.; Han, Yi; Jayaseelan, Joy C.; Kovar, Christie; Mathew, Tittu; Muzny, Donna M.; Ongeri, Fiona; Pu, Ling-Ling; Qu, Jiaxin; Thornton, Rebecca L.; Worley, Kim C.; Wu, Yuan-Qing; Linares, Mauricio; Blaxter, Mark L.; Constant, Richard H. ffrench; Joron, Mathieu; Kronforst, Marcus R.; Mullen, Sean P.; Reed, Robert D.; Scherer, Steven E.; Richards, Stephen; Mallet, James; McMillan, W. Owen; Jiggins, Chris D.

    2012-01-01

    The evolutionary importance of hybridization and introgression has long been debated1. We used genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation2-5 . We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,657 predicted genes for Heliconius, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organisation has remained broadly conserved since the Cretaceous, when butterflies split from the silkmoth lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, H. melpomene, H. timareta, and H. elevatus, especially at two genomic regions that control mimicry pattern. Closely related Heliconius species clearly exchange protective colour pattern genes promiscuously, implying a major role for hybridization in adaptive radiation. PMID:22722851

  15. Comparative Analysis of Genome Sequences Covering the Seven Cronobacter Species

    PubMed Central

    Cummings, Craig A.; Shih, Rita; Degoricija, Lovorka; Rico, Alain; Brzoska, Pius; Hamby, Stephen E.; Masood, Naqash; Hariri, Sumyya; Sonbol, Hana; Chuzhanova, Nadia; McClelland, Michael; Furtado, Manohar R.; Forsythe, Stephen J.

    2012-01-01

    Background Species of Cronobacter are widespread in the environment and are occasional food-borne pathogens associated with serious neonatal diseases, including bacteraemia, meningitis, and necrotising enterocolitis. The genus is composed of seven species: C. sakazakii, C. malonaticus, C. turicensis, C. dublinensis, C. muytjensii, C. universalis, and C. condimenti. Clinical cases are associated with three species, C. malonaticus, C. turicensis and, in particular, with C. sakazakii multilocus sequence type 4. Thus, it is plausible that virulence determinants have evolved in certain lineages. Methodology/Principal Findings We generated high quality sequence drafts for eleven Cronobacter genomes representing the seven Cronobacter species, including an ST4 strain of C. sakazakii. Comparative analysis of these genomes together with the two publicly available genomes revealed Cronobacter has over 6,000 genes in one or more strains and over 2,000 genes shared by all Cronobacter. Considerable variation in the presence of traits such as type six secretion systems, metal resistance (tellurite, copper and silver), and adhesins were found. C. sakazakii is unique in the Cronobacter genus in encoding genes enabling the utilization of exogenous sialic acid which may have clinical significance. The C. sakazakii ST4 strain 701 contained additional genes as compared to other C. sakazakii but none of them were known specific virulence-related genes. Conclusions/Significance Genome comparison revealed that pair-wise DNA sequence identity varies between 89 and 97% in the seven Cronobacter species, and also suggested various degrees of divergence. Sets of universal core genes and accessory genes unique to each strain were identified. These gene sequences can be used for designing genus/species specific detection assays. Genes encoding adhesins, T6SS, and metal resistance genes as well as prophages are found in only subsets of genomes and have contributed considerably to the variation of

  16. High frequency of Acinetobacter soli among Acinetobacter isolates causing bacteremia at a tertiary hospital in Japan.

    PubMed

    Endo, Shiro; Yano, Hisakazu; Kanamori, Hajime; Inomata, Shinya; Aoyagi, Tetsuji; Hatta, Masumitsu; Gu, Yoshiaki; Tokuda, Koichi; Kitagawa, Miho; Kaku, Mitsuo

    2014-03-01

    Acinetobacter baumannii is generally the most frequently isolated Acinetobacter species. Sequence analysis techniques allow reliable identification of Acinetobacter isolates at the species level. Forty-eight clinical isolates of Acinetobacter spp. were obtained from blood cultures at Tohoku University Hospital. These isolates were identified at the species level by partial sequencing of the RNA polymerase β-subunit (rpoB), 16S rRNA, and gyrB genes. Then further characterization was done by using the PCR for detection of OXA-type β-lactamase gene clusters, metallo-β-lactamases, and carO genes. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing were also performed. The most frequent isolate was Acinetobacter soli (27.1%). Six of the 13 A. soli isolates were carbapenem nonsusceptible, and all of these isolates produced IMP-1. PFGE revealed that the 13 A. soli isolates were divided into 8 clusters. This study demonstrated that A. soli accounted for a high proportion of Acinetobacter isolates causing bacteremia at a Japanese tertiary hospital. Non-A. baumannii species were identified more frequently than A. baumannii and carbapenem-nonsusceptible isolates were found among the non-A. baumannii strains. These results emphasize the importance of performing epidemiological investigations of Acinetobacter species.

  17. Retrotransposon populations of Vicia species with varying genome size.

    PubMed

    Hill, Pamela; Burford, Debbie; Martin, David M A; Flavell, Andrew J

    2005-06-01

    The (non-LTR) LINE and Ty3-gypsy-type LTR retrotransposon populations of three Vicia species that differ in genome size (Vicia faba, Vicia melanops and Vicia sativa) have been characterised. In each species the LINE retrotransposons comprise a complex, very heterogeneous set of sequences, while the Ty3-gypsy elements are much more homogeneous. Copy numbers of all three retrotransposon groups (Ty1-copia, Ty3-gypsy and LINE) in these species have been estimated by random genomic sequencing and Southern hybridisation analysis. The Ty3-gypsy elements are extremely numerous in all species, accounting for 18-35% of their genomes. The Ty1-copia group elements are somewhat less abundant and LINE elements are present in still lower amounts. Collectively, 20-45% of the genomes of these three Vicia species are comprised of retrotransposons. These data show that the three retrotransposon groups have proliferated to different extents in members of the Vicia genus and high proliferation has been associated with homogenisation of the retrotransposon population.

  18. Role of hospital surfaces in the transmission of emerging health care-associated pathogens: norovirus, Clostridium difficile, and Acinetobacter species.

    PubMed

    Weber, David J; Rutala, William A; Miller, Melissa B; Huslage, Kirk; Sickbert-Bennett, Emily

    2010-06-01

    Health care-associated infections (HAI) remain a major cause of patient morbidity and mortality. Although the main source of nosocomial pathogens is likely the patient's endogenous flora, an estimated 20% to 40% of HAI have been attributed to cross infection via the hands of health care personnel, who have become contaminated from direct contact with the patient or indirectly by touching contaminated environmental surfaces. Multiple studies strongly suggest that environmental contamination plays an important role in the transmission of methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus spp. More recently, evidence suggests that environmental contamination also plays a role in the nosocomial transmission of norovirus, Clostridium difficile, and Acinetobacter spp. All 3 pathogens survive for prolonged periods of time in the environment, and infections have been associated with frequent surface contamination in hospital rooms and health care worker hands. In some cases, the extent of patient-to-patient transmission has been found to be directly proportional to the level of environmental contamination. Improved cleaning/disinfection of environmental surfaces and hand hygiene have been shown to reduce the spread of all of these pathogens. Importantly, norovirus and C difficile are relatively resistant to the most common surface disinfectants and waterless alcohol-based antiseptics. Current hand hygiene guidelines and recommendations for surface cleaning/disinfection should be followed in managing outbreaks because of these emerging pathogens.

  19. The genomes of four tapeworm species reveal adaptations to parasitism.

    PubMed

    Tsai, Isheng J; Zarowiecki, Magdalena; Holroyd, Nancy; Garciarrubio, Alejandro; Sanchez-Flores, Alejandro; Brooks, Karen L; Tracey, Alan; Bobes, Raúl J; Fragoso, Gladis; Sciutto, Edda; Aslett, Martin; Beasley, Helen; Bennett, Hayley M; Cai, Jianping; Camicia, Federico; Clark, Richard; Cucher, Marcela; De Silva, Nishadi; Day, Tim A; Deplazes, Peter; Estrada, Karel; Fernández, Cecilia; Holland, Peter W H; Hou, Junling; Hu, Songnian; Huckvale, Thomas; Hung, Stacy S; Kamenetzky, Laura; Keane, Jacqueline A; Kiss, Ferenc; Koziol, Uriel; Lambert, Olivia; Liu, Kan; Luo, Xuenong; Luo, Yingfeng; Macchiaroli, Natalia; Nichol, Sarah; Paps, Jordi; Parkinson, John; Pouchkina-Stantcheva, Natasha; Riddiford, Nick; Rosenzvit, Mara; Salinas, Gustavo; Wasmuth, James D; Zamanian, Mostafa; Zheng, Yadong; Cai, Xuepeng; Soberón, Xavier; Olson, Peter D; Laclette, Juan P; Brehm, Klaus; Berriman, Matthew

    2013-04-04

    Tapeworms (Cestoda) cause neglected diseases that can be fatal and are difficult to treat, owing to inefficient drugs. Here we present an analysis of tapeworm genome sequences using the human-infective species Echinococcus multilocularis, E. granulosus, Taenia solium and the laboratory model Hymenolepis microstoma as examples. The 115- to 141-megabase genomes offer insights into the evolution of parasitism. Synteny is maintained with distantly related blood flukes but we find extreme losses of genes and pathways that are ubiquitous in other animals, including 34 homeobox families and several determinants of stem cell fate. Tapeworms have specialized detoxification pathways, metabolism that is finely tuned to rely on nutrients scavenged from their hosts, and species-specific expansions of non-canonical heat shock proteins and families of known antigens. We identify new potential drug targets, including some on which existing pharmaceuticals may act. The genomes provide a rich resource to underpin the development of urgently needed treatments and control.

  20. Genetic environment of the KPC gene in Acinetobacter baumannii ST2 clone from Puerto Rico and genomic insights into its drug resistance.

    PubMed

    Martinez, Teresa; Martinez, Idali; Vazquez, Guillermo J; Aquino, Edna E; Robledo, Iraida E

    2016-08-01

    Carbapenems are considered the last-resort antibiotics to treat infections caused by multidrug-resistant Gram-negative bacilli. The Klebsiella pneumoniae carbapenemase (KPC) enzyme hydrolyses β-lactam antibiotics including the carbapenems. KPC has been detected worldwide in Enterobacteriaceae and Pseudomonas aeruginosa isolates associated with transposon Tn4401 commonly located in plasmids. Acinetobacter baumannii has become an important multidrug-resistant nosocomial pathogen. KPC-producing A. baumannii has been reported to date only in Puerto Rico. The objective of this study was to determine the whole genomic sequence of a KPC-producing A. baumannii in order to (i) define its allelic diversity, (ii) identify the location and genetic environment of the blaKPC and (iii) detect additional mechanisms of antimicrobial resistance. Next-generation sequencing, Southern blot, PFGE, multilocus sequence typing and bioinformatics analysis were performed. The organism was assigned to the international ST2 clone. The blaKPC-2 was identified on a novel truncated version of Tn4401e (tentatively named Tn4401h), located in the chromosome within an IncA/C plasmid fragment derived from an Enterobacteriaceae, probably owing to insertion sequence IS26. A chromosomally located truncated Tn1 transposon harbouring a blaTEM-1 was found in a novel genetic environment within an antimicrobial resistance cluster. Additional resistance mechanisms included efflux pumps, non-β-lactam antibiotic inactivating enzymes within and outside a resistance island, two class 1 integrons, In439 and the novel In1252, as well as mutations in the topoisomerase and DNA gyrase genes which confer resistance to quinolones. The presence of the blaKPC in an already globally disseminated A. baumannii ST2 presents a serious threat of further dissemination.

  1. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.

    PubMed

    2012-07-05

    The evolutionary importance of hybridization and introgression has long been debated. Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species. Here we use genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation. We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,669 predicted genes, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organization has remained broadly conserved since the Cretaceous period, when butterflies split from the Bombyx (silkmoth) lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, Heliconius melpomene, Heliconius timareta and Heliconius elevatus, especially at two genomic regions that control mimicry pattern. We infer that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.

  2. Genome skimming identifies polymorphism in tern populations and species

    PubMed Central

    2012-01-01

    Background Terns (Charadriiformes: Sterninae) are a lineage of cosmopolitan shorebirds with a disputed evolutionary history that comprises several species of conservation concern. As a non-model system in genetics, previous study has left most of the nuclear genome unexplored, and population-level studies are limited to only 15% of the world's species of terns and noddies. Screening of polymorphic nuclear sequence markers is needed to enhance genetic resolution because of supposed low mitochondrial mutation rate, documentation of nuclear insertion of hypervariable mitochondrial regions, and limited success of microsatellite enrichment in terns. Here, we investigated the phylogenetic and population genetic utility for terns and relatives of a variety of nuclear markers previously developed for other birds and spanning the nuclear genome. Markers displaying a variety of mutation rates from both the nuclear and mitochondrial genome were tested and prioritized according to optimal cross-species amplification and extent of genetic polymorphism between (1) the main tern clades and (2) individual Royal Terns (Thalasseus maxima) breeding on the US East Coast. Results Results from this genome skimming effort yielded four new nuclear sequence-based markers for tern phylogenetics and 11 intra-specific polymorphic markers. Further, comparison between the two genomes indicated a phylogenetic conflict at the base of terns, involving the inclusion (mitochondrial) or exclusion (nuclear) of the Angel Tern (Gygis alba). Although limited mitochondrial variation was confirmed, both nuclear markers and a short tandem repeat in the mitochondrial control region indicated the presence of considerable genetic variation in Royal Terns at a regional scale. Conclusions These data document the value of intronic markers to the study of terns and allies. We expect that these and additional markers attained through next-generation sequencing methods will accurately map the genetic origin and

  3. Genomic analysis of the native European Solanum species, S. dulcamara

    PubMed Central

    2013-01-01

    Background Solanum dulcamara (bittersweet, climbing nightshade) is one of the few species of the Solanaceae family native to Europe. As a common weed it is adapted to a wide range of ecological niches and it has long been recognized as one of the alternative hosts for pathogens and pests responsible for many important diseases in potato, such as Phytophthora. At the same time, it may represent an alternative source of resistance genes against these diseases. Despite its unique ecology and potential as a genetic resource, genomic research tools are lacking for S. dulcamara. We have taken advantage of next-generation sequencing to speed up research on and use of this non-model species. Results In this work, we present the first large-scale characterization of the S. dulcamara transcriptome. Through comparison of RNAseq reads from two different accessions, we were able to predict transcript-based SNP and SSR markers. Using the SNP markers in combination with genomic AFLP and CAPS markers, the first genome-wide genetic linkage map of bittersweet was generated. Based on gene orthology, the markers were anchored to the genome of related Solanum species (tomato, potato and eggplant), revealing both conserved and novel chromosomal rearrangements. This allowed a better estimation of the evolutionary moment of rearrangements in a number of cases and showed that chromosomal breakpoints are regularly re-used. Conclusion Knowledge and tools developed as part of this study pave the way for future genomic research and exploitation of this wild Solanum species. The transcriptome assembly represents a resource for functional analysis of genes underlying interesting biological and agronomical traits and, in the absence of the full genome, provides a reference for RNAseq gene expression profiling aimed at understanding the unique biology of S. dulcamara. Cross-species orthology-based marker selection is shown to be a powerful tool to quickly generate a comparative genetic map, which

  4. Evaluation of the Bruker Biotyper Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Identification of Blood Isolates of Acinetobacter Species

    PubMed Central

    Hsueh, Po-Ren; Kuo, Lu-Cheng; Chang, Tsung-Chain; Lee, Tai-Fen; Teng, Shih-Hua; Chuang, Yu-Chung; Teng, Lee-Jene

    2014-01-01

    Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) (Bruker Biotyper) was able to accurately identify 98.6% (142/144) of Acinetobacter baumannii isolates, 72.4% (63/87) of A. nosocomialis isolates, and 97.6% (41/42) of A. pittii isolates. All Acinetobacter junii, A. ursingii, A. johnsonii, and A. radioresistens isolates (n = 28) could also be identified correctly by Bruker Biotyper. PMID:24899038

  5. Minocycline activity tested against Acinetobacter baumannii complex, Stenotrophomonas maltophilia, and Burkholderia cepacia species complex isolates from a global surveillance program (2013).

    PubMed

    Flamm, Robert K; Castanheira, Mariana; Streit, Jennifer M; Jones, Ronald N

    2016-07-01

    Clinical isolates of Acinetobacter baumannii complex (1312), Stenotrophomonas maltophilia (464), and Burkholderia cepacia species complex (30) were selected from medical centers in the United States (USA), Europe and the Mediterranean (EU-M) region, Latin America, and Asia Pacific. Only one isolate per infected patient episode was included and local identifications were confirmed by the monitoring laboratory. Susceptibility testing was performed at the monitoring laboratory using the reference broth microdilution method as described by Clinical and Laboratory Standards Institute (CLSI). A. baumannii complex were classified as MDR (multi-drug resistant [MDR]; nonsusceptible to ≥1 agent in ≥3 antimicrobial classes) and extensively drug-resistant (XDR; nonsusceptible to ≥1 agent in all but ≤2 antimicrobial classes). A total of 81.6% of A. baumannii complex were MDR. Colistin was the most active agent against MDR A. baumannii complex. Minocycline was the most active "tetracycline" against these organisms based on susceptibility. Against B. cepacia, trimethoprim-sulfamethoxazole (MIC90, 2 μg/mL; 100.0% susceptible) was the most active agent tested. Overall, minocycline was the most active tetracycline tested against A. baumannii complex and S. maltophilia isolates collected from patients throughout EU-M, USA, Latin America, and the Asia-Pacific. Minocycline, particularly the intravenous formulation, has activity against several ESKAPE pathogens and merits consideration in seriously ill patients where treatment options may be limited due to the presence of MDR bacteria.

  6. Mapping whole genome shotgun sequence and variant calling in mammalian species without their reference genomes.

    PubMed

    Kalbfleisch, Ted; Heaton, Michael P

    2013-01-01

    Genomics research in mammals has produced reference genome sequences that are essential for identifying variation associated with disease.  High quality reference genome sequences are now available for humans, model species, and economically important agricultural animals.  Comparisons between these species have provided unique insights into mammalian gene function.  However, the number of species with reference genomes is small compared to those needed for studying molecular evolutionary relationships in the tree of life.  For example, among the even-toed ungulates there are approximately 300 species whose phylogenetic relationships have been calculated in the 10k trees project.  Only six of these have reference genomes:  cattle, swine, sheep, goat, water buffalo, and bison.  Although reference sequences will eventually be developed for additional hoof stock, the resources in terms of time, money, infrastructure and expertise required to develop a quality reference genome may be unattainable for most species for at least another decade.  In this work we mapped 35 Gb of next generation sequence data of a Katahdin sheep to its own species' reference genome ( Ovis aries Oar3.1) and to that of a species that diverged 15 to 30 million years ago ( Bos taurus UMD3.1).  In total, 56% of reads covered 76% of UMD3.1 to an average depth of 6.8 reads per site, 83 million variants were identified, of which 78 million were homozygous and likely represent interspecies nucleotide differences. Excluding repeat regions and sex chromosomes, nearly 3.7 million heterozygous sites were identified in this animal vs. bovine UMD3.1, representing polymorphisms occurring in sheep.  Of these, 41% could be readily mapped to orthologous positions in ovine Oar3.1 with 80% corroborated as heterozygous.  These variant sites, identified via interspecies mapping could be used for comparative genomics, disease association studies, and ultimately to understand mammalian gene

  7. Draft genome sequence of the oilseed species Ricinus communis.

    PubMed

    Chan, Agnes P; Crabtree, Jonathan; Zhao, Qi; Lorenzi, Hernan; Orvis, Joshua; Puiu, Daniela; Melake-Berhan, Admasu; Jones, Kristine M; Redman, Julia; Chen, Grace; Cahoon, Edgar B; Gedil, Melaku; Stanke, Mario; Haas, Brian J; Wortman, Jennifer R; Fraser-Liggett, Claire M; Ravel, Jacques; Rabinowicz, Pablo D

    2010-09-01

    Castor bean (Ricinus communis) is an oilseed crop that belongs to the spurge (Euphorbiaceae) family, which comprises approximately 6,300 species that include cassava (Manihot esculenta), rubber tree (Hevea brasiliensis) and physic nut (Jatropha curcas). It is primarily of economic interest as a source of castor oil, used for the production of high-quality lubricants because of its high proportion of the unusual fatty acid ricinoleic acid. However, castor bean genomics is also relevant to biosecurity as the seeds contain high levels of ricin, a highly toxic, ribosome-inactivating protein. Here we report the draft genome sequence of castor bean (4.6-fold coverage), the first for a member of the Euphorbiaceae. Whereas most of the key genes involved in oil synthesis and turnover are single copy, the number of members of the ricin gene family is larger than previously thought. Comparative genomics analysis suggests the presence of an ancient hexaploidization event that is conserved across the dicotyledonous lineage.

  8. Draft Genome Sequence of an Aflatoxigenic Aspergillus Species, A. bombycis

    PubMed Central

    Moore, Geromy G.; Mack, Brian M.; Beltz, Shannon B.; Gilbert, Matthew K.

    2016-01-01

    Aspergillus bombycis was first isolated from silkworm frass in Japan. It has been reportedly misidentified as A. nomius due to their macro-morphological and chemotype similarities. We sequenced the genome of the A. bombycis Type strain and found it to be comparable in size (37 Mb), as well as in numbers of predicted genes (12,266), to other sequenced Aspergilli. The aflatoxin gene cluster in this strain is similar in size and the genes are oriented the same as other B- + G-aflatoxin producing species, and this strain contains a complete but nonfunctional gene cluster for the production of cyclopiazonic acid. Our findings also showed that the A. bombycis Type strain contains a single MAT1-2 gene indicating that this species is likely heterothallic (self-infertile). This draft genome will contribute to our understanding of the genes and pathways necessary for aflatoxin synthesis as well as the evolutionary relationships of aflatoxigenic fungi. PMID:27664179

  9. Identification of a new allelic variant of the Acinetobacter baumannii cephalosporinase, ADC-7 beta-lactamase: defining a unique family of class C enzymes.

    PubMed

    Hujer, Kristine M; Hamza, Nashaat S; Hujer, Andrea M; Perez, Federico; Helfand, Marion S; Bethel, Christopher R; Thomson, Jodi M; Anderson, Vernon E; Barlow, Miriam; Rice, Louis B; Tenover, Fred C; Bonomo, Robert A

    2005-07-01

    Acinetobacter spp. are emerging as opportunistic hospital pathogens that demonstrate resistance to many classes of antibiotics. In a metropolitan hospital in Cleveland, a clinical isolate of Acinetobacter baumannii that tested resistant to cefepime and ceftazidime (MIC = 32 microg/ml) was identified. Herein, we sought to determine the molecular basis for the extended-spectrum-cephalosporin resistance. Using analytical isoelectric focusing, a beta-lactamase with a pI of > or = 9.2 was detected. PCR amplification with specific A. baumannii cephalosporinase primers yielded a 1,152-bp product which, when sequenced, identified a novel 383-amino-acid class C enzyme. Expressed in Escherichia coli DH10B, this beta-lactamase demonstrated greater resistance against ceftazidime and cefotaxime than cefepime (4.0 microg/ml versus 0.06 microg/ml). The kinetic characteristics of this beta-lactamase were similar to other cephalosporinases found in Acinetobacter spp. In addition, this cephalosporinase was inhibited by meropenem, imipenem, ertapenem, and sulopenem (K(i) < 40 microM). The amino acid compositions of this novel enzyme and other class C beta-lactamases thus far described for A. baumannii, Acinetobacter genomic species 3, and Oligella urethralis in Europe and South Africa suggest that this cephalosporinase defines a unique family of class C enzymes. We propose a uniform designation for this family of cephalosporinases (Acinetobacter-derived cephalosporinases [ADC]) found in Acinetobacter spp. and identify this enzyme as ADC-7 beta-lactamase. The coalescence of Acinetobacter ampC beta-lactamases into a single common ancestor and the substantial phylogenetic distance separating them from other ampC genes support the logical value of developing a system of nomenclature for these Acinetobacter cephalosporinase genes.

  10. Identification of a New Allelic Variant of the Acinetobacter baumannii Cephalosporinase, ADC-7 β-Lactamase: Defining a Unique Family of Class C Enzymes‡

    PubMed Central

    Hujer, Kristine M.; Hamza, Nashaat S.; Hujer, Andrea M.; Perez, Federico; Helfand, Marion S.; Bethel, Christopher R.; Thomson, Jodi M.; Anderson, Vernon E.; Barlow, Miriam; Rice, Louis B.; Tenover, Fred C.; Bonomo, Robert A.

    2005-01-01

    Acinetobacter spp. are emerging as opportunistic hospital pathogens that demonstrate resistance to many classes of antibiotics. In a metropolitan hospital in Cleveland, a clinical isolate of Acinetobacter baumannii that tested resistant to cefepime and ceftazidime (MIC = 32 μg/ml) was identified. Herein, we sought to determine the molecular basis for the extended-spectrum-cephalosporin resistance. Using analytical isoelectric focusing, a β-lactamase with a pI of ≥9.2 was detected. PCR amplification with specific A. baumannii cephalosporinase primers yielded a 1,152-bp product which, when sequenced, identified a novel 383-amino-acid class C enzyme. Expressed in Escherichia coli DH10B, this β-lactamase demonstrated greater resistance against ceftazidime and cefotaxime than cefepime (4.0 μg/ml versus 0.06 μg/ml). The kinetic characteristics of this β-lactamase were similar to other cephalosporinases found in Acinetobacter spp. In addition, this cephalosporinase was inhibited by meropenem, imipenem, ertapenem, and sulopenem (Ki < 40 μM). The amino acid compositions of this novel enzyme and other class C β-lactamases thus far described for A. baumannii, Acinetobacter genomic species 3, and Oligella urethralis in Europe and South Africa suggest that this cephalosporinase defines a unique family of class C enzymes. We propose a uniform designation for this family of cephalosporinases (Acinetobacter-derived cephalosporinases [ADC]) found in Acinetobacter spp. and identify this enzyme as ADC-7 β-lactamase. The coalescence of Acinetobacter ampC β-lactamases into a single common ancestor and the substantial phylogenetic distance separating them from other ampC genes support the logical value of developing a system of nomenclature for these Acinetobacter cephalosporinase genes. PMID:15980372

  11. Prevalence and antimicrobial susceptibility of Acinetobacter spp. isolated from meat.

    PubMed

    Carvalheira, Ana; Casquete, Rocio; Silva, Joana; Teixeira, Paula

    2017-02-21

    The prevalence and antibiotic resistance of Acinetobacter spp. from fifty samples of meat (chicken, turkey, beef and pork) were evaluated. Acinetobacter spp. was recovered from all samples and the clonal relatedness of 223 isolates identified to belong to the genus Acinetobacter was established by PFGE. A high genetic diversity was observed and 166 isolates from different samples, 141 representing different PFGE profiles, were further identified to the species level by rpoB gene sequencing. Thirteen distinct Acinetobacter species were identified among 156 isolates. The remaining ten isolates may represent three putatively novel species since rpoB sequence homologies with type strains of all available described Acinetobacter species, were <95%. The most common species was Acinetobacter guillouiae with a prevalence of 34.9%. However 18.7% of the strains belong to the Acinetobacter baumannii group (n=31) which include the species Acinetobacter baumannii (n=7), Acinetobacter pittii (n=12), Acinetobacter seifertii (n=8) and Acinetobacter nosocomialis (n=4) that are the species most frequently associated with nosocomial infections worldwide. In general, strains were resistant to some of the antimicrobials most frequently used to treat Acinetobacter infections such as piperacillin-tazobactam (64.9% of strains resistant), ceftazidime (43.5%), ciprofloxacin (42.9%), as well as to colistin (41.7%) and polymyxin B (35.1%), the last-resort drugs to treat infections caused by multidrug-resistant Acinetobacter. The percentage of resistant strains to trimethoprim-sulfamethoxazole, tetracycline, aminoglycosides (amikacin and tobramycin) and ampicillin-sulbactam was >10% (23.2%, 23.2%, 14.3%, 12.5%, 12.5%, respectively). However, resistances to meropenem, imipenem and minocycline were only sporadically observed (8.3%, 1.2% and 1.2%, respectively). Overall, 51.2% of the strains were considered as multidrug-resistant (MDR) and 9.6% as extensively drug-resistant (XDR). The prevalence

  12. Genomic approaches for interrogating the biochemistry of medicinal plant species

    PubMed Central

    Góngora-Castillo, Elsa; Fedewa, Greg; Yeo, Yunsoo; Chappell, Joe; DellaPenna, Dean; Buell, C. Robin

    2013-01-01

    Development of next-generation sequencing, coupled with the advancement of computational methods, has allowed researchers to access the transcriptomes of recalcitrant genomes such as those of medicinal plant species. Through the sequencing of even a few cDNA libraries, a broad representation of the transcriptome of any medicinal plant species can be obtained, providing a robust resource for gene discovery and downstream biochemical pathway discovery. When coupled to estimation of expression abundances in specific tissues from a developmental series, biotic stress, abiotic stress, or elicitor challenge, informative coexpression and differential expression estimates on a whole transcriptome level can be obtained to identify candidates for function discovery. PMID:23084937

  13. Complete Mitochondrial Genome of Anoplocephala magna Solidifying the Species

    PubMed Central

    Guo, Aijiang

    2016-01-01

    The 2 species of the genus Anoplocephala (Anoplocephalidae), A. perfoliata and A. magna, are among the most important equine cestode parasites. However, there is little information about their differences at the molecular level. The present study revealed that the mitochondrial (mt) genome of A. magna was 13,759 bp in size and 700 bp shorter than that of A. perfoliata. The 2 species includes 2 rRNA, 22 tRNA, and 12 protein-coding genes each. The size of each of the 36 genes was the same as that of A. perfoliata, except for cox1, rrnL, trnC, trnS2(UCN), trnG, trnH, trnQ, and trnP. In the full mitochondrial genome, the sequence similarity was 87.1%. The divergence in the nucleotide and amino acid sequences of individual protein-coding genes ranged from 11.1% to 16% and 6.8% to 16.4%, respectively. The 2 noncoding regions of the mt genome of A. magna were 199 bp and 271 bp in length, while the equivalent regions in A. perfoliata were 875 bp and 276 bp, respectively. The results of this study support the proposal that A. magna and A. perfoliata are separate species, consistent with previous morphological analyses. PMID:27417096

  14. Medically Relevant Acinetobacter Species Require a Type II Secretion System and Specific Membrane-Associated Chaperones for the Export of Multiple Substrates and Full Virulence

    PubMed Central

    Harding, Christian M.; Kinsella, Rachel L.; Palmer, Lauren D.; Skaar, Eric P.; Feldman, Mario F.

    2016-01-01

    Acinetobacter baumannii, A. nosocomialis, and A. pittii have recently emerged as opportunistic human pathogens capable of causing severe human disease; however, the molecular mechanisms employed by Acinetobacter to cause disease remain poorly understood. Many pathogenic members of the genus Acinetobacter contain genes predicted to encode proteins required for the biogenesis of a type II secretion system (T2SS), which have been shown to mediate virulence in many Gram-negative organisms. Here we demonstrate that Acinetobacter nosocomialis strain M2 produces a functional T2SS, which is required for full virulence in both the Galleria mellonella and murine pulmonary infection models. Importantly, this is the first bona fide secretion system shown to be required for virulence in Acinetobacter. Using bioinformatics, proteomics, and mutational analyses, we show that Acinetobacter employs its T2SS to export multiple substrates, including the lipases LipA and LipH as well as the protease CpaA. Furthermore, the Acinetobacter T2SS, which is found scattered amongst five distinct loci, does not contain a dedicated pseudopilin peptidase, but instead relies on the type IV prepilin peptidase, reinforcing the common ancestry of these two systems. Lastly, two of the three secreted proteins characterized in this study require specific chaperones for secretion. These chaperones contain an N-terminal transmembrane domain, are encoded adjacently to their cognate effector, and their disruption abolishes type II secretion of their cognate effector. Bioinformatic analysis identified putative chaperones located adjacent to multiple previously known type II effectors from several Gram-negative bacteria, which suggests that T2SS chaperones constitute a separate class of membrane-associated chaperones mediating type II secretion. PMID:26764912

  15. Medically Relevant Acinetobacter Species Require a Type II Secretion System and Specific Membrane-Associated Chaperones for the Export of Multiple Substrates and Full Virulence.

    PubMed

    Harding, Christian M; Kinsella, Rachel L; Palmer, Lauren D; Skaar, Eric P; Feldman, Mario F

    2016-01-01

    Acinetobacter baumannii, A. nosocomialis, and A. pittii have recently emerged as opportunistic human pathogens capable of causing severe human disease; however, the molecular mechanisms employed by Acinetobacter to cause disease remain poorly understood. Many pathogenic members of the genus Acinetobacter contain genes predicted to encode proteins required for the biogenesis of a type II secretion system (T2SS), which have been shown to mediate virulence in many Gram-negative organisms. Here we demonstrate that Acinetobacter nosocomialis strain M2 produces a functional T2SS, which is required for full virulence in both the Galleria mellonella and murine pulmonary infection models. Importantly, this is the first bona fide secretion system shown to be required for virulence in Acinetobacter. Using bioinformatics, proteomics, and mutational analyses, we show that Acinetobacter employs its T2SS to export multiple substrates, including the lipases LipA and LipH as well as the protease CpaA. Furthermore, the Acinetobacter T2SS, which is found scattered amongst five distinct loci, does not contain a dedicated pseudopilin peptidase, but instead relies on the type IV prepilin peptidase, reinforcing the common ancestry of these two systems. Lastly, two of the three secreted proteins characterized in this study require specific chaperones for secretion. These chaperones contain an N-terminal transmembrane domain, are encoded adjacently to their cognate effector, and their disruption abolishes type II secretion of their cognate effector. Bioinformatic analysis identified putative chaperones located adjacent to multiple previously known type II effectors from several Gram-negative bacteria, which suggests that T2SS chaperones constitute a separate class of membrane-associated chaperones mediating type II secretion.

  16. Lactobacillus paracasei Comparative Genomics: Towards Species Pan-Genome Definition and Exploitation of Diversity

    PubMed Central

    Smokvina, Tamara; Wels, Michiel; Polka, Justyna; Chervaux, Christian; Brisse, Sylvain; Boekhorst, Jos; Vlieg, Johan E. T. van Hylckama; Siezen, Roland J.

    2013-01-01

    Lactobacillus paracasei is a member of the normal human and animal gut microbiota and is used extensively in the food industry in starter cultures for dairy products or as probiotics. With the development of low-cost, high-throughput sequencing techniques it has become feasible to sequence many different strains of one species and to determine its “pan-genome”. We have sequenced the genomes of 34 different L. paracasei strains, and performed a comparative genomics analysis. We analysed genome synteny and content, focussing on the pan-genome, core genome and variable genome. Each genome was shown to contain around 2800–3100 protein-coding genes, and comparative analysis identified over 4200 ortholog groups that comprise the pan-genome of this species, of which about 1800 ortholog groups make up the conserved core. Several factors previously associated with host-microbe interactions such as pili, cell-envelope proteinase, hydrolases p40 and p75 or the capacity to produce short branched-chain fatty acids (bkd operon) are part of the L. paracasei core genome present in all analysed strains. The variome consists mainly of hypothetical proteins, phages, plasmids, transposon/conjugative elements, and known functions such as sugar metabolism, cell-surface proteins, transporters, CRISPR-associated proteins, and EPS biosynthesis proteins. An enormous variety and variability of sugar utilization gene cassettes were identified, with each strain harbouring between 25–53 cassettes, reflecting the high adaptability of L. paracasei to different niches. A phylogenomic tree was constructed based on total genome contents, and together with an analysis of horizontal gene transfer events we conclude that evolution of these L. paracasei strains is complex and not always related to niche adaptation. The results of this genome content comparison was used, together with high-throughput growth experiments on various carbohydrates, to perform gene-trait matching analysis, in order to

  17. Mitochondrial Genome Supports Sibling Species of Angiostrongylus costaricensis (Nematoda: Angiostrongylidae)

    PubMed Central

    Yong, Hoi-Sen; Song, Sze-Looi; Eamsobhana, Praphathip; Goh, Share-Yuan; Lim, Phaik-Eem; Chow, Wan-Loo; Chan, Kok-Gan; Abrahams-Sandi, Elizabeth

    2015-01-01

    Angiostrongylus costaricensis is a zoonotic parasitic nematode that causes abdominal or intestinal angiostrongyliasis in humans. It is endemic to the Americas. Although the mitochondrial genome of the Brazil taxon has been published, there is no available mitochondrial genome data on the Costa Rica taxon. We report here the complete mitochondrial genome of the Costa Rica taxon and its genetic differentiation from the Brazil taxon. The whole mitochondrial genome was obtained from next-generation sequencing of genomic DNA. It had a total length of 13,652 bp, comprising 36 genes (12 protein-coding genes—PCGs, 2 rRNA and 22 tRNA genes) and a control region (A + T rich non-coding region). It is longer than that of the Brazil taxon (13,585 bp). The larger mitogenome size of the Costa Rica taxon is due to the size of the control region as the Brazil taxon has a shorter length (265 bp) than the Costa Rica taxon (318 bp). The size of 6 PCGs and the start codon for ATP6, CYTB and NAD5 genes are different between the Costa Rica and Brazil taxa. Additionally, the two taxa differ in the stop codon of 6 PCGs. Molecular phylogeny based on 12 PCGs was concordant with two rRNA, 22 tRNA and 36 mitochondrial genes. The two taxa have a genetic distance of p = 16.2% based on 12 PCGs, p = 15.3% based on 36 mitochondrial genes, p = 13.1% based on 2 rRNA genes and p = 10.7% based on 22 tRNA genes, indicating status of sibling species. The Costa Rica and Brazil taxa of A. costaricensis are proposed to be accorded specific status as members of a species complex. PMID:26230642

  18. Complete Genome Sequences of 12 Species of Stable Defined Moderately Diverse Mouse Microbiota 2

    PubMed Central

    Uchimura, Yasuhiro; Wyss, Madeleine; Brugiroux, Sandrine; Limenitakis, Julien P.; Stecher, Bärbel; McCoy, Kathy D.

    2016-01-01

    We report here the complete genome sequences of 12 bacterial species of stable defined moderately diverse mouse microbiota 2 (sDMDMm2) used to colonize germ-free mice with defined microbes. Whole-genome sequencing of these species was performed using the PacBio sequencing platform yielding circularized genome sequences of all 12 species. PMID:27634994

  19. Karyotype and genome size in Euterpe Mart. (Arecaceae) species

    PubMed Central

    Oliveira, Ludmila Cristina; de Oliveira, Maria do Socorro Padilha; Davide, Lisete Chamma; Torres, Giovana Augusta

    2016-01-01

    Abstract Euterpe (Martius, 1823), a genus from Central and South America, has species with high economic importance in Brazil, because of their palm heart and fruits, known as açaí berries. Breeding programs have been conducted to increase yield and establish cultivation systems to replace the extraction of wild material. These programs need basic information about the genome of these species to better explore the available genetic variability. The aim of this study was to compare Euterpe edulis (Martius, 1824), Euterpe oleracea (Martius, 1824) and Euterpe precatoria (Martius, 1842), with regard to karyotype, type of interphase nucleus and nuclear DNA amount. Metaphase chromosomes and interphase nuclei from root tip meristematic cells were obtained by the squashing technique and solid stained for microscope analysis. The DNA amount was estimated by flow cytometry. There were previous reports on the chromosome number of Euterpe edulis and Euterpe oleracea, but chromosome morphology of these two species and the whole karyotype of Euterpe precatoria are reported for the first time. The species have 2n=36, a number considered as a pleisomorphic feature in Arecoideae since the modern species, according to floral morphology, have the lowest chromosome number (2n=28 and 2n=30). The three Euterpe species also have the same type of interphase nuclei, classified as semi-reticulate. The species differed on karyotypic formulas, on localization of secondary constriction and genome size. The data suggest that the main forces driving Euterpe karyotype evolution were structural rearrangements, such as inversions and translocations that alter chromosome morphology, and either deletion or amplification that led to changes in chromosome size. PMID:27186334

  20. Karyotype and genome size in Euterpe Mart. (Arecaceae) species.

    PubMed

    Oliveira, Ludmila Cristina; de Oliveira, Maria do Socorro Padilha; Davide, Lisete Chamma; Torres, Giovana Augusta

    2016-01-01

    Euterpe (Martius, 1823), a genus from Central and South America, has species with high economic importance in Brazil, because of their palm heart and fruits, known as açaí berries. Breeding programs have been conducted to increase yield and establish cultivation systems to replace the extraction of wild material. These programs need basic information about the genome of these species to better explore the available genetic variability. The aim of this study was to compare Euterpe edulis (Martius, 1824), Euterpe oleracea (Martius, 1824) and Euterpe precatoria (Martius, 1842), with regard to karyotype, type of interphase nucleus and nuclear DNA amount. Metaphase chromosomes and interphase nuclei from root tip meristematic cells were obtained by the squashing technique and solid stained for microscope analysis. The DNA amount was estimated by flow cytometry. There were previous reports on the chromosome number of Euterpe edulis and Euterpe oleracea, but chromosome morphology of these two species and the whole karyotype of Euterpe precatoria are reported for the first time. The species have 2n=36, a number considered as a pleisomorphic feature in Arecoideae since the modern species, according to floral morphology, have the lowest chromosome number (2n=28 and 2n=30). The three Euterpe species also have the same type of interphase nuclei, classified as semi-reticulate. The species differed on karyotypic formulas, on localization of secondary constriction and genome size. The data suggest that the main forces driving Euterpe karyotype evolution were structural rearrangements, such as inversions and translocations that alter chromosome morphology, and either deletion or amplification that led to changes in chromosome size.

  1. The Population Structure of Acinetobacter baumannii: Expanding Multiresistant Clones from an Ancestral Susceptible Genetic Pool

    PubMed Central

    Diancourt, Laure; Passet, Virginie; Nemec, Alexandr; Dijkshoorn, Lenie; Brisse, Sylvain

    2010-01-01

    Outbreaks of hospital infections caused by multidrug resistant Acinetobacter baumannii strains are of increasing concern worldwide. Although it has been reported that particular outbreak strains are geographically widespread, little is known about the diversity and phylogenetic relatedness of A. baumannii clonal groups. Sequencing of internal portions of seven housekeeping genes (total 2,976 nt) was performed in 154 A. baumannii strains covering the breadth of known diversity and including representatives of previously recognized international clones, and in 19 representatives of other Acinetobacter species. Restricted amounts of diversity and a star-like phylogeny reveal that A. baumannii is a genetically compact species that suffered a severe bottleneck in the recent past, possibly linked to a restricted ecological niche. A. baumannii is neatly demarcated from its closest relative (genomic species 13TU) and other Acinetobacter species. Multilocus sequence typing analysis demonstrated that the previously recognized international clones I to III correspond to three clonal complexes, each made of a central, predominant genotype and few single locus variants, a hallmark of recent clonal expansion. Whereas antimicrobial resistance was almost universal among isolates of these and a novel international clone (ST15), isolates of the other genotypes were mostly susceptible. This dichotomy indicates that antimicrobial resistance is a major selective advantage that drives the ongoing rapid clonal expansion of these highly problematic agents of nosocomial infections. PMID:20383326

  2. The bacterial species definition in the genomic era

    PubMed Central

    Konstantinidis, Konstantinos T; Ramette, Alban; Tiedje, James M

    2006-01-01

    The bacterial species definition, despite its eminent practical significance for identification, diagnosis, quarantine and diversity surveys, remains a very difficult issue to advance. Genomics now offers novel insights into intra-species diversity and the potential for emergence of a more soundly based system. Although we share the excitement, we argue that it is premature for a universal change to the definition because current knowledge is based on too few phylogenetic groups and too few samples of natural populations. Our analysis of five important bacterial groups suggests, however, that more stringent standards for species may be justifiable when a solid understanding of gene content and ecological distinctiveness becomes available. Our analysis also reveals what is actually encompassed in a species according to the current standards, in terms of whole-genome sequence and gene-content diversity, and shows that this does not correspond to coherent clusters for the environmental Burkholderia and Shewanella genera examined. In contrast, the obligatory pathogens, which have a very restricted ecological niche, do exhibit clusters. Therefore, the idea of biologically meaningful clusters of diversity that applies to most eukaryotes may not be universally applicable in the microbial world, or if such clusters exist, they may be found at different levels of distinction. PMID:17062412

  3. Phenotypic and Molecular Characterization of Acinetobacter Clinical Isolates Obtained from Inmates of California Correctional Facilities▿†

    PubMed Central

    Golanbar, Galarah D.; Lam, Christopher K.; Chu, Yi-Ming; Cueva, Carla; Tan, Stephanie W.; Silva, Isba; Xu, H. Howard

    2011-01-01

    Acinetobacter spp. increasingly have been wreaking havoc in hospitals and communities worldwide. Although much has been reported regarding Acinetobacter isolates responsible for nosocomial infections, little is known about these organisms in correctional facilities. In this study, we performed species identification, examined the antibiotic resistance profiles, and determined the mechanisms of resistance and clonal relationships of 123 Acinetobacter isolates obtained from inmates of 20 California correctional facilities (CCFs). We found that 57.7% of the isolates belong to A. baumannii, followed by isolates of Acinetobacter genomic species 3 (gen. sp. 3; 23.6%) and of Acinetobacter gen. sp. 13TU (10.6%). Multidrug-resistant (MDR) CCF isolates were found in only six CCFs. Additionally, DNA sequences of gyrA and parC genes were consistent with fluoroquinolone (FQ) susceptibility phenotypes. Furthermore, the presence of class 1 integrons was detected in 15 CCF isolates, all of which are MDR. Integron-associated gene cassettes encode several aminoglycoside modification enzymes, which correlate with most of the aminoglycoside-resistant phenotypes. Antimicrobial susceptibility testing in the presence of Phe-Arg-β-naphthylamide dihydrochloride and 1-(1-naphthylmethyl)-piperazine indicated the involvement of efflux pumps in the FQ resistance of only a few CCF isolates. Finally, genetic profiling showed that there was no evidence of A. baumannii outbreaks in CCFs. Instead, our analyses revealed only limited clonal dissemination of mostly non-MDR A. baumannii strains in a few facilities. This study represents the first report to characterize phenotypic and molecular features of Acinetobacter isolates in correctional facilities, which provides a baseline for monitoring the antimicrobial resistance changes and dissemination patterns of these organisms in such specialized institutions. PMID:21450955

  4. Genome Evolution in Three Species of Cactophilic Drosophila

    PubMed Central

    Sanchez-Flores, Alejandro; Peñaloza, Fernando; Carpinteyro-Ponce, Javier; Nazario-Yepiz, Nestor; Abreu-Goodger, Cei; Machado, Carlos A.; Markow, Therese Ann

    2016-01-01

    We report genomes of two species of cactophilic Drosophila: Drosophila arizonae and D. navojoa. These two are the closest relatives of D. mojavensis, forming the D. mojavensis cluster. D. mojavensis and D. arizonae diverged from D. navojoa ∼5.8 Mya, while the split between D. arizonae and D. mojavensis is more recent, at 1.5 Mya. Together the three genomes provide opportunities to examine genomic changes associated with speciation and host shifts in this ecologically defined group of flies. The three species are also separated by fixed inversion differences in three of their six chromosomes. While the levels of nucleotide divergence in the colinear chromosomes are significantly lower than in the inverted chromosomes, consistent with a past role of the inversions in preventing gene flow, the patterns differ among the inverted chromosomes when the locations of nucleotides inside or outside of the inversions are considered. For Muller element E, there is greater divergence external to the inversion breakpoints. For Muller A, the divergence is slightly higher inside the inversions, while for Muller B, the breakpoints and hence the difference in substitutions in relation to the inversions could not be determined. The differences among the inverted chromosomes, especially once the breakpoints are clearly established, could aid in dating the origins of the inversions. PMID:27489210

  5. Transposable elements and small RNAs: Genomic fuel for species diversity

    PubMed Central

    Hoffmann, Federico G; McGuire, Liam P; Counterman, Brian A; Ray, David A

    2015-01-01

    While transposable elements (TE) have long been suspected of involvement in species diversification, identifying specific roles has been difficult. We recently found evidence of TE-derived regulatory RNAs in a species-rich family of bats. The TE-derived small RNAs are temporally associated with the burst of species diversification, suggesting that they may have been involved in the processes that led to the diversification. In this commentary, we expand on the ideas that were briefly touched upon in that manuscript. Specifically, we suggest avenues of research that may help to identify the roles that TEs may play in perturbing regulatory pathways. Such research endeavors may serve to inform evolutionary biologists of the ways that TEs have influenced the genomic and taxonomic diversity around us. PMID:26904375

  6. Transposable elements and small RNAs: Genomic fuel for species diversity.

    PubMed

    Hoffmann, Federico G; McGuire, Liam P; Counterman, Brian A; Ray, David A

    2015-01-01

    While transposable elements (TE) have long been suspected of involvement in species diversification, identifying specific roles has been difficult. We recently found evidence of TE-derived regulatory RNAs in a species-rich family of bats. The TE-derived small RNAs are temporally associated with the burst of species diversification, suggesting that they may have been involved in the processes that led to the diversification. In this commentary, we expand on the ideas that were briefly touched upon in that manuscript. Specifically, we suggest avenues of research that may help to identify the roles that TEs may play in perturbing regulatory pathways. Such research endeavors may serve to inform evolutionary biologists of the ways that TEs have influenced the genomic and taxonomic diversity around us.

  7. Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences.

    PubMed

    Wambugu, Peterson W; Brozynska, Marta; Furtado, Agnelo; Waters, Daniel L; Henry, Robert J

    2015-09-10

    Rice is the most important crop in the world, acting as the staple food for over half of the world's population. The evolutionary relationships of cultivated rice and its wild relatives have remained contentious and inconclusive. Here we report on the use of whole chloroplast sequences to elucidate the evolutionary and phylogenetic relationships in the AA genome Oryza species, representing the primary gene pool of rice. This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species. The pan tropical distribution of these rice relatives was found to be explained by long distance dispersal within the last million years. The analysis resulted in a clustering pattern that showed strong geographical differentiation. The species were defined in two primary clades with a South American/African clade with two species, O glumaepatula and O longistaminata, distinguished from all other species. The largest clade was comprised of an Australian clade including newly identified taxa and the African and Asian clades. This refined knowledge of the relationships between cultivated rice and the related wild species provides a strong foundation for more targeted use of wild genetic resources in rice improvement and efforts to ensure their conservation.

  8. Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences

    PubMed Central

    Wambugu, Peterson W.; Brozynska, Marta; Furtado, Agnelo; Waters, Daniel L.; Henry, Robert J.

    2015-01-01

    Rice is the most important crop in the world, acting as the staple food for over half of the world’s population. The evolutionary relationships of cultivated rice and its wild relatives have remained contentious and inconclusive. Here we report on the use of whole chloroplast sequences to elucidate the evolutionary and phylogenetic relationships in the AA genome Oryza species, representing the primary gene pool of rice. This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species. The pan tropical distribution of these rice relatives was found to be explained by long distance dispersal within the last million years. The analysis resulted in a clustering pattern that showed strong geographical differentiation. The species were defined in two primary clades with a South American/African clade with two species, O glumaepatula and O longistaminata, distinguished from all other species. The largest clade was comprised of an Australian clade including newly identified taxa and the African and Asian clades. This refined knowledge of the relationships between cultivated rice and the related wild species provides a strong foundation for more targeted use of wild genetic resources in rice improvement and efforts to ensure their conservation. PMID:26355750

  9. Diverse responses to UV light exposure in Acinetobacter include the capacity for DNA damage-induced mutagenesis in the opportunistic pathogens Acinetobacter baumannii and Acinetobacter ursingii.

    PubMed

    Hare, Janelle M; Bradley, James A; Lin, Ching-li; Elam, Tyler J

    2012-03-01

    Error-prone and error-free DNA damage repair responses that are induced in most bacteria after exposure to various chemicals, antibiotics or radiation sources were surveyed across the genus Acinetobacter. The error-prone SOS mutagenesis response occurs when DNA damage induces a cell's umuDC- or dinP-encoded error-prone polymerases. The model strain Acinetobacter baylyi ADP1 possesses an unusual, regulatory umuD allele (umuDAb) with an extended 5' region and only incomplete fragments of umuC. Diverse Acinetobacter species were investigated for the presence of umuDC and their ability to conduct UV-induced mutagenesis. Unlike ADP1, most Acinetobacter strains possessed multiple umuDC loci containing either umuDAb or a umuD allele resembling that of Escherichia coli. The nearly omnipresent umuDAb allele was the ancestral umuD in Acinetobacter, with horizontal gene transfer accounting for over half of the umuDC operons. Despite multiple umuD(Ab)C operons in many strains, only three species conducted UV-induced mutagenesis: Acinetobacter baumannii, Acinetobacter ursingii and Acinetobacter beijerinckii. The type of umuDC locus or mutagenesis phenotype a strain possessed was not correlated with its error-free response of survival after UV exposure, but similar diversity was apparent. The survival of 30 Acinetobacter strains after UV treatment ranged over five orders of magnitude, with the Acinetobacter calcoaceticus-A. baumannii (Acb) complex and haemolytic strains having lower survival than non-Acb or non-haemolytic strains. These observations demonstrate that a genus can possess a range of DNA damage response mechanisms, and suggest that DNA damage-induced mutation could be an important part of the evolution of the emerging pathogens A. baumannii and A. ursingii.

  10. Genomes, diversity and resistance gene analogues in Musa species.

    PubMed

    Azhar, M; Heslop-Harrison, J S

    2008-01-01

    Resistance genes (R genes) in plants are abundant and may represent more than 1% of all the genes. Their diversity is critical to the recognition and response to attack from diverse pathogens. Like many other crops, banana and plantain face attacks from potentially devastating fungal and bacterial diseases, increased by a combination of worldwide spread of pathogens, exploitation of a small number of varieties, new pathogen mutations, and the lack of effective, benign and cheap chemical control. The challenge for plant breeders is to identify and exploit genetic resistances to diseases, which is particularly difficult in banana and plantain where the valuable cultivars are sterile, parthenocarpic and mostly triploid so conventional genetic analysis and breeding is impossible. In this paper, we review the nature of R genes and the key motifs, particularly in the Nucleotide Binding Sites (NBS), Leucine Rich Repeat (LRR) gene class. We present data about identity, nature and evolutionary diversity of the NBS domains of Musa R genes in diploid wild species with the Musa acuminata (A), M. balbisiana (B), M. schizocarpa (S), M. textilis (T), M. velutina and M. ornata genomes, and from various cultivated hybrid and triploid accessions, using PCR primers to isolate the domains from genomic DNA. Of 135 new sequences, 75% of the sequenced clones had uninterrupted open reading frames (ORFs), and phylogenetic UPGMA tree construction showed four clusters, one from Musa ornata, one largely from the B and T genomes, one from A and M. velutina, and the largest with A, B, T and S genomes. Only genes of the coiled-coil (non-TIR) class were found, typical of the grasses and presumably monocotyledons. The analysis of R genes in cultivated banana and plantain, and their wild relatives, has implications for identification and selection of resistance genes within the genus which may be useful for plant selection and breeding and also for defining relationships and genome evolution

  11. The Complete Chloroplast Genome Sequences of Six Rehmannia Species

    PubMed Central

    Zeng, Shuyun; Zhou, Tao; Han, Kai; Yang, Yanci; Zhao, Jianhua; Liu, Zhan-Lin

    2017-01-01

    Rehmannia is a non-parasitic genus in Orobanchaceae including six species mainly distributed in central and north China. Its phylogenetic position and infrageneric relationships remain uncertain due to potential hybridization and polyploidization. In this study, we sequenced and compared the complete chloroplast genomes of six Rehmannia species using Illumina sequencing technology to elucidate the interspecific variations. Rehmannia plastomes exhibited typical quadripartite and circular structures with good synteny of gene order. The complete genomes ranged from 153,622 bp to 154,055 bp in length, including 133 genes encoding 88 proteins, 37 tRNAs, and 8 rRNAs. Three genes (rpoA, rpoC2, accD) have potentially experienced positive selection. Plastome size variation of Rehmannia was mainly ascribed to the expansion and contraction of the border regions between the inverted repeat (IR) region and the single-copy (SC) regions. Despite of the conserved structure in Rehmannia plastomes, sequence variations provide useful phylogenetic information. Phylogenetic trees of 23 Lamiales species reconstructed with the complete plastomes suggested that Rehmannia was monophyletic and sister to the clade of Lindenbergia and the parasitic taxa in Orobanchaceae. The interspecific relationships within Rehmannia were completely different with the previous studies. In future, population phylogenomic works based on plastomes are urgently needed to clarify the evolutionary history of Rehmannia. PMID:28294981

  12. Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies.

    PubMed

    Sessegolo, Camille; Burlet, Nelly; Haudry, Annabelle

    2016-08-01

    While the evolutionary mechanisms driving eukaryote genome size evolution are still debated, repeated element content appears to be crucial. Here, we reconstructed the phylogeny and identified repeats in the genome of 26 Drosophila exhibiting a twofold variation in genome size. The content in transposable elements (TEs) is highly correlated to genome size evolution among these closely related species. We detected a strong phylogenetic signal on the evolution of both genome size and TE content, and a genome contraction in the Drosophila melanogaster subgroup.

  13. Genome Sequence of Cronobacter sakazakii BAA-894 and Comparative Genomic Hybridization Analysis with Other Cronobacter Species

    PubMed Central

    Kucerova, Eva; Clifton, Sandra W.; Xia, Xiao-Qin; Long, Fred; Porwollik, Steffen; Fulton, Lucinda; Fronick, Catrina; Minx, Patrick; Kyung, Kim; Warren, Wesley; Fulton, Robert; Feng, Dongyan; Wollam, Aye; Shah, Neha; Bhonagiri, Veena; Nash, William E.; Hallsworth-Pepin, Kymberlie; Wilson, Richard K.

    2010-01-01

    Background The genus Cronobacter (formerly called Enterobacter sakazakii) is composed of five species; C. sakazakii, C. malonaticus, C. turicensis, C. muytjensii, and C. dublinensis. The genus includes opportunistic human pathogens, and the first three species have been associated with neonatal infections. The most severe diseases are caused in neonates and include fatal necrotizing enterocolitis and meningitis. The genetic basis of the diversity within the genus is unknown, and few virulence traits have been identified. Methodology/Principal Findings We report here the first sequence of a member of this genus, C. sakazakii strain BAA-894. The genome of Cronobacter sakazakii strain BAA-894 comprises a 4.4 Mb chromosome (57% GC content) and two plasmids; 31 kb (51% GC) and 131 kb (56% GC). The genome was used to construct a 387,000 probe oligonucleotide tiling DNA microarray covering the whole genome. Comparative genomic hybridization (CGH) was undertaken on five other C. sakazakii strains, and representatives of the four other Cronobacter species. Among 4,382 annotated genes inspected in this study, about 55% of genes were common to all C. sakazakii strains and 43% were common to all Cronobacter strains, with 10–17% absence of genes. Conclusions/Significance CGH highlighted 15 clusters of genes in C. sakazakii BAA-894 that were divergent or absent in more than half of the tested strains; six of these are of probable prophage origin. Putative virulence factors were identified in these prophage and in other variable regions. A number of genes unique to Cronobacter species associated with neonatal infections (C. sakazakii, C. malonaticus and C. turicensis) were identified. These included a copper and silver resistance system known to be linked to invasion of the blood-brain barrier by neonatal meningitic strains of Escherichia coli. In addition, genes encoding for multidrug efflux pumps and adhesins were identified that were unique to C. sakazakii strains from

  14. The Ups and Downs of Genome Size Evolution in Polyploid Species of Nicotiana (Solanaceae)

    PubMed Central

    Leitch, I. J.; Hanson, L.; Lim, K. Y.; Kovarik, A.; Chase, M. W.; Clarkson, J. J.; Leitch, A. R.

    2008-01-01

    Background In studies looking at individual polyploid species, the most common patterns of genomic change are that either genome size in the polyploid is additive (i.e. the sum of parental genome donors) or there is evidence of genome downsizing. Reports showing an increase in genome size are rare. In a large-scale analysis of 3008 species, genome downsizing was shown to be a widespread biological response to polyploidy. Polyploidy in the genus Nicotiana (Solanaceae) is common with approx. 40 % of the approx. 75 species being allotetraploid. Recent advances in understanding phylogenetic relationships of Nicotiana species and dating polyploid formation enable a temporal dimension to be added to the analysis of genome size evolution in these polyploids. Methods Genome sizes were measured in 18 species of Nicotiana (nine diploids and nine polyploids) ranging in age from <200 000 years to approx. 4·5 Myr old, to determine the direction and extent of genome size change following polyploidy. These data were combined with data from genomic in situ hybridization and increasing amounts of information on sequence composition in Nicotiana to provide insights into the molecular basis of genome size changes. Key Results and Conclusions By comparing the expected genome size of the polyploid (based on summing the genome size of species identified as either a parent or most closely related to the diploid progenitors) with the observed genome size, four polyploids showed genome downsizing and five showed increases. There was no discernable pattern in the direction of genome size change with age of polyploids, although with increasing age the amount of genome size change increased. In older polyploids (approx. 4·5 million years old) the increase in genome size was associated with loss of detectable genomic in situ hybridization signal, whereas some hybridization signal was still detected in species exhibiting genome downsizing. The possible significance of these results is

  15. The Complete Chloroplast Genomes of Three Cardiocrinum (Liliaceae) Species: Comparative Genomic and Phylogenetic Analyses

    PubMed Central

    Lu, Rui-Sen; Li, Pan; Qiu, Ying-Xiong

    2017-01-01

    The genus Cardiocrinum (Endlicher) Lindley (Liliaceae) comprises three herbaceous perennial species that are distributed in East Asian temperate-deciduous forests. Although all three Cardiocrinum species have horticultural and medical uses, studies related to species identification and molecular phylogenetic analysis of this genus have not been reported. Here, we report the complete chloroplast (cp) sequences of each Cardiocrinum species using Illumina paired-end sequencing technology. The cp genomes of C. giganteum, C. cathayanum, and C. cordatum were found to be 152,653, 152,415, and 152,410 bp in length, respectively, including a pair of inverted repeat (IR) regions (26,364–26,500 bp) separated by a large single-copy (LSC) region (82,186–82,368 bp) and a small single-copy (SSC) region (17,309–17,344 bp). Each cp genome contained the same 112 unique genes consisting of 30 transfer RNA genes, 4 ribosomal RNA genes, and 78 protein-coding genes. Gene content, gene order, AT content, and IR/SC boundary structures were almost the same among the three Cardiocrinum cp genomes, yet their lengths varied due to contraction/expansion of the IR/SC borders. Simple sequence repeat (SSR) analysis further indicated the richest SSRs in these cp genomes to be A/T mononucleotides. A total of 45, 57, and 45 repeats were identified in C. giganteum, C. cathayanum, and C. cordatum, respectively. Six cpDNA markers (rps19, rpoC2-rpoC1, trnS-psbZ, trnM-atpE, psaC-ndhE, ycf15-ycf1) with the percentage of variable sites higher than 0.95% were identified. Phylogenomic analyses of the complete cp genomes and 74 protein-coding genes strongly supported the monophyly of Cardiocrinum and a sister relationship between C. cathayanum and C. cordatum. The availability of these cp genomes provides valuable genetic information for further population genetics and phylogeography studies on Cardiocrinum. PMID:28119727

  16. Genome Sequences of Four Acinetobacter baumannii-A. calcoaceticus Complex Isolates from Combat-Related Infections Sustained in the Middle East

    DTIC Science & Technology

    2014-02-06

    prevalent bacterial causes of combat-related infections on the battlefield. Antibiotic resistance and a poor understanding of the protective host immune...Combat-Related Infections Sustained in the Middle East Report Title Acinetobacter baumannii is among the most prevalent bacterial causes of combat...most prevalent bacterial causes of combat-related infections on the battlefield. Antibiotic resistance and a poor understanding of the protective host

  17. A case of community-acquired Acinetobacter junii-johnsonii cellulitis.

    PubMed

    Henao-Martínez, Andrés F; González-Fontal, Guido R; Johnson, Steven

    2012-06-01

    Acinetobacter skin and soft tissue infection outside of the traumatic wound setting are rare occurrences. The majority of cases occur in the presence of significant comorbilities and by Acinetobacter baumanii. Herein a case is reported of community-onset, health-care-associated, non-traumatic cellulitis caused by Acinetobacter, species junii-johnsonii with bacteremia. This is the first reported case of Acinetobacter junii-johnsonii skin and soft tissue infection. Hemorrhagic bullae might be one of the clinical features of Acinetobacter cellulitis.

  18. Biosystematics and evolutionary relationships of perennial Triticeae species revealed by genomic analyses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Literature published after 1984 were reviewed to address: (1) genome relationships among monogenomic diploid species, (2) progenitors of the unknown Y genome in Elymus polyploids, X in Thinopyrum intermedium, and Xm in Leymus, and (3) genome constitutions of some perennial Triticeae species that wer...

  19. Crossing the species barrier: genomic hotspots of introgression between two highly divergent Ciona intestinalis species.

    PubMed

    Roux, Camille; Tsagkogeorga, Georgia; Bierne, Nicolas; Galtier, Nicolas

    2013-07-01

    Inferring a realistic demographic model from genetic data is an important challenge to gain insights into the historical events during the speciation process and to detect molecular signatures of selection along genomes. Recent advances in divergence population genetics have reported that speciation in face of gene flow occurred more frequently than theoretically expected, but the approaches used did not account for genome-wide heterogeneity (GWH) in introgression rates. Here, we investigate the impact of GWH on the inference of divergence with gene flow between two cryptic species of the marine model Ciona intestinalis by analyzing polymorphism and divergence patterns in 852 protein-coding sequence loci. These morphologically similar entities are highly diverged molecular-wise, but evidence of hybridization has been reported in both laboratory and field studies. We compare various speciation models and test for GWH under the approximate Bayesian computation framework. Our results demonstrate the presence of significant extents of gene flow resulting from a recent secondary contact after >3 My of divergence in isolation. The inferred rates of introgression are relatively low, highly variable across loci and mostly unidirectional, which is consistent with the idea that numerous genetic incompatibilities have accumulated over time throughout the genomes of these highly diverged species. A genomic map of the level of gene flow identified two hotspots of introgression, that is, large genome regions of unidirectional introgression. This study clarifies the history and degree of isolation of two cryptic and partially sympatric model species and provides a methodological framework to investigate GWH at various stages of speciation process.

  20. Principles of Genome Evolution in the Drosophila melanogaster Species Group

    PubMed Central

    Ranz, José M; Maurin, Damien; Chan, Yuk S; von Grotthuss, Marcin; Hillier, LaDeana W; Roote, John; Ashburner, Michael; Bergman, Casey M

    2007-01-01

    That closely related species often differ by chromosomal inversions was discovered by Sturtevant and Plunkett in 1926. Our knowledge of how these inversions originate is still very limited, although a prevailing view is that they are facilitated by ectopic recombination events between inverted repetitive sequences. The availability of genome sequences of related species now allows us to study in detail the mechanisms that generate interspecific inversions. We have analyzed the breakpoint regions of the 29 inversions that differentiate the chromosomes of Drosophila melanogaster and two closely related species, D. simulans and D. yakuba, and reconstructed the molecular events that underlie their origin. Experimental and computational analysis revealed that the breakpoint regions of 59% of the inversions (17/29) are associated with inverted duplications of genes or other nonrepetitive sequences. In only two cases do we find evidence for inverted repetitive sequences in inversion breakpoints. We propose that the presence of inverted duplications associated with inversion breakpoint regions is the result of staggered breaks, either isochromatid or chromatid, and that this, rather than ectopic exchange between inverted repetitive sequences, is the prevalent mechanism for the generation of inversions in the melanogaster species group. Outgroup analysis also revealed evidence for widespread breakpoint recycling. Lastly, we have found that expression domains in D. melanogaster may be disrupted in D. yakuba, bringing into question their potential adaptive significance. PMID:17550304

  1. Structure and biosynthesis of fimsbactins A-F, siderophores from Acinetobacter baumannii and Acinetobacter baylyi.

    PubMed

    Proschak, Anna; Lubuta, Patrice; Grün, Peter; Löhr, Frank; Wilharm, Gottfried; De Berardinis, Veronique; Bode, Helge B

    2013-03-18

    Novel chatechol/hydroxamate siderophores (named "fimsbactins") were identified in Acinetobacter baumannii ATCC 17978 and Acinetobacter baylyi ADP1. The major compound, fimsbactin A, was isolated from low-iron cultures of A. baylyi ADP1, and its chemical structure was elucidated by mass spectrometry, and detailed (1)H, (13)C and (15)N NMR spectroscopy. From inverse feeding experiments following HPLC-MS analysis, the structures of five additional derivatives were elucidated. The gene cluster encoding the fimsbactin synthetase (fbs) was identified in both genomes, and mutants in fbs genes in A. baylyi were analyzed, thus allowing prediction of the fimsbactin biosynthesis pathway.

  2. Whole genome comparative analysis of channel catfish (Ictalurus punctatus) with four model fish species

    PubMed Central

    2013-01-01

    Background Comparative mapping is a powerful tool to study evolution of genomes. It allows transfer of genome information from the well-studied model species to non-model species. Catfish is an economically important aquaculture species in United States. A large amount of genome resources have been developed from catfish including genetic linkage maps, physical maps, BAC end sequences (BES), integrated linkage and physical maps using BES-derived markers, physical map contig-specific sequences, and draft genome sequences. Application of such genome resources should allow comparative analysis at the genome scale with several other model fish species. Results In this study, we conducted whole genome comparative analysis between channel catfish and four model fish species with fully sequenced genomes, zebrafish, medaka, stickleback and Tetraodon. A total of 517 Mb draft genome sequences of catfish were anchored to its genetic linkage map, which accounted for 62% of the total draft genome sequences. Based on the location of homologous genes, homologous chromosomes were determined among catfish and the four model fish species. A large number of conserved syntenic blocks were identified. Analysis of the syntenic relationships between catfish and the four model fishes supported that the catfish genome is most similar to the genome of zebrafish. Conclusion The organization of the catfish genome is similar to that of the four teleost species, zebrafish, medaka, stickleback, and Tetraodon such that homologous chromosomes can be identified. Within each chromosome, extended syntenic blocks were evident, but the conserved syntenies at the chromosome level involve extensive inter-chromosomal and intra-chromosomal rearrangements. This whole genome comparative map should facilitate the whole genome assembly and annotation in catfish, and will be useful for genomic studies of various other fish species. PMID:24215161

  3. Beta-Lactamase Encoded Genes blaTEM and blaCTX Among Acinetobacter baumannii Species Isolated From Medical Devices of Intensive Care Units in Tehran Hospitals

    PubMed Central

    Khalilzadegan, Sara; Sade, Mojtaba; Godarzi, Hussein; Eslami, Gita; Hallajzade, Masoumeh; Fallah, Fatemeh; Yadegarnia, Davood

    2016-01-01

    Background Excessive consumption of antimicrobial materials in hospitals is considered as the main encoder leading to the emergence, development and acquisition of new bacterial resistance to beta-lactamase. Objectives Owing to the lack of proper information regarding the mechanism of the bacterial resistance to antibiotics and responsible genes in the country, the current study aimed to consider the resistance or sensitivity of the Acinetobacter baumannii multi drug resistant (MDR) isolates facing 2% glutaraldehyde. The study was conducted in the selected intensive care units in Tehran hospitals, Iran, in 2013. Materials and Methods In this study conducted over a period of 10 months, A. baumannii species were isolated by bacterial culture following biochemical tests from intensive care units (ICUs) of some hospitals in Tehran, Iran (Fayazbaksh, Taleghani, Imam Khomeini, Valiasr, Labafinejad). The resistance and sensitivity of the isolates to antibiotics were considered according to the clinical and laboratory standard institute CLSI (2012) guidelines. By multiplex PCR method, blaCTX and blaTEM genes were detected and finally, MDR strains were treated with 2% glutaraldehyde. PCR was used for each strain of MDR using specific primers. Results In the current study, 131 A. baumannii isolates (22.3%) out of 588 were studied. The level of resistance to various antibiotics was in the range of 69.4% to 100%. The frequencies of blaTEM and blaCTX genes were 3.2% and 19.4%, respectively. MIC50% and MIC90% of imipenem and meropenem antibiotics were 32 ± 1 µg/mL and 64 ± 1 µg/mL, respectively (P < 0.9). However no resistance to glutaraldehyde was observed. Different bands of MDR strains were observed in the PCR product by electrophoresis. Conclusions It seems that besides the variety and prevalence of blaTEM and blaCTX, enormous mechanisms such as porin and leaking systems (efflux pumps) are responsible for the information of the A. baumannii resistance to disinfectants

  4. Differential paralog divergence modulates genome evolution across yeast species

    PubMed Central

    Lynch, Bryony; Huang, Mei; Alcantara, Erica; DeSevo, Christopher G.; Pai, Dave A.; Hoang, Margaret L.

    2017-01-01

    Evolutionary outcomes depend not only on the selective forces acting upon a species, but also on the genetic background. However, large timescales and uncertain historical selection pressures can make it difficult to discern such important background differences between species. Experimental evolution is one tool to compare evolutionary potential of known genotypes in a controlled environment. Here we utilized a highly reproducible evolutionary adaptation in Saccharomyces cerevisiae to investigate whether experimental evolution of other yeast species would select for similar adaptive mutations. We evolved populations of S. cerevisiae, S. paradoxus, S. mikatae, S. uvarum, and interspecific hybrids between S. uvarum and S. cerevisiae for ~200–500 generations in sulfate-limited continuous culture. Wild-type S. cerevisiae cultures invariably amplify the high affinity sulfate transporter gene, SUL1. However, while amplification of the SUL1 locus was detected in S. paradoxus and S. mikatae populations, S. uvarum cultures instead selected for amplification of the paralog, SUL2. We measured the relative fitness of strains bearing deletions and amplifications of both SUL genes from different species, confirming that, converse to S. cerevisiae, S. uvarum SUL2 contributes more to fitness in sulfate limitation than S. uvarum SUL1. By measuring the fitness and gene expression of chimeric promoter-ORF constructs, we were able to delineate the cause of this differential fitness effect primarily to the promoter of S. uvarum SUL1. Our data show evidence of differential sub-functionalization among the sulfate transporters across Saccharomyces species through recent changes in noncoding sequence. Furthermore, these results show a clear example of how such background differences due to paralog divergence can drive changes in genome evolution. PMID:28196070

  5. Genome size variation among sex types in dioecious and triecious Caricaceae species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Caricaceae is a small family consisting of 35 species of varying sexual systems and includes economically important fruit crop, Carica papaya, and other species of “highland papayas”. Flow cytometry was used to obtain genome sizes for 11 species in three genera of Caricaceae to determine if genome s...

  6. Telling plant species apart with DNA: from barcodes to genomes.

    PubMed

    Hollingsworth, Peter M; Li, De-Zhu; van der Bank, Michelle; Twyford, Alex D

    2016-09-05

    Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity-yet many tens of thousands of species await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols and being backward compatible with existing barcodes; and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature does, however, present a major informatics challenge for upscaling to large sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'.

  7. Telling plant species apart with DNA: from barcodes to genomes

    PubMed Central

    Li, De-Zhu; van der Bank, Michelle

    2016-01-01

    Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity—yet many tens of thousands of species await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols and being backward compatible with existing barcodes; and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature does, however, present a major informatics challenge for upscaling to large sample sets. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481790

  8. Draft genome sequence of an aflatoxigenic Aspergillus species, A. bombycis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genome of the A. bombycis Type strain was sequenced using a Personal Genome Machine, followed by annotation of its predicted genes. The genome size for A. bombycis was found to be approximately 37 Mb and contained 12,266 genes. This announcement introduces a sequenced genome for an aflatoxigenic...

  9. Insertions or Deletions (Indels) in the rrn 16S-23S rRNA Gene Internal Transcribed Spacer Region (ITS) Compromise the Typing and Identification of Strains within the Acinetobacter calcoaceticus-baumannii (Acb) Complex and Closely Related Members

    PubMed Central

    Maslunka, Christopher; Gifford, Bianca; Tucci, Joseph; Gürtler, Volker; Seviour, Robert J.

    2014-01-01

    To determine whether ITS sequences in the rrn operon are suitable for identifying individual Acinetobacter Acb complex members, we analysed length and sequence differences between multiple ITS copies within the genomes of individual strains. Length differences in ITS reported previously between A. nosocomialis BCRC15417T (615 bp) and other strains (607 bp) can be explained by presence of an insertion (indel 13i/1) in the longer ITS variant. The same Indel 13i/1 was also found in ITS sequences of ten strains of A. calcoaceticus, all 639 bp long, and the 628 bp ITS of Acinetobacter strain BENAB127. Four additional indels (13i/2–13i/5) were detected in Acinetobacter strain c/t13TU 10090 ITS length variants (608, 609, 620, 621 and 630 bp). These ITS variants appear to have resulted from horizontal gene transfer involving other Acinetobacter species or in some cases unrelated bacteria. Although some ITS copies in strain c/t13TU 10090 are of the same length (620 bp) as those in Acinetobacter strains b/n1&3, A. pittii (10 strains), A. calcoaceticus and A. oleivorans (not currently acknowledged as an Acb member), their individual ITS sequences differ. Thus ITS length by itself can not by itself be used to identify Acb complex strains. A shared indel in ITS copies in two separate Acinetobacter species compromises the specificity of ITS targeted probes, as shown with the Aun-3 probe designed to target the ITS in A. pitti. The presence of indel 13i/5 in the ITS of Acinetobacter strain c/t13TU means it too responded positively to this probe. Thus, neither ITS sequencing nor the currently available ITS targeted probes can distinguish reliably between Acb member species. PMID:25141005

  10. Comparative genomics reveals evidence of marine adaptation in Salinispora species

    PubMed Central

    2012-01-01

    Background Actinobacteria represent a consistent component of most marine bacterial communities yet little is known about the mechanisms by which these Gram-positive bacteria adapt to life in the marine environment. Here we employed a phylogenomic approach to identify marine adaptation genes in marine Actinobacteria. The focus was on the obligate marine actinomycete genus Salinispora and the identification of marine adaptation genes that have been acquired from other marine bacteria. Results Functional annotation, comparative genomics, and evidence of a shared evolutionary history with bacteria from hyperosmotic environments were used to identify a pool of more than 50 marine adaptation genes. An Actinobacterial species tree was used to infer the likelihood of gene gain or loss in accounting for the distribution of each gene. Acquired marine adaptation genes were associated with electron transport, sodium and ABC transporters, and channels and pores. In addition, the loss of a mechanosensitive channel gene appears to have played a major role in the inability of Salinispora strains to grow following transfer to low osmotic strength media. Conclusions The marine Actinobacteria for which genome sequences are available are broadly distributed throughout the Actinobacterial phylogenetic tree and closely related to non-marine forms suggesting they have been independently introduced relatively recently into the marine environment. It appears that the acquisition of transporters in Salinispora spp. represents a major marine adaptation while gene loss is proposed to play a role in the inability of this genus to survive outside of the marine environment. This study reveals fundamental differences between marine adaptations in Gram-positive and Gram-negative bacteria and no common genetic basis for marine adaptation among the Actinobacteria analyzed. PMID:22401625

  11. Plasmid carriage of bla NDM-1 in clinical Acinetobacter baumannii isolates from India.

    PubMed

    Jones, Lim S; Toleman, Mark A; Weeks, Janis L; Howe, Robin A; Walsh, Timothy R; Kumarasamy, Karthikeyan K

    2014-07-01

    NDM-1 probably emerged in Acinetobacter species prior to its dissemination among Enterobacteriaceae, and NDM-1-like enzymes are increasingly reported in Acinetobacter species. Here, we report on the genetic context of blaNDM-1 in the earliest known NDM-1-producing organisms, clinical isolates of Acinetobacter from India in 2005. These strains harbor blaNDM-1 plasmids of different sizes. The gene is associated with the remnants of the Tn125 transposon normally associated with blaNDM-1 in Acinetobacter spp. The transposon has been disrupted by the IS26 insertion and subsequent movement events.

  12. Salt adaptation in Acinetobacter baylyi: identification and characterization of a secondary glycine betaine transporter.

    PubMed

    Sand, Miriam; de Berardinis, Veronique; Mingote, Ana; Santos, Helena; Göttig, Stephan; Müller, Volker; Averhoff, Beate

    2011-10-01

    Members of the genus Acinetobacter are well known for their metabolic versatility that allows them to adapt to different ecological niches. Here, we have addressed how the model strain Acinetobacter baylyi copes with different salinities and low water activities. A. baylyi tolerates up to 900 mM sodium salts and even higher concentrations of potassium chloride. Growth at high salinities was better in complex than in mineral medium and addition of glycine betaine stimulated growth at high salinities in mineral medium. Cells grown at high salinities took up glycine betaine from the medium. Uptake of glycine betaine was energy dependent and dependent on a salinity gradient across the membrane. Inspection of the genome sequence revealed two potential candidates for glycine betaine transport, both encoding potential secondary transporters, one of the major facilitator superfamily (MFS) class (ACIAD2280) and one of the betaine/choline/carnitine transporter (BCCT) family (ACIAD3460). The latter is essential for glycine betaine transport in A. baylyi. The broad distribution of ACIAD3460 homologues indicates the essential role of secondary transporters in the adaptation of Acinetobacter species to osmotic stress.

  13. The draft genome sequence of Xanthomonas species strain Nyagatare, isolated from diseased bean in Rwanda.

    PubMed

    Aritua, Valente; Musoni, Augustine; Kabeja, Alice; Butare, Louis; Mukamuhirwa, Floride; Gahakwa, Daphrose; Kato, Fred; Abang, Mathew M; Buruchara, Robin; Sapp, Melanie; Harrison, James; Studholme, David J; Smith, Julian

    2015-02-01

    We announce the genome sequence for Xanthomonas species strain Nyagatare, isolated from beans showing unusual disease symptoms in Rwanda. This strain represents the first sequenced genome belonging to an as-yet undescribed Xanthomonas species known as species-level clade 1. It has at least 100 kb of genomic sequence that shows little or no sequence similarity to other xanthomonads, including a unique lipopolysaccharide synthesis gene cluster. At least one genomic region appears to have been acquired from relatives of Agrobacterium or Rhizobium species. The genome encodes homologues of only three known type-three secretion system effectors: AvrBs2, XopF1 and AvrXv4. Availability of the genome sequence will facilitate development of molecular tools for detection and diagnostics for this newly discovered pathogen of beans and facilitate epidemiological investigations of a potential causal link between this pathogen and the disease outbreak.

  14. Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies

    PubMed Central

    Burlet, Nelly

    2016-01-01

    While the evolutionary mechanisms driving eukaryote genome size evolution are still debated, repeated element content appears to be crucial. Here, we reconstructed the phylogeny and identified repeats in the genome of 26 Drosophila exhibiting a twofold variation in genome size. The content in transposable elements (TEs) is highly correlated to genome size evolution among these closely related species. We detected a strong phylogenetic signal on the evolution of both genome size and TE content, and a genome contraction in the Drosophila melanogaster subgroup. PMID:27576524

  15. What Can Comparative Genomics Tell Us About Species Concepts in the Genus Aspergillus?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding the nature of species’ boundaries is a fundamental question in evolutionary biology. The availability of genomes from several species of the genus Aspergillus allows us for the first time to examine the demarcation of fungal species at the whole-genome level. Here, we examine four ca...

  16. Genome analysis of 7 Kengyilia (Triticeae Poaceae) species with FISH and GISH

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome composition of and genetic relationships among seven Kengyilia species were assessed using a technique of sequential FISH (fluorescence in situ hybridization) and GISH (genomic in situ hybridization). Five of these 7 species, K. kokonorica, K. rigidula, K. hirsula, K. grandiglumis, and K. th...

  17. Development of a real-time PCR assay for the rapid detection of Acinetobacter baumannii from whole blood samples.

    PubMed

    De Gregorio, Eliana; Roscetto, Emanuela; Iula, Vita Dora; Martinucci, Marianna; Zarrilli, Raffaele; Di Nocera, Pier Paolo; Catania, Maria Rosaria

    2015-04-01

    Acinetobacter baumannii is a multidrug-resistant pathogen associated with severe infections in hospitalized patients, including pneumonia, urinary and bloodstream infections. Rapid detection of A. baumannii infection is crucial for timely treatment of septicemic patients. The aim of the present study was to develop a specific marker for a quantitative polymerase chain reaction (PCR) assay for the detection of A. baumannii. The target gene chosen is the biofilm-associated protein (bap) gene, encoding a cell surface protein involved in biofilm formation. The assay is specific for A. baumannii, allowing its discrimination from different species of Acinetobacter and other clinically relevant bacterial pathogens. The assay is able to detect one genomic copy of A. baumannii, corresponding to 4 fg of purified DNA, and 20 colony-forming units/ml using DNA extracted from spiked whole blood samples.

  18. Investigating hookworm genomes by comparative analysis of two Ancylostoma species

    PubMed Central

    Mitreva, Makedonka; McCarter, James P; Arasu, Prema; Hawdon, John; Martin, John; Dante, Mike; Wylie, Todd; Xu, Jian; Stajich, Jason E; Kapulkin, Wadim; Clifton, Sandra W; Waterston, Robert H; Wilson, Richard K

    2005-01-01

    Background Hookworms, infecting over one billion people, are the mostly closely related major human parasites to the model nematode Caenorhabditis elegans. Applying genomics techniques to these species, we analyzed 3,840 and 3,149 genes from Ancylostoma caninum and A. ceylanicum. Results Transcripts originated from libraries representing infective L3 larva, stimulated L3, arrested L3, and adults. Most genes are represented in single stages including abundant transcripts like hsp-20 in infective L3 and vit-3 in adults. Over 80% of the genes have homologs in C. elegans, and nearly 30% of these were with observable RNA interference phenotypes. Homologies were identified to nematode-specific and clade V specific gene families. To study the evolution of hookworm genes, 574 A. caninum / A. ceylanicum orthologs were identified, all of which were found to be under purifying selection with distribution ratios of nonsynonymous to synonymous amino acid substitutions similar to that reported for C. elegans / C. briggsae orthologs. The phylogenetic distance between A. caninum and A. ceylanicum is almost identical to that for C. elegans / C. briggsae. Conclusion The genes discovered should substantially accelerate research toward better understanding of the parasites' basic biology as well as new therapies including vaccines and novel anthelmintics. PMID:15854223

  19. Origin in Acinetobacter guillouiae and dissemination of the aminoglycoside-modifying enzyme Aph(3')-VI.

    PubMed

    Yoon, Eun-Jeong; Goussard, Sylvie; Touchon, Marie; Krizova, Lenka; Cerqueira, Gustavo; Murphy, Cheryl; Lambert, Thierry; Grillot-Courvalin, Catherine; Nemec, Alexandr; Courvalin, Patrice

    2014-10-21

    The amikacin resistance gene aphA6 was first detected in the nosocomial pathogen Acinetobacter baumannii and subsequently in other genera. Analysis of 133 whole-genome sequences covering the taxonomic diversity of Acinetobacter spp. detected aphA6 in the chromosome of 2 isolates of A. guillouiae, which is an environmental species, 1 of 8 A. parvus isolates, and 5 of 34 A. baumannii isolates. The gene was also present in 29 out of 36 A. guillouiae isolates screened by PCR, indicating that it is ancestral to this species. The Pnative promoter for aphA6 in A. guillouiae and A. parvus was replaced in A. baumannii by PaphA6, which was generated by use of the insertion sequence ISAba125, which brought a -35 sequence. Study of promoter strength in Escherichia coli and A. baumannii indicated that PaphA6 was four times more potent than Pnative. There was a good correlation between aminoglycoside MICs and aphA6 transcription in A. guillouiae isolates that remained susceptible to amikacin. The marked topology differences of the phylogenetic trees of aphA6 and of the hosts strongly support its recent direct transfer within Acinetobacter spp. and also to evolutionarily remote bacterial genera. Concomitant expression of aphA6 must have occurred because, contrary to the donors, it can confer resistance to the new hosts. Mobilization and expression of aphA6 via composite transposons and the upstream IS-generating hybrid PaphA6, followed by conjugation, seems the most plausible mechanism. This is in agreement with the observation that, in the recipients, aphA6 is carried by conjugative plasmids and flanked by IS that are common in Acinetobacter spp. Our data indicate that resistance genes can also be found in susceptible environmental bacteria. Importance: We speculated that the aphA6 gene for an enzyme that confers resistance to amikacin, the most active aminoglycoside for the treatment of nosocomial infections due to Acinetobacter spp., originated in this genus before

  20. Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation

    PubMed Central

    Clarkson, Chris S.; Weetman, David; Essandoh, John; Yawson, Alexander E.; Maslen, Gareth; Manske, Magnus; Field, Stuart G.; Webster, Mark; Antão, Tiago; MacInnis, Bronwyn; Kwiatkowski, Dominic; Donnelly, Martin J.

    2014-01-01

    Adaptive introgression can provide novel genetic variation to fuel rapid evolutionary responses, though it may be counterbalanced by potential for detrimental disruption of the recipient genomic background. We examine the extent and impact of recent introgression of a strongly selected insecticide-resistance mutation (Vgsc-1014F) located within one of two exceptionally large genomic islands of divergence separating the Anopheles gambiae species pair. Here we show that transfer of the Vgsc mutation results in homogenization of the entire genomic island region (~1.5% of the genome) between species. Despite this massive disruption, introgression is clearly adaptive with a dramatic rise in frequency of Vgsc-1014F and no discernable impact on subsequent reproductive isolation between species. Our results show (1) how resilience of genomes to massive introgression can permit rapid adaptive response to anthropogenic selection and (2) that even extreme prominence of genomic islands of divergence can be an unreliable indicator of importance in speciation. PMID:24963649

  1. Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation.

    PubMed

    Clarkson, Chris S; Weetman, David; Essandoh, John; Yawson, Alexander E; Maslen, Gareth; Manske, Magnus; Field, Stuart G; Webster, Mark; Antão, Tiago; MacInnis, Bronwyn; Kwiatkowski, Dominic; Donnelly, Martin J

    2014-06-25

    Adaptive introgression can provide novel genetic variation to fuel rapid evolutionary responses, though it may be counterbalanced by potential for detrimental disruption of the recipient genomic background. We examine the extent and impact of recent introgression of a strongly selected insecticide-resistance mutation (Vgsc-1014F) located within one of two exceptionally large genomic islands of divergence separating the Anopheles gambiae species pair. Here we show that transfer of the Vgsc mutation results in homogenization of the entire genomic island region (~1.5% of the genome) between species. Despite this massive disruption, introgression is clearly adaptive with a dramatic rise in frequency of Vgsc-1014F and no discernable impact on subsequent reproductive isolation between species. Our results show (1) how resilience of genomes to massive introgression can permit rapid adaptive response to anthropogenic selection and (2) that even extreme prominence of genomic islands of divergence can be an unreliable indicator of importance in speciation.

  2. Diversity and Clinical Impact of Acinetobacter baumannii Colonization and Infection at a Military Medical Center ▿

    PubMed Central

    Petersen, Kyle; Cannegieter, Suzanne C.; van der Reijden, Tanny J.; van Strijen, Beppie; You, David M.; Babel, Britta S.; Philip, Andrew I.; Dijkshoorn, Lenie

    2011-01-01

    The epidemiology of Acinetobacter baumannii emerging in combat casualties is poorly understood. We analyzed 65 (54 nonreplicate) Acinetobacter isolates from 48 patients (46 hospitalized and 2 outpatient trainees entering the military) from October 2004 to October 2005 for genotypic similarities, time-space relatedness, and antibiotic susceptibility. Clinical and surveillance cultures were compared by amplified fragment length polymorphism (AFLP) genomic fingerprinting to each other and to strains of a reference database. Antibiotic susceptibility was determined, and multiplex PCR was performed for OXA-23-like, -24-like, -51-like, and -58-like carbapenemases. Records were reviewed for overlapping hospital stays of the most frequent genotypes, and risk ratios were calculated for any association of genotype with severity of Acute Physiology and Chronic Health Evaluation II (APACHE II) score or injury severity score (ISS) and previous antibiotic use. Nineteen genotypes were identified; two predominated, one consistent with an emerging novel international clone and the other unique to our database. Both predominant genotypes were carbapenem resistant, were present at another hospital before patients' admission to our facility, and were associated with higher APACHE II scores, higher ISSs, and previous carbapenem antibiotics in comparison with other genotypes. One predominated in wound and respiratory isolates, and the other predominated in wound and skin surveillance samples. Several other genotypes were identified as European clones I to III. Acinetobacter genotypes from recruits upon entry to the military, unlike those in hospitalized patients, did not include carbapenem-resistant genotypes. Acinetobacter species isolated from battlefield casualties are diverse, including genotypes belonging to European clones I to III. Two carbapenem-resistant genotypes were epidemic, one of which appeared to belong to a novel international clone. PMID:21084513

  3. Diversity and clinical impact of Acinetobacter baumannii colonization and infection at a military medical center.

    PubMed

    Petersen, Kyle; Cannegieter, Suzanne C; van der Reijden, Tanny J; van Strijen, Beppie; You, David M; Babel, Britta S; Philip, Andrew I; Dijkshoorn, Lenie

    2011-01-01

    The epidemiology of Acinetobacter baumannii emerging in combat casualties is poorly understood. We analyzed 65 (54 nonreplicate) Acinetobacter isolates from 48 patients (46 hospitalized and 2 outpatient trainees entering the military) from October 2004 to October 2005 for genotypic similarities, time-space relatedness, and antibiotic susceptibility. Clinical and surveillance cultures were compared by amplified fragment length polymorphism (AFLP) genomic fingerprinting to each other and to strains of a reference database. Antibiotic susceptibility was determined, and multiplex PCR was performed for OXA-23-like, -24-like, -51-like, and -58-like carbapenemases. Records were reviewed for overlapping hospital stays of the most frequent genotypes, and risk ratios were calculated for any association of genotype with severity of Acute Physiology and Chronic Health Evaluation II (APACHE II) score or injury severity score (ISS) and previous antibiotic use. Nineteen genotypes were identified; two predominated, one consistent with an emerging novel international clone and the other unique to our database. Both predominant genotypes were carbapenem resistant, were present at another hospital before patients' admission to our facility, and were associated with higher APACHE II scores, higher ISSs, and previous carbapenem antibiotics in comparison with other genotypes. One predominated in wound and respiratory isolates, and the other predominated in wound and skin surveillance samples. Several other genotypes were identified as European clones I to III. Acinetobacter genotypes from recruits upon entry to the military, unlike those in hospitalized patients, did not include carbapenem-resistant genotypes. Acinetobacter species isolated from battlefield casualties are diverse, including genotypes belonging to European clones I to III. Two carbapenem-resistant genotypes were epidemic, one of which appeared to belong to a novel international clone.

  4. The Complete Chloroplast Genome Sequences of Five Epimedium Species: Lights into Phylogenetic and Taxonomic Analyses

    PubMed Central

    Zhang, Yanjun; Du, Liuwen; Liu, Ao; Chen, Jianjun; Wu, Li; Hu, Weiming; Zhang, Wei; Kim, Kyunghee; Lee, Sang-Choon; Yang, Tae-Jin; Wang, Ying

    2016-01-01

    Epimedium L. is a phylogenetically and economically important genus in the family Berberidaceae. We here sequenced the complete chloroplast (cp) genomes of four Epimedium species using Illumina sequencing technology via a combination of de novo and reference-guided assembly, which was also the first comprehensive cp genome analysis on Epimedium combining the cp genome sequence of E. koreanum previously reported. The five Epimedium cp genomes exhibited typical quadripartite and circular structure that was rather conserved in genomic structure and the synteny of gene order. However, these cp genomes presented obvious variations at the boundaries of the four regions because of the expansion and contraction of the inverted repeat (IR) region and the single-copy (SC) boundary regions. The trnQ-UUG duplication occurred in the five Epimedium cp genomes, which was not found in the other basal eudicotyledons. The rapidly evolving cp genome regions were detected among the five cp genomes, as well as the difference of simple sequence repeats (SSR) and repeat sequence were identified. Phylogenetic relationships among the five Epimedium species based on their cp genomes showed accordance with the updated system of the genus on the whole, but reminded that the evolutionary relationships and the divisions of the genus need further investigation applying more evidences. The availability of these cp genomes provided valuable genetic information for accurately identifying species, taxonomy and phylogenetic resolution and evolution of Epimedium, and assist in exploration and utilization of Epimedium plants. PMID:27014326

  5. Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

    PubMed Central

    2009-01-01

    The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10 000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16 203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60 000 living species). In this proposal, we present precise counts for these 16 203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry. PMID:19892720

  6. Similarities and differences in the nuclear genome organization within Pooideae species revealed by comparative genomic in situ hybridization (GISH).

    PubMed

    Majka, Joanna; Majka, Maciej; Kwiatek, Michał; Wiśniewska, Halina

    2016-10-14

    In this paper, we highlight the affinity between the genomes of key representatives of the Pooideae subfamily, revealed at the chromosomal level by genomic in situ hybridization (GISH). The analyses were conducted using labeled probes from each species to hybridize with chromosomes of every species used in this study based on a "round robin" rule. As a result, the whole chromosomes or chromosome regions were distinguished or variable types of signals were visualized to prove the different levels of the relationships between genomes used in this study. We observed the unexpected lack of signals in secondary constrictions of rye (RR) chromosomes probed by triticale (AABBRR) genomic DNA. We have also identified unlabeled chromosome regions, which point to species-specific sequences connected with disparate pathways of chromosome differentiation. Our results revealed a conservative character of coding sequence of 35S rDNA among selected species of the genera Aegilops, Brachypodium, Festuca, Hordeum, Lolium, Secale, and Triticum. In summary, we showed strong relationships in genomic DNA sequences between species which have been previously reported to be phylogenetically distant.

  7. Acinetobacter junii as an aetiological agent of corneal ulcer.

    PubMed

    Broniek, G; Langwińska-Wośko, E; Szaflik, J; Wróblewska, M

    2014-12-01

    Rods of the Acinetobacter genus are present mainly in the external environment (e.g. water, soil) and in animals, while in humans they may comprise physiological flora. The main pathogenic species is Acinetobacter baumannii complex, which constitutes a common cause of nosocomial infections, particularly in patients with underlying diseases and risk factors (e.g. prior broad-spectrum antibiotic therapy, malignancy, central venous catheter, mechanical ventilation); however, infections of the eye caused by strains of Acinetobacter spp. are very rare. We report a unique case of community-acquired corneal ulcer caused by Acinetobacter non-baumannii (possibly A. junii), in a patient with no risk factors identified. The case highlights the need for obtaining a sample from the cornea for bacteriological culture in the case of suspected ophthalmic infection as identification of the pathogen, and assessment of its susceptibility profile enables proper antibiotic therapy, improves the outcome and may constitute an eyesight-saving management.

  8. Comparative Analysis of Begonia Plastid Genomes and Their Utility for Species-Level Phylogenetics.

    PubMed

    Harrison, Nicola; Harrison, Richard J; Kidner, Catherine A

    2016-01-01

    Recent, rapid radiations make species-level phylogenetics difficult to resolve. We used a multiplexed, high-throughput sequencing approach to identify informative genomic regions to resolve phylogenetic relationships at low taxonomic levels in Begonia from a survey of sixteen species. A long-range PCR method was used to generate draft plastid genomes to provide a strong phylogenetic backbone, identify fast evolving regions and provide informative molecular markers for species-level phylogenetic studies in Begonia.

  9. Comparative Analysis of Begonia Plastid Genomes and Their Utility for Species-Level Phylogenetics

    PubMed Central

    Harrison, Nicola; Harrison, Richard J.

    2016-01-01

    Recent, rapid radiations make species-level phylogenetics difficult to resolve. We used a multiplexed, high-throughput sequencing approach to identify informative genomic regions to resolve phylogenetic relationships at low taxonomic levels in Begonia from a survey of sixteen species. A long-range PCR method was used to generate draft plastid genomes to provide a strong phylogenetic backbone, identify fast evolving regions and provide informative molecular markers for species-level phylogenetic studies in Begonia. PMID:27058864

  10. Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex.

    PubMed

    Vijay, Nagarjun; Bossu, Christen M; Poelstra, Jelmer W; Weissensteiner, Matthias H; Suh, Alexander; Kryukov, Alexey P; Wolf, Jochen B W

    2016-10-31

    Uncovering the genetic basis of species diversification is a central goal in evolutionary biology. Yet, the link between the accumulation of genomic changes during population divergence and the evolutionary forces promoting reproductive isolation is poorly understood. Here, we analysed 124 genomes of crow populations with various degrees of genome-wide differentiation, with parallelism of a sexually selected plumage phenotype, and ongoing hybridization. Overall, heterogeneity in genetic differentiation along the genome was best explained by linked selection exposed on a shared genome architecture. Superimposed on this common background, we identified genomic regions with signatures of selection specific to independent phenotypic contact zones. Candidate pigmentation genes with evidence for divergent selection were only partly shared, suggesting context-dependent selection on a multigenic trait architecture and parallelism by pathway rather than by repeated single-gene effects. This study provides insight into how various forms of selection shape genome-wide patterns of genomic differentiation as populations diverge.

  11. Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

    PubMed Central

    Vijay, Nagarjun; Bossu, Christen M.; Poelstra, Jelmer W.; Weissensteiner, Matthias H.; Suh, Alexander; Kryukov, Alexey P.; Wolf, Jochen B. W.

    2016-01-01

    Uncovering the genetic basis of species diversification is a central goal in evolutionary biology. Yet, the link between the accumulation of genomic changes during population divergence and the evolutionary forces promoting reproductive isolation is poorly understood. Here, we analysed 124 genomes of crow populations with various degrees of genome-wide differentiation, with parallelism of a sexually selected plumage phenotype, and ongoing hybridization. Overall, heterogeneity in genetic differentiation along the genome was best explained by linked selection exposed on a shared genome architecture. Superimposed on this common background, we identified genomic regions with signatures of selection specific to independent phenotypic contact zones. Candidate pigmentation genes with evidence for divergent selection were only partly shared, suggesting context-dependent selection on a multigenic trait architecture and parallelism by pathway rather than by repeated single-gene effects. This study provides insight into how various forms of selection shape genome-wide patterns of genomic differentiation as populations diverge. PMID:27796282

  12. The Complete Chloroplast Genome of Wild Rice (Oryza minuta) and Its Comparison to Related Species

    PubMed Central

    Asaf, Sajjad; Waqas, Muhammad; Khan, Abdul L.; Khan, Muhammad A.; Kang, Sang-Mo; Imran, Qari M.; Shahzad, Raheem; Bilal, Saqib; Yun, Byung-Wook; Lee, In-Jung

    2017-01-01

    Oryza minuta, a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites. The genomic organization, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. Approximately 30 forward, 28 tandem and 20 palindromic repeats were detected in the O. minuta cp genome. Comparison of the complete O. minuta cp genome with another eleven Oryza species showed a high degree of sequence similarity and relatively high divergence of intergenic spacers. Phylogenetic analyses were conducted based on the complete genome sequence, 65 shared genes and matK gene showed same topologies and O. minuta forms a single clade with parental O. punctata. Thus, the complete O. minuta cp genome provides interesting insights and valuable information that can be used to identify related species and reconstruct its phylogeny. PMID:28326093

  13. Functional organization of the genome may shape the species boundary in the house mouse.

    PubMed

    Janoušek, Václav; Munclinger, Pavel; Wang, Liuyang; Teeter, Katherine C; Tucker, Priscilla K

    2015-05-01

    Genomic features such as rate of recombination and differentiation have been suggested to play a role in species divergence. However, the relationship of these phenomena to functional organization of the genome in the context of reproductive isolation remains unexplored. Here, we examine genomic characteristics of the species boundaries between two house mouse subspecies (Mus musculus musculus/M. m. domesticus). These taxa form a narrow semipermeable zone of secondary contact across Central Europe. Due to the incomplete nature of reproductive isolation, gene flow in the zone varies across the genome. We present an analysis of genomic differentiation, rate of recombination, and functional composition of genes relative to varying amounts of introgression. We assessed introgression using 1,316 autosomal single nucleotide polymorphism markers, previously genotyped in hybrid populations from three transects. We found a significant relationship between amounts of introgression and both genomic differentiation and rate of recombination with genomic regions of reduced introgression associated with higher genomic differentiation and lower rates of recombination, and the opposite for genomic regions of extensive introgression. We also found a striking functional polarization of genes based on where they are expressed in the cell. Regions of elevated introgression exhibit a disproportionate number of genes involved in signal transduction functioning at the cell periphery, among which olfactory receptor genes were found to be the most prominent group. Conversely, genes expressed intracellularly and involved in DNA binding were the most prevalent in regions of reduced introgression. We hypothesize that functional organization of the genome is an important driver of species divergence.

  14. Roegneria alashanica Keng: a species with the StStSt(Y)St(Y) genome constitution.

    PubMed

    Wang, Richard R-C; Jensen, Kevin B

    2017-03-17

    The genome constitution of tetraploid Roegneria alashanica Keng has been in question for a long time. Most scientific studies have suggested that R. alashanica had two versions of the St genome, St1St2, similar to that of Pseudoroegneria elytrigioides (C. Yen & J.L. Yang) B.R. Lu. A study, however, concluded that R. alashanica had the StY genome formula typical for tetraploid species of Roegneria. For the present study, R. alashanica, Elymus longearistatus (Bioss.) Tzvelev (StY genomes), Pseudoroegneria strigosa (M. Bieb.) Á. Löve (St), Pseudoroegneria libanoctica (Hackel) D.R. Dewey (St), and Pseudoroegneria spicata (Pursh) Á. Löve (St) were screened for the Y-genome specific marker B14(F+R)269. All E. longearistatus plants expressed intense bands specific to the Y genome. Only 6 of 10 R. alashanica plants exhibited relatively faint bands for the STS marker. Previously, the genome in species of Pseudoroegneria exhibiting such faint Y-genome specific marker was designated as St(Y). Based on these results, R. alashanica lacks the Y genome in E. longearistatus but likely possess two remotely related St genomes, St and St(Y). According to its genome constitution, R. alashanica should be classified in the genus Pseudoroenera and given the new name Pseudoroegneria alashanica (Keng) R.R.-C. Wang and K.B. Jensen.

  15. Carbapenem-resistance and pathogenicity of bovine Acinetobacter indicus-like isolates.

    PubMed

    Klotz, Peter; Göttig, Stephan; Leidner, Ursula; Semmler, Torsten; Scheufen, Sandra; Ewers, Christa

    2017-01-01

    relatedness to isolates from human clinical sources requires further investigations regarding the pathogenic potential, genomic characteristics, zoonotic risk and putative additional sources of this new Acinetobacter species.

  16. Carbapenem-resistance and pathogenicity of bovine Acinetobacter indicus-like isolates

    PubMed Central

    Leidner, Ursula; Semmler, Torsten; Scheufen, Sandra; Ewers, Christa

    2017-01-01

    relatedness to isolates from human clinical sources requires further investigations regarding the pathogenic potential, genomic characteristics, zoonotic risk and putative additional sources of this new Acinetobacter species. PMID:28207789

  17. The genomic organization of Ty3/gypsy-like retrotransposons in Helianthus (Asteraceae) homoploid hybrid species.

    PubMed

    Staton, S Evan; Ungerer, Mark C; Moore, Richard C

    2009-09-01

    The origin of new diploid, or homoploid, hybrid species is associated with rapid genomic restructuring in the hybrid neospecies. This mode of speciation has been best characterized in wild sunflower species in the genus Helianthus, where three homoploid hybrid species (H. anomalus, H. deserticola, and H. paradoxus) have independently arisen via ancient hybridization events between the same two parental species (H. annuus and H. petiolaris). Most previous work examining genomic restructuring in these sunflower hybrid species has focused on chromosomal rearrangements. However, the origin of all three homoploid hybrid sunflower species also is associated with massive proliferation events of Ty3/gypsy-like retrotransposons in the hybrid species' genomes. We compared the genomic organization of these elements in the parent species and two of the homoploid hybrid species using fluorescence in situ hybridization (FISH). We found a significant expansion of Ty3/gypsy-like retrotransposons confined to the pericentromeric regions of two hybrid sunflower species, H. deserticola and H. paradoxus. In contrast, we detected no significant increase in the frequency or extent of dispersed retrotransposon populations in the hybrid species within the resolution limits of our assay. We discuss the potential role that transposable element proliferation and localization plays in the evolution of homoploid hybrid species.

  18. The genomic impact of 100 million years of social evolution in seven ant species.

    PubMed

    Gadau, Jürgen; Helmkampf, Martin; Nygaard, Sanne; Roux, Julien; Simola, Daniel F; Smith, Chris R; Suen, Garret; Wurm, Yannick; Smith, Christopher D

    2012-01-01

    Ants (Hymenoptera, Formicidae) represent one of the most successful eusocial taxa in terms of both their geographic distribution and species number. The publication of seven ant genomes within the past year was a quantum leap for socio- and ant genomics. The diversity of social organization in ants makes them excellent model organisms to study the evolution of social systems. Comparing the ant genomes with those of the honeybee, a lineage that evolved eusociality independently from ants, and solitary insects suggests that there are significant differences in key aspects of genome organization between social and solitary insects, as well as among ant species. Altogether, these seven ant genomes open exciting new research avenues and opportunities for understanding the genetic basis and regulation of social species, and adaptive complex systems in general.

  19. Comparative Genomics of Bacillus species and its Relevance in Industrial Microbiology

    PubMed Central

    Sharma, Archana; Satyanarayana, T

    2013-01-01

    With the advent of high throughput sequencing platforms and relevant analytical tools, the rate of microbial genome sequencing has accelerated which has in turn led to better understanding of microbial molecular biology and genetics. The complete genome sequences of important industrial organisms provide opportunities for human health, industry, and the environment. Bacillus species are the dominant workhorses in industrial fermentations. Today, genome sequences of several Bacillus species are available, and comparative genomics of this genus helps in understanding their physiology, biochemistry, and genetics. The genomes of these bacterial species are the sources of many industrially important enzymes and antibiotics and, therefore, provide an opportunity to tailor enzymes with desired properties to suit a wide range of applications. A comparative account of strengths and weaknesses of the different sequencing platforms are also highlighted in the review. PMID:26217108

  20. Bacterial genomic epidemiology, from local outbreak characterization to species-history reconstruction

    PubMed Central

    Gaiarsa, Stefano; De Marco, Leone; Comandatore, Francesco; Marone, Piero; Bandi, Claudio; Sassera, Davide

    2015-01-01

    Bacteriology has embraced the next-generation sequencing revolution, swiftly moving from the time of single genome sequencing to the age of genomic epidemiology. Hundreds and now even thousands of genomes are being sequenced for single bacterial species, allowing unprecedented levels of resolution and insight in the evolution and epidemic diffusion of the main bacterial pathogens. Here, we present a review of some of the most recent and groundbreaking studies in this field. PMID:26878934

  1. Amplification of a single-locus variable-number direct repeats with restriction fragment length polymorphism (DR-PCR/RFLP) for genetic typing of Acinetobacter baumannii strains.

    PubMed

    Nowak-Zaleska, Alicja; Krawczyk, Beata; Kotłowski, Roman; Mikucka, Agnieszka; Gospodarek, Eugenia

    2008-01-01

    In search of an effective DNA typing technique for Acinetobacter baumannii strains for hospital epidemiology use, the performance and convenience of a new target sequence was evaluated. Using known genomic sequences of Acinetobacter baumannii strains AR 319754 and ATCC 17978, we developed single-locus variable-number direct-repeat analysis using polymerase chain reaction-restriction fragment length polymorphism (DR-PCR/RFLP) method. A total of 90 Acinetobacter baumannii strains isolated from patients of the Clinical Hospital in Bydgoszcz, Poland, were examined. Initially, all strains were typed using macrorestriction analysis of the chromosomal DNA by pulsed-field gel electrophoresis (REA-PFGE). Digestion of the chromosomal DNA with the ApaI endonuclease and separation of the fragments by PFGE revealed 21 unique types. Application of DR-PCR/RFLP resulted in recognition of 12 clusters. The results showed that the DR-PCR/RFLP method is less discriminatory than REA-PFGE, however, the novel genotyping method can be used as an alternative technique for generating DNA profiles in epidemiological studies of intra-species genetic relatedness of Acinetobacter baumannii strains.

  2. Developing informative microsatellite makers for non-model species using reference mapping against a model species' genome.

    PubMed

    Hung, Chih-Ming; Yu, Ai-Yun; Lai, Yu-Ting; Shaner, Pei-Jen L

    2016-03-15

    Microsatellites have a wide range of applications from behavioral biology, evolution, to agriculture-based breeding programs. The recent progress in the next-generation sequencing technologies and the rapidly increasing number of published genomes may greatly enhance the current applications of microsatellites by turning them from anonymous to informative markers. Here we developed an approach to anchor microsatellite markers of any target species in a genome of a related model species, through which the genomic locations of the markers, along with any functional genes potentially linked to them, can be revealed. We mapped the shotgun sequence reads of a non-model rodent species Apodemus semotus against the genome of a model species, Mus musculus, and presented 24 polymorphic microsatellite markers with detailed background information for A. semotus in this study. The developed markers can be used in other rodent species, especially those that are closely related to A. semotus or M. musculus. Compared to the traditional approaches based on DNA cloning, our approach is likely to yield more loci for the same cost. This study is a timely demonstration of how a research team can efficiently generate informative (neutral or function-associated) microsatellite markers for their study species and unique biological questions.

  3. Insights into the Musa genome: Syntenic relationships to rice and between Musa species

    PubMed Central

    Lescot, Magali; Piffanelli, Pietro; Ciampi, Ana Y; Ruiz, Manuel; Blanc, Guillaume; Leebens-Mack, Jim; da Silva, Felipe R; Santos, Candice MR; D'Hont, Angélique; Garsmeur, Olivier; Vilarinhos, Alberto D; Kanamori, Hiroyuki; Matsumoto, Takashi; Ronning, Catherine M; Cheung, Foo; Haas, Brian J; Althoff, Ryan; Arbogast, Tammy; Hine, Erin; Pappas, Georgios J; Sasaki, Takuji; Souza, Manoel T; Miller, Robert NG; Glaszmann, Jean-Christophe; Town, Christopher D

    2008-01-01

    Background Musa species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale analyses of Musa genomic sequence have been conducted. This study compares genomic sequence in two Musa species with orthologous regions in the rice genome. Results We produced 1.4 Mb of Musa sequence from 13 BAC clones, annotated and analyzed them along with 4 previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with eudicot and Poaceae genomes. Comparison with rice revealed microsynteny regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The divergence time distributions for Musa-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong evidence for a large-scale duplication event in the Musa lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from M. acuminata and M. balbisiana revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya. Conclusion These results point to the utility of comparative analyses between distantly-related monocot species such as rice and Musa for improving our understanding of monocot genome evolution. Sequencing the genome of M. acuminata would provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivated Musa polyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic traits for breeding purposes

  4. A draft physical map of a D-genome cotton species (Gossypium raimondii)

    PubMed Central

    2010-01-01

    Background Genetically anchored physical maps of large eukaryotic genomes have proven useful both for their intrinsic merit and as an adjunct to genome sequencing. Cultivated tetraploid cottons, Gossypium hirsutum and G. barbadense, share a common ancestor formed by a merger of the A and D genomes about 1-2 million years ago. Toward the long-term goal of characterizing the spectrum of diversity among cotton genomes, the worldwide cotton community has prioritized the D genome progenitor Gossypium raimondii for complete sequencing. Results A whole genome physical map of G. raimondii, the putative D genome ancestral species of tetraploid cottons was assembled, integrating genetically-anchored overgo hybridization probes, agarose based fingerprints and 'high information content fingerprinting' (HICF). A total of 13,662 BAC-end sequences and 2,828 DNA probes were used in genetically anchoring 1585 contigs to a cotton consensus genetic map, and 370 and 438 contigs, respectively to Arabidopsis thaliana (AT) and Vitis vinifera (VV) whole genome sequences. Conclusion Several lines of evidence suggest that the G. raimondii genome is comprised of two qualitatively different components. Much of the gene rich component is aligned to the Arabidopsis and Vitis vinifera genomes and shows promise for utilizing translational genomic approaches in understanding this important genome and its resident genes. The integrated genetic-physical map is of value both in assembling and validating a planned reference sequence. PMID:20569427

  5. Genome Sizes of Nine Insect Species Determined by Flow Cytometry and k-mer Analysis

    PubMed Central

    He, Kang; Lin, Kejian; Wang, Guirong; Li, Fei

    2016-01-01

    The flow cytometry method was used to estimate the genome sizes of nine agriculturally important insects, including two coleopterans, five Hemipterans, and two hymenopterans. Among which, the coleopteran Lissorhoptrus oryzophilus (Kuschel) had the largest genome of 981 Mb. The average genome size was 504 Mb, suggesting that insects have a moderate-size genome. Compared with the insects in other orders, hymenopterans had small genomes, which were averagely about ~200 Mb. We found that the genome sizes of four insect species were different between male and female, showing the organismal complexity of insects. The largest difference occurred in the coconut leaf beetle Brontispa longissima (Gestro). The male coconut leaf beetle had a 111 Mb larger genome than females, which might be due to the chromosome number difference between the sexes. The results indicated that insect invasiveness was not related to genome size. We also determined the genome sizes of the small brown planthopper Laodelphax striatellus (Fallén) and the parasitic wasp Macrocentrus cingulum (Brischke) using k-mer analysis with Illunima Solexa sequencing data. There were slight differences in the results from the two methods. k-mer analysis indicated that the genome size of L. striatellus was 500–700 Mb and that of M. cingulum was ~150 Mb. In all, the genome sizes information presented here should be helpful for designing the genome sequencing strategy when necessary. PMID:27932995

  6. Genome Sequence of Two Novel Species of Torque Teno Minivirus from the Human Oral Cavity

    PubMed Central

    Parras-Moltó, Marcos; Suárez-Rodríguez, Patricia; Eguia, Asier; Aguirre-Urizar, José Manuel

    2014-01-01

    Anelloviridae is a family of circular, single-stranded DNA viruses highly prevalent among humans. We report the genome sequence of two torque teno miniviruses found in human oral mucosa samples. Genome organization, phylogenetic analysis, and pairwise comparisons reveal that they belong to novel species within the Betatorquevirus genus. PMID:25291759

  7. Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species

    PubMed Central

    Irizarry, Kristopher J. L.; Bryant, Doug; Kalish, Jordan; Eng, Curtis; Schmidt, Peggy L.; Barrett, Gini; Barr, Margaret C.

    2016-01-01

    Many endangered captive populations exhibit reduced genetic diversity resulting in health issues that impact reproductive fitness and quality of life. Numerous cost effective genomic sequencing and genotyping technologies provide unparalleled opportunity for incorporating genomics knowledge in management of endangered species. Genomic data, such as sequence data, transcriptome data, and genotyping data, provide critical information about a captive population that, when leveraged correctly, can be utilized to maximize population genetic variation while simultaneously reducing unintended introduction or propagation of undesirable phenotypes. Current approaches aimed at managing endangered captive populations utilize species survival plans (SSPs) that rely upon mean kinship estimates to maximize genetic diversity while simultaneously avoiding artificial selection in the breeding program. However, as genomic resources increase for each endangered species, the potential knowledge available for management also increases. Unlike model organisms in which considerable scientific resources are used to experimentally validate genotype-phenotype relationships, endangered species typically lack the necessary sample sizes and economic resources required for such studies. Even so, in the absence of experimentally verified genetic discoveries, genomics data still provides value. In fact, bioinformatics and comparative genomics approaches offer mechanisms for translating these raw genomics data sets into integrated knowledge that enable an informed approach to endangered species management. PMID:27376076

  8. Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species.

    PubMed

    Irizarry, Kristopher J L; Bryant, Doug; Kalish, Jordan; Eng, Curtis; Schmidt, Peggy L; Barrett, Gini; Barr, Margaret C

    2016-01-01

    Many endangered captive populations exhibit reduced genetic diversity resulting in health issues that impact reproductive fitness and quality of life. Numerous cost effective genomic sequencing and genotyping technologies provide unparalleled opportunity for incorporating genomics knowledge in management of endangered species. Genomic data, such as sequence data, transcriptome data, and genotyping data, provide critical information about a captive population that, when leveraged correctly, can be utilized to maximize population genetic variation while simultaneously reducing unintended introduction or propagation of undesirable phenotypes. Current approaches aimed at managing endangered captive populations utilize species survival plans (SSPs) that rely upon mean kinship estimates to maximize genetic diversity while simultaneously avoiding artificial selection in the breeding program. However, as genomic resources increase for each endangered species, the potential knowledge available for management also increases. Unlike model organisms in which considerable scientific resources are used to experimentally validate genotype-phenotype relationships, endangered species typically lack the necessary sample sizes and economic resources required for such studies. Even so, in the absence of experimentally verified genetic discoveries, genomics data still provides value. In fact, bioinformatics and comparative genomics approaches offer mechanisms for translating these raw genomics data sets into integrated knowledge that enable an informed approach to endangered species management.

  9. Sampling strategies for whole genome association studies in aquaculture and outcrossing plant species.

    PubMed

    Hayes, B J; MacLeod, I M; Baranski, M

    2009-12-01

    A number of farmed species are characterized by breeding populations of large full-sib families, including aquaculture species and outcrossing plant species. Whole genome association studies in such species must account for stratification arising from the full-sib family structure to avoid high rates of false discovery. Here, we demonstrate the value of selective genotyping strategies which balance the contribution of families across high and low phenotypes to greatly reduce rates of false discovery with a minimal effect on power.

  10. Molecular epidemiology of Acinetobacter baumannii and Acinetobacter nosocomialis in Germany over a 5-year period (2005-2009).

    PubMed

    Schleicher, X; Higgins, P G; Wisplinghoff, H; Körber-Irrgang, B; Kresken, M; Seifert, H

    2013-08-01

    To investigate the species distribution within the Acinetobacter calcoaceticus-Acinetobacter baumannii complex and the molecular epidemiology of A. baumannii and Acinetobacter nosocomialis, 376 Acinetobacter isolates were collected prospectively from hospitalized patients at 15 medical centres in Germany during three surveillance studies conducted over a 5-year period. Species identification was performed by molecular methods. Imipenem minimum inhibitory concentrations (MIC) were determined by broth microdilution. The prevalence of the most common carbapenemase-encoding genes was investigated by oxacillinase (OXA) -multiplex polymerase chain reaction (PCR). The molecular epidemiology was investigated by repetitive sequence-based PCR (rep-PCR; DiversiLab™). Acinetobacter pittii was the most prevalent Acinetobacter species (n = 193), followed by A. baumannii (n = 140), A. calcoaceticus (n = 10) and A. nosocomialis (n = 8). The majority of A. baumannii was represented by sporadic isolates (n = 70, 50%) that showed unique rep-PCR patterns, 25 isolates (18%) clustered with one or two other isolates, and only 45 isolates (32%) belonged to one of the previously described international clonal lineages. The most prevalent clonal lineage was international clone (IC) 2 (n = 34) and IC 1 (n = 6). According to CLSI, 25 A. baumannii isolates were non-susceptible to imipenem (MIC ≥ 8 mg/L), all of which produced an OXA-58-like or OXA-23-like carbapenemase. The rate of imipenem susceptibility among A. baumannii isolates decreased from 96% in 2005 to 76% in 2009. All other Acinetobacter isolates were susceptible to imipenem. The population structure of carbapenem-susceptible A. baumannii in Germany is highly diverse. Imipenem non-susceptibility was strongly associated with the clonal lineages IC 2 and IC 1. These data underscore the high clonality of carbapenem-resistant A. baumannii isolates.

  11. INVESTIGATIONS INTO MOLECULAR PATHWAYS IN THE POST GENOME ERA: CROSS SPECIES COMPARATIVE GENOMICS APPROACH

    EPA Science Inventory


    Genome sequencing efforts in the past decade were aimed at generating draft sequences of many prokaryotic and eukaryotic model organisms. Successful completion of unicellular eukaryotes, worm, fly and human genome have opened up the new field of molecular biology and function...

  12. Using comparative genomic hybridization to survey genomic sequence divergence across species: a proof-of-concept from Drosophila

    PubMed Central

    2010-01-01

    Background Genome-wide analysis of sequence divergence among species offers profound insights into the evolutionary processes that shape lineages. When full-genome sequencing is not feasible for a broad comparative study, we propose the use of array-based comparative genomic hybridization (aCGH) in order to identify orthologous genes with high sequence divergence. Here we discuss experimental design, statistical power, success rate, sources of variation and potential confounding factors. We used a spotted PCR product microarray platform from Drosophila melanogaster to assess sequence divergence on a gene-by-gene basis in three fully sequenced heterologous species (D. sechellia, D. simulans, and D. yakuba). Because complete genome assemblies are available for these species this study presents a powerful test for the use of aCGH as a tool to measure sequence divergence. Results We found a consistent and linear relationship between hybridization ratio and sequence divergence of the sample to the platform species. At higher levels of sequence divergence (< 92% sequence identity to D. melanogaster) ~84% of features had significantly less hybridization to the array in the heterologous species than the platform species, and thus could be identified as "diverged". At lower levels of divergence (≥ 97% identity), only 13% of genes were identified as diverged. While ~40% of the variation in hybridization ratio can be accounted for by variation in sequence identity of the heterologous sample relative to D. melanogaster, other individual characteristics of the DNA sequences, such as GC content, also contribute to variation in hybridization ratio, as does technical variation. Conclusions Here we demonstrate that aCGH can accurately be used as a proxy to estimate genome-wide divergence, thus providing an efficient way to evaluate how evolutionary processes and genomic architecture can shape species diversity in non-model systems. Given the increased number of species for which

  13. Genome Editing in C. elegans and Other Nematode Species

    PubMed Central

    Sugi, Takuma

    2016-01-01

    Caenorhabditis elegans, a 1 mm long free-living nematode, is a popular model animal that has been widely utilized for genetic investigations of various biological processes. Characteristic features that make C. elegans a powerful model of choice for eukaryotic genetic studies include its rapid life cycle (development from egg to adult in 3.5 days at 20 °C), well-annotated genome, simple morphology (comprising only 959 somatic cells in the hermaphrodite), and transparency (which facilitates non-invasive fluorescence observations). However, early approaches to introducing mutations in the C. elegans genome, such as chemical mutagenesis and imprecise excision of transposons, have required large-scale mutagenesis screens. To avoid this laborious and time-consuming procedure, genome editing technologies have been increasingly used in nematodes including C. briggsae and Pristionchus pacificus, thereby facilitating their genetic analyses. Here, I review the recent progress in genome editing technologies using zinc-finger nucleases (ZFNs), transcriptional activator-like nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 in nematodes and offer perspectives on their use in the future. PMID:26927083

  14. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species.

    PubMed

    Kim, Seungill; Park, Minkyu; Yeom, Seon-In; Kim, Yong-Min; Lee, Je Min; Lee, Hyun-Ah; Seo, Eunyoung; Choi, Jaeyoung; Cheong, Kyeongchae; Kim, Ki-Tae; Jung, Kyongyong; Lee, Gir-Won; Oh, Sang-Keun; Bae, Chungyun; Kim, Saet-Byul; Lee, Hye-Young; Kim, Shin-Young; Kim, Myung-Shin; Kang, Byoung-Cheorl; Jo, Yeong Deuk; Yang, Hee-Bum; Jeong, Hee-Jin; Kang, Won-Hee; Kwon, Jin-Kyung; Shin, Chanseok; Lim, Jae Yun; Park, June Hyun; Huh, Jin Hoe; Kim, June-Sik; Kim, Byung-Dong; Cohen, Oded; Paran, Ilan; Suh, Mi Chung; Lee, Saet Buyl; Kim, Yeon-Ki; Shin, Younhee; Noh, Seung-Jae; Park, Junhyung; Seo, Young Sam; Kwon, Suk-Yoon; Kim, Hyun A; Park, Jeong Mee; Kim, Hyun-Jin; Choi, Sang-Bong; Bosland, Paul W; Reeves, Gregory; Jo, Sung-Hwan; Lee, Bong-Woo; Cho, Hyung-Taeg; Choi, Hee-Seung; Lee, Min-Soo; Yu, Yeisoo; Do Choi, Yang; Park, Beom-Seok; van Deynze, Allen; Ashrafi, Hamid; Hill, Theresa; Kim, Woo Taek; Pai, Hyun-Sook; Ahn, Hee Kyung; Yeam, Inhwa; Giovannoni, James J; Rose, Jocelyn K C; Sørensen, Iben; Lee, Sang-Jik; Kim, Ryan W; Choi, Ik-Young; Choi, Beom-Soon; Lim, Jong-Sung; Lee, Yong-Hwan; Choi, Doil

    2014-03-01

    Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense. The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species.

  15. Survey and analysis of simple sequence repeats (SSRs) in three genomes of Candida species.

    PubMed

    Jia, Dongmei

    2016-06-15

    Simple sequence repeats (SSRs) or microsatellites, which composed of tandem repeated short units of 1-6 bp, have been paying attention continuously. Here, the distribution, composition and polymorphism of microsatellites and compound microsatellites were analyzed in three available genomes of Candida species (Candida dubliniensis, Candida glabrata and Candida orthopsilosis). The results show that there were 118,047, 66,259 and 61,119 microsatellites in genomes of C. dubliniensis, C. glabrata and C. orthopsilosis, respectively. The SSRs covered more than 1/3 length of genomes in the three species. The microsatellites, which just consist of bases A and (or) T, such as (A)n, (T)n, (AT)n, (TA)n, (AAT)n, (TAA)n, (TTA)n, (ATA)n, (ATT)n and (TAT)n, were predominant in the three genomes. The length of microsatellites was focused on 6 bp and 9 bp either in the three genomes or in its coding sequences. What's more, the relative abundance (19.89/kbp) and relative density (167.87 bp/kbp) of SSRs in sequence of mitochondrion of C. glabrata were significantly great than that in any one of genomes or chromosomes of the three species. In addition, the distance between any two adjacent microsatellites was an important factor to influence the formation of compound microsatellites. The analysis may be helpful for further studying the roles of microsatellites in genomes' origination, organization and evolution of Candida species.

  16. The evolution of polyploid wheats: identification of the A genome donor species.

    PubMed

    Dvorák, J; Terlizzi, P; Zhang, H B; Resta, P

    1993-02-01

    Cytogenetic work has shown that the tetraploid wheats, Triticum turgidum and T. timopheevii, and the hexaploid wheat T. aestivum have one pair of A genomes, whereas hexaploid T. zhukovskyi has two. Variation in 16 repeated nucleotide sequences was used to identify sources of the A genomes. The A genomes of T. turgidum, T. timopheevii, and T. aestivum were shown to be contributed by T. urartu. Little divergence in the repeated nucleotide sequences was detected in the A genomes of these species from the genome of T. urartu. In T. zhukovskyi one A genome was contributed by T. urartu and the other was contributed by T. monococcum. It is concluded that T. zhukovskyi originated from hybridization of T. timopheevii with T. monococcum. The repeated nucleotide sequence profiles in the A genomes of T. zhukovskyi showed reduced correspondence with those in the genomes of both ancestral species, T. urartu and T. monococcum. This differentiation is attributed to heterogenetic chromosome pairing and segregation among chromosomes of the two A genomes in T. zhukovskyi.

  17. Identification of a whitefly species by genomic and behavioral studies

    USGS Publications Warehouse

    Perring, T.M.; Cooper, A.D.; Rodriguez, R.J.; Farrar, C.A.; Bellows, T.S.

    1993-01-01

    An introduced whitefly species, responsible for over a half billion dollars in damage to U.S. agricultural production in 1991, is morphologically indistinguishable from Bemisia tabaci (Gennadius). However, with the use of polymerase chain reaction-based DNA differentiation tests, allozymic frequency analyses, crossing experiments, and mating behavior studies, the introduced whitefly is found to be a distinct species. Recognition of this new species, the silverleaf whitefly, is critical in the search for management options.

  18. Genomic evidence of rapid, global-scale gene flow in a Sulfolobus species.

    PubMed

    Mao, Dominic; Grogan, Dennis

    2012-08-01

    Local populations of Sulfolobus islandicus diverge genetically with geographical separation, and this has been attributed to restricted transfer of propagules imposed by the unfavorable spatial distribution of acidic geothermal habitat. We tested the generality of genetic divergence with distance in Sulfolobus species by analyzing genomes of Sulfolobus acidocaldarius drawn from three populations separated by more than 8000 km. In sharp contrast to S. islandicus, the geographically diverse S. acidocaldarius genomes proved to be nearly identical. We could not link the difference in genome conservation between the two species to a corresponding difference in genome stability or ecological factors affecting propagule dispersal. The results provide the first evidence that genetic isolation of local populations does not result primarily from properties intrinsic to Sulfolobus and the severe discontinuity of its geothermal habitat, but varies with species, and thus may reflect biotic interactions that act after propagule dispersal.

  19. Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence

    PubMed Central

    2010-01-01

    Background The Ralstonia solanacearum species complex includes thousands of strains pathogenic to an unusually wide range of plant species. These globally dispersed and heterogeneous strains cause bacterial wilt diseases, which have major socio-economic impacts. Pathogenicity is an ancestral trait in R. solanacearum and strains with high genetic variation can be subdivided into four phylotypes, correlating to isolates from Asia (phylotype I), the Americas (phylotype IIA and IIB), Africa (phylotype III) and Indonesia (phylotype IV). Comparison of genome sequences strains representative of this phylogenetic diversity can help determine which traits allow this bacterium to be such a pathogen of so many different plant species and how the bacteria survive in many different habitats. Results The genomes of three tomato bacterial wilt pathogens, CFBP2957 (phy. IIA), CMR15 (phy. III) and PSI07 (phy. IV) were sequenced and manually annotated. These genomes were compared with those of three previously sequenced R. solanacearum strains: GMI1000 (tomato, phy. I), IPO1609 (potato, phy. IIB), and Molk2 (banana, phy. IIB). The major genomic features (size, G+C content, number of genes) were conserved across all of the six sequenced strains. Despite relatively high genetic distances (calculated from average nucleotide identity) and many genomic rearrangements, more than 60% of the genes of the megaplasmid and 70% of those on the chromosome are syntenic. The three new genomic sequences revealed the presence of several previously unknown traits, probably acquired by horizontal transfers, within the genomes of R. solanacearum, including a type IV secretion system, a rhi-type anti-mitotic toxin and two small plasmids. Genes involved in virulence appear to be evolving at a faster rate than the genome as a whole. Conclusions Comparative analysis of genome sequences and gene content confirmed the differentiation of R. solanacearum species complex strains into four phylotypes. Genetic

  20. Genetic snapshots of the Rhizobium species NGR234 genome

    PubMed Central

    Viprey, Virginie; Rosenthal, André; Broughton, William J; Perret, Xavier

    2000-01-01

    Background: In nitrate-poor soils, many leguminous plants form nitrogen-fixing symbioses with members of the bacterial family Rhizobiaceae. We selected Rhizobium sp. NGR234 for its exceptionally broad host range, which includes more than I 12 genera of legumes. Unlike the genome of Bradyrhizobium japonicum, which is composed of a single 8.7 Mb chromosome, that of NGR234 is partitioned into three replicons: a chromosome of about 3.5 Mb, a megaplasmid of more than 2 Mb (pNGR234b) and pNGR234a, a 536,165 bp plasmid that carries most of the genes required for symbioses with legumes. Symbiotic loci represent only a small portion of all the genes coded by rhizobial genomes, however. To rapidly characterize the two largest replicons of NGR234, the genome of strain ANU265 (a derivative strain cured of pNGR234a) was analyzed by shotgun sequencing. Results: Homology searches of public databases with 2,275 random sequences of strain ANU265 resulted in the identification of 1,130 putative protein-coding sequences, of which 922 (41%) could be classified into functional groups. In contrast to the 18% of insertion-like sequences (ISs) found on the symbiotic plasmid pNGR234a, only 2.2% of the shotgun sequences represent known ISs, suggesting that pNGR234a is enriched in such elements. Hybridization data also indicate that the density of known transposable elements is higher in pNGR234b (the megaplasmid) than on the chromosome. Rhizobium-specific intergenic mosaic elements (RIMEs) were found in 35 shotgun sequences, 6 of which carry RIME2 repeats previously thought to be present only in Rhizobium meliloti. As non-overlapping shotgun sequences together represent approximately 10% of ANU265 genome, the chromosome and megaplasmid may carry a total of over 200 RIMEs. Conclusions: 'Skimming' the genome of Rhizobium sp. NGR234 sheds new light on the fine structure and evolution of its replicons, as well as on the integration of symbiotic functions in the genome of a soil bacterium

  1. Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level

    PubMed Central

    Tian, Xinpeng; Zhang, Zhewen; Yang, Tingting; Chen, Meili; Li, Jie; Chen, Fei; Yang, Jin; Li, Wenjie; Zhang, Bing; Zhang, Zhang; Wu, Jiayan; Zhang, Changsheng; Long, Lijuan; Xiao, Jingfa

    2016-01-01

    Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea’s genetic data sources. PMID:27446038

  2. Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level.

    PubMed

    Tian, Xinpeng; Zhang, Zhewen; Yang, Tingting; Chen, Meili; Li, Jie; Chen, Fei; Yang, Jin; Li, Wenjie; Zhang, Bing; Zhang, Zhang; Wu, Jiayan; Zhang, Changsheng; Long, Lijuan; Xiao, Jingfa

    2016-01-01

    Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea's genetic data sources.

  3. Bloodstream infection caused by Acinetobacter junii in a patient with acute lymphoblastic leukaemia after allogenic haematopoietic cell transplantation.

    PubMed

    Cayô, Rodrigo; Yañez San Segundo, Lucrecia; Pérez del Molino Bernal, Inmaculada Concepción; García de la Fuente, Celia; Bermúdez Rodríguez, Maria Aranzazu; Calvo, Jorge; Martínez-Martínez, Luis

    2011-03-01

    Acinetobacter junii is a rare human pathogen associated with bacteraemia in neonates and paediatric oncology patients. We present a case of A. junii causing bacteraemia in an adult transplant patient with leukaemia. The correct identification of Acinetobacter species can highlight the clinical significance of the different species of this genus.

  4. The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis.

    PubMed

    Zuo, Li-Hui; Shang, Ai-Qin; Zhang, Shuang; Yu, Xiao-Yue; Ren, Ya-Chao; Yang, Min-Sheng; Wang, Jin-Mao

    2017-01-01

    Elm (Ulmus) has a long history of use as a high-quality heavy hardwood famous for its resistance to drought, cold, and salt. It grows in temperate, warm temperate, and subtropical regions. This is the first report of Ulmaceae chloroplast genomes by de novo sequencing. The Ulmus chloroplast genomes exhibited a typical quadripartite structure with two single-copy regions (long single copy [LSC] and short single copy [SSC] sections) separated by a pair of inverted repeats (IRs). The lengths of the chloroplast genomes from five Ulmus ranged from 158,953 to 159,453 bp, with the largest observed in Ulmus davidiana and the smallest in Ulmus laciniata. The genomes contained 137-145 protein-coding genes, of which Ulmus davidiana var. japonica and U. davidiana had the most and U. pumila had the fewest. The five Ulmus species exhibited different evolutionary routes, as some genes had been lost. In total, 18 genes contained introns, 13 of which (trnL-TAA+, trnL-TAA-, rpoC1-, rpl2-, ndhA-, ycf1, rps12-, rps12+, trnA-TGC+, trnA-TGC-, trnV-TAC-, trnI-GAT+, and trnI-GAT) were shared among all five species. The intron of ycf1 was the longest (5,675bp) while that of trnF-AAA was the smallest (53bp). All Ulmus species except U. davidiana exhibited the same degree of amplification in the IR region. To determine the phylogenetic positions of the Ulmus species, we performed phylogenetic analyses using common protein-coding genes in chloroplast sequences of 42 other species published in NCBI. The cluster results showed the closest plants to Ulmaceae were Moraceae and Cannabaceae, followed by Rosaceae. Ulmaceae and Moraceae both belonged to Urticales, and the chloroplast genome clustering results were consistent with their traditional taxonomy. The results strongly supported the position of Ulmaceae as a member of the order Urticales. In addition, we found a potential error in the traditional taxonomies of U. davidiana and U. davidiana var. japonica, which should be confirmed with a

  5. The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis

    PubMed Central

    Zhang, Shuang; Yu, Xiao-Yue; Ren, Ya-Chao; Yang, Min-Sheng; Wang, Jin-Mao

    2017-01-01

    Elm (Ulmus) has a long history of use as a high-quality heavy hardwood famous for its resistance to drought, cold, and salt. It grows in temperate, warm temperate, and subtropical regions. This is the first report of Ulmaceae chloroplast genomes by de novo sequencing. The Ulmus chloroplast genomes exhibited a typical quadripartite structure with two single-copy regions (long single copy [LSC] and short single copy [SSC] sections) separated by a pair of inverted repeats (IRs). The lengths of the chloroplast genomes from five Ulmus ranged from 158,953 to 159,453 bp, with the largest observed in Ulmus davidiana and the smallest in Ulmus laciniata. The genomes contained 137–145 protein-coding genes, of which Ulmus davidiana var. japonica and U. davidiana had the most and U. pumila had the fewest. The five Ulmus species exhibited different evolutionary routes, as some genes had been lost. In total, 18 genes contained introns, 13 of which (trnL-TAA+, trnL-TAA−, rpoC1-, rpl2-, ndhA-, ycf1, rps12-, rps12+, trnA-TGC+, trnA-TGC-, trnV-TAC-, trnI-GAT+, and trnI-GAT) were shared among all five species. The intron of ycf1 was the longest (5,675bp) while that of trnF-AAA was the smallest (53bp). All Ulmus species except U. davidiana exhibited the same degree of amplification in the IR region. To determine the phylogenetic positions of the Ulmus species, we performed phylogenetic analyses using common protein-coding genes in chloroplast sequences of 42 other species published in NCBI. The cluster results showed the closest plants to Ulmaceae were Moraceae and Cannabaceae, followed by Rosaceae. Ulmaceae and Moraceae both belonged to Urticales, and the chloroplast genome clustering results were consistent with their traditional taxonomy. The results strongly supported the position of Ulmaceae as a member of the order Urticales. In addition, we found a potential error in the traditional taxonomies of U. davidiana and U. davidiana var. japonica, which should be confirmed with a

  6. Genome Sequence of the Thermophile Bacillus coagulans Hammer, the Type Strain of the Species

    PubMed Central

    Su, Fei; Tao, Fei; Tang, Hongzhi

    2012-01-01

    Here we announce a 3.0-Mb assembly of the Bacillus coagulans Hammer strain, which is the type strain of the species within the genus Bacillus. Genomic analyses based on the sequence may provide insights into the phylogeny of the species and help to elucidate characteristics of the poorly studied strains of Bacillus coagulans. PMID:23105047

  7. Draft Genome Sequence of Bacillus Species from the Rhizosphere of the Desert Plant Rhazya stricta

    PubMed Central

    Abo-Aba, S. E. M.; Sabir, Jamal S. M.; Baeshen, Mohammed N.; Sabir, Meshaal J.; Mutwakil, Mohammed H. Z.; Baeshen, Nabih A.; D’Amore, Rosalinda

    2015-01-01

    In order to better understand the ecology and diversity of microbes in the rhizosphere of desert plants, we undertook a survey of Bacillus species isolated from soil around Rhazya stricta plants from the area around Jeddah, in The Kingdom, Saudi Arabia. We have sequenced the genomes of 8 Bacillus isolates representing four different species. PMID:26543104

  8. Comparative Species Divergence across Eight Triplets of Spiny Lizards (Sceloporus) Using Genomic Sequence Data

    PubMed Central

    Leaché, Adam D.; Harris, Rebecca B.; Maliska, Max E.; Linkem, Charles W.

    2013-01-01

    Species divergence is typically thought to occur in the absence of gene flow, but many empirical studies are discovering that gene flow may be more pervasive during species formation. Although many examples of divergence with gene flow have been identified, few clades have been investigated in a comparative manner, and fewer have been studied using genome-wide sequence data. We contrast species divergence genetic histories across eight triplets of North American Sceloporus lizards using a maximum likelihood implementation of the isolation–migration (IM) model. Gene flow at the time of species divergence is modeled indirectly as variation in species divergence time across the genome or explicitly using a migration rate parameter. Likelihood ratio tests (LRTs) are used to test the null model of no gene flow at speciation against these two alternative gene flow models. We also use the Akaike information criterion to rank the models. Hundreds of loci are needed for the LRTs to have statistical power, and we use genome sequencing of reduced representation libraries to obtain DNA sequence alignments at many loci (between 340 and 3,478; mean = 1,678) for each triplet. We find that current species distributions are a poor predictor of whether a species pair diverged with gene flow. Interrogating the genome using the triplet method expedites the comparative study of species divergence history and the estimation of genetic parameters associated with speciation. PMID:24259316

  9. What can comparative genomics tell us about species concepts in the genus Aspergillus?

    SciTech Connect

    Rokas, Antonis; payne, gary; Federova, Natalie D.; Baker, Scott E.; Machida, Masa; yu, Jiujiang; georgianna, D. R.; Dean, Ralph A.; Bhatnagar, Deepak; Cleveland, T. E.; Wortman, Jennifer R.; Maiti, R.; Joardar, V.; Amedeo, Paolo; Denning, David W.; Nierman, William C.

    2007-12-15

    Understanding the nature of species" boundaries is a fundamental question in evolutionary biology. The availability of genomes from several species of the genus Aspergillus allows us for the first time to examine the demarcation of fungal species at the whole-genome level. Here, we examine four case studies, two of which involve intraspecific comparisons, whereas the other two deal with interspecific genomic comparisons between closely related species. These four comparisons reveal significant variation in the nature of species boundaries across Aspergillus. For example, comparisons between A. fumigatus and Neosartorya fischeri (the teleomorph of A. fischerianus) and between A. oryzae and A. flavus suggest that measures of sequence similarity and species-specific genes are significantly higher for the A. fumigatus - N. fischeri pair. Importantly, the values obtained from the comparison between A. oryzae and A. flavus are remarkably similar to those obtained from an intra-specific comparison of A. fumigatus strains, giving support to the proposal that A. oryzae represents a distinct ecotype of A. flavus and not a distinct species. We argue that genomic data can aid Aspergillus taxonomy by serving as a source of novel and unprecedented amounts of comparative data, as a resource for the development of additional diagnostic tools, and finally as a knowledge database about the biological differences between strains and species.

  10. Comparative Analyses Of The ‘Candidatus Liberibacter’ Species Reductive Genome Features

    Technology Transfer Automated Retrieval System (TEKTRAN)

    ‘Candidatus Liberibacter’ species are gram-negative a-proteobacteria that are associated with some destructive plant diseases such as citrus Huanglongbing and potato ‘zebra chip’. These bacteria are transmitted by psyllids and are classified into four species. Using whole genome amplification and 45...

  11. Genome sequence of the thermophile Bacillus coagulans Hammer, the type strain of the species.

    PubMed

    Su, Fei; Tao, Fei; Tang, Hongzhi; Xu, Ping

    2012-11-01

    Here we announce a 3.0-Mb assembly of the Bacillus coagulans Hammer strain, which is the type strain of the species within the genus Bacillus. Genomic analyses based on the sequence may provide insights into the phylogeny of the species and help to elucidate characteristics of the poorly studied strains of Bacillus coagulans.

  12. Phylogenomic Analyses and Reclassification of Species within the Genus Tsukamurella: Insights to Species Definition in the Post-genomic Era

    PubMed Central

    Teng, Jade L. L.; Tang, Ying; Huang, Yi; Guo, Feng-Biao; Wei, Wen; Chen, Jonathan H. K.; Wong, Samson S. Y.; Lau, Susanna K. P.; Woo, Patrick C. Y.

    2016-01-01

    Owing to the highly similar phenotypic profiles, protein spectra and 16S rRNA gene sequences observed between three pairs of Tsukamurella species (Tsukamurella pulmonis/Tsukamurella spongiae, Tsukamurella tyrosinosolvens/Tsukamurella carboxy-divorans, and Tsukamurella pseudospumae/Tsukamurella sunchonensis), we hypothesize that and the six Tsukamurella species may have been misclassified and that there may only be three Tsukamurella species. In this study, we characterized the type strains of these six Tsukamurella species by tradition DNA–DNA hybridization (DDH) and “digital DDH” after genome sequencing to determine their exact taxonomic positions. Traditional DDH showed 81.2 ± 0.6% to 99.7 ± 1.0% DNA–DNA relatedness between the two Tsukamurella species in each of the three pairs, which was above the threshold for same species designation. “Digital DDH” based on Genome-To-Genome Distance Calculator and Average Nucleotide Identity for the three pairs also showed similarity results in the range of 82.3–92.9 and 98.1–99.1%, respectively, in line with results of traditional DDH. Based on these evidence and according to Rules 23a and 42 of the Bacteriological Code, we propose that T. spongiae Olson et al. 2007, should be reclassified as a later heterotypic synonym of T. pulmonis Yassin et al. 1996, T. carboxydivorans Park et al. 2009, as a later heterotypic synonym of T. tyrosinosolvens Yassin et al. 1997, and T. sunchonensis Seong et al. 2008 as a later heterotypic synonym of T. pseudospumae Nam et al. 2004. With the advancement of genome sequencing technologies, classification of bacterial species can be readily achieved by “digital DDH” than traditional DDH. PMID:27493643

  13. Draft Genome Sequences of Two Pathogenic Corynebacterial Species Isolated from Cows

    PubMed Central

    Guimarães, Luis Carlos; Lopes, Thiago; Ramos, Rommel Thiago Jucá; Carneiro, Adriana Ribeiro; Cavalcante, Ana Lídia Queiroz; Barreto, Diego; de Sá, Pablo Caracciolo Gomes; Veras, Adonney Allan Oliveira; Rocha, Flávia Souza; Bagano, Priscilla; Pereira, Felipe Luiz; Dorella, Fernanda Alves; Leal, Carlos Augusto; Carvalho, Alex Fiorini; Bizet, Chantal; Guiso, Nicole; Badell, Edgar; Figueiredo, Henrique César Pereira; Azevedo, Vasco; Silva, Artur

    2016-01-01

    The species Corynebacterium renale, Corynebacterium pilosum, and Corynebacterium cystitidis were initially thought to be the same species C. renale, but with different immunological types. These bacteria are the causative agent of cystitis, urethritis and pyelonephritis and are found usually as constituents of the normal flora in the lower urogenital tract of cattle. Therefore, we present the draft genome sequences of two pathogenic Corynebacterium species: C. renale CIP 52.96 and C. pilosum CIP 103422. The genome sequences of these species have 2,322,762 bp with 2,218 protein encoding genes and 2,548,014 bp with 2,428 protein encoding genes, respectively. These genomes can help clarify the virulence mechanisms of these unknown bacteria and enable the development of more effective methods for control. PMID:26958092

  14. Gene duplication, population genomics, and species-level differentiation within a tropical mountain shrub.

    PubMed

    Mastretta-Yanes, Alicia; Zamudio, Sergio; Jorgensen, Tove H; Arrigo, Nils; Alvarez, Nadir; Piñero, Daniel; Emerson, Brent C

    2014-09-14

    Gene duplication leads to paralogy, which complicates the de novo assembly of genotyping-by-sequencing (GBS) data. The issue of paralogous genes is exacerbated in plants, because they are particularly prone to gene duplication events. Paralogs are normally filtered from GBS data before undertaking population genomics or phylogenetic analyses. However, gene duplication plays an important role in the functional diversification of genes and it can also lead to the formation of postzygotic barriers. Using populations and closely related species of a tropical mountain shrub, we examine 1) the genomic differentiation produced by putative orthologs, and 2) the distribution of recent gene duplication among lineages and geography. We find high differentiation among populations from isolated mountain peaks and species-level differentiation within what is morphologically described as a single species. The inferred distribution of paralogs among populations is congruent with taxonomy and shows that GBS could be used to examine recent gene duplication as a source of genomic differentiation of nonmodel species.

  15. Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction

    PubMed Central

    Fournier, Pierre-Edouard; El Karkouri, Khalid; Leroy, Quentin; Robert, Catherine; Giumelli, Bernadette; Renesto, Patricia; Socolovschi, Cristina; Parola, Philippe; Audic, Stéphane; Raoult, Didier

    2009-01-01

    Background The Rickettsia genus includes 25 validated species, 17 of which are proven human pathogens. Among these, the pathogenicity varies greatly, from the highly virulent R. prowazekii, which causes epidemic typhus and kills its arthropod host, to the mild pathogen R. africae, the agent of African tick-bite fever, which does not affect the fitness of its tick vector. Results We evaluated the clonality of R. africae in 70 patients and 155 ticks, and determined its genome sequence, which comprises a circular chromosome of 1,278,540 bp including a tra operon and an unstable 12,377-bp plasmid. To study the genetic characteristics associated with virulence, we compared this species to R. prowazekii, R. rickettsii and R. conorii. R. africae and R. prowazekii have, respectively, the less and most decayed genomes. Eighteen genes are present only in R. africae including one with a putative protease domain upregulated at 37°C. Conclusion Based on these data, we speculate that a loss of regulatory genes causes an increase of virulence of rickettsial species in ticks and mammals. We also speculate that in Rickettsia species virulence is mostly associated with gene loss. The genome sequence was deposited in GenBank under accession number [GenBank: NZ_AAUY01000001]. PMID:19379498

  16. Comparative Analysis of the Complete Chloroplast Genomes of Five Quercus Species

    PubMed Central

    Yang, Yanci; Zhou, Tao; Duan, Dong; Yang, Jia; Feng, Li; Zhao, Guifang

    2016-01-01

    Quercus is considered economically and ecologically one of the most important genera in the Northern Hemisphere. Oaks are taxonomically perplexing because of shared interspecific morphological traits and intraspecific morphological variation, which are mainly attributed to hybridization. Universal plastid markers cannot provide a sufficient number of variable sites to explore the phylogeny of this genus, and chloroplast genome-scale data have proven to be useful in resolving intractable phylogenetic relationships. In this study, the complete chloroplast genomes of four Quercus species were sequenced, and one published chloroplast genome of Quercus baronii was retrieved for comparative analyses. The five chloroplast genomes ranged from 161,072 bp (Q. baronii) to 161,237 bp (Q. dolicholepis) in length, and their gene organization and order, and GC content, were similar to those of other Fagaceae species. We analyzed nucleotide substitutions, indels, and repeats in the chloroplast genomes, and found 19 relatively highly variable regions that will potentially provide plastid markers for further taxonomic and phylogenetic studies within Quercus. We observed that four genes (ndhA, ndhK, petA, and ycf1) were subject to positive selection. The phylogenetic relationships of the Quercus species inferred from the chloroplast genomes obtained moderate-to-high support, indicating that chloroplast genome data may be useful in resolving relationships in this genus. PMID:27446185

  17. The complete chloroplast genome sequences for four Amaranthus species (Amaranthaceae)1

    PubMed Central

    Chaney, Lindsay; Mangelson, Ryan; Ramaraj, Thiruvarangan; Jellen, Eric N.; Maughan, Peter J.

    2016-01-01

    Premise of the study: The amaranth genus contains many important grain and weedy species. We further our understanding of the genus through the development of a complete reference chloroplast genome. Methods and Results: A high-quality Amaranthus hypochondriacus (Amaranthaceae) chloroplast genome assembly was developed using long-read technology. This reference genome was used to reconstruct the chloroplast genomes for two closely related grain species (A. cruentus and A. caudatus) and their putative progenitor (A. hybridus). The reference genome was 150,518 bp and possesses a circular structure of two inverted repeats (24,352 bp) separated by small (17,941 bp) and large (83,873 bp) single-copy regions; it encodes 111 genes, 72 for proteins. Relative to the reference chloroplast genome, an average of 210 single-nucleotide polymorphisms (SNPs) and 122 insertion/deletion polymorphisms (indels) were identified across the analyzed genomes. Conclusions: This reference chloroplast genome, along with the reported simple sequence repeats, SNPs, and indels, is an invaluable genetic resource for studying the phylogeny and genetic diversity within the amaranth genus. PMID:27672525

  18. Genome-Wide Identification and Transferability of Microsatellite Markers between Palmae Species

    PubMed Central

    Xiao, Yong; Xia, Wei; Ma, Jianwei; Mason, Annaliese S.; Fan, Haikuo; Shi, Peng; Lei, Xintao; Ma, Zilong; Peng, Ming

    2016-01-01

    The Palmae family contains 202 genera and approximately 2800 species. Except for Elaeis guineensis and Phoenix dactylifera, almost no genetic and genomic information is available for Palmae species. Therefore, this is an obstacle to the conservation and genetic assessment of Palmae species, especially those that are currently endangered. The study was performed to develop a large number of microsatellite markers which can be used for genetic analysis in different Palmae species. Based on the assembled genome of E. guineensis and P. dactylifera, a total of 814 383 and 371 629 microsatellites were identified. Among these microsatellites identified in E. guineensis, 734 509 primer pairs could be designed from the flanking sequences of these microsatellites. The majority (618 762) of these designed primer pairs had in silico products in the genome of E. guineensis. These 618 762 primer pairs were subsequently used to in silico amplify the genome of P. dactylifera. A total of 7 265 conserved microsatellites were identified between E. guineensis and P. dactylifera. One hundred and thirty-five primer pairs flanking the conserved SSRs were stochastically selected and validated to have high cross-genera transferability, varying from 16.7 to 93.3% with an average of 73.7%. These genome-wide conserved microsatellite markers will provide a useful tool for genetic assessment and conservation of different Palmae species in the future. PMID:27826307

  19. Genome-wide characterization of microsatellites in Triticeae species: abundance, distribution and evolution

    PubMed Central

    Deng, Pingchuan; Wang, Meng; Feng, Kewei; Cui, Licao; Tong, Wei; Song, Weining; Nie, Xiaojun

    2016-01-01

    Microsatellites are an important constituent of plant genome and distributed across entire genome. In this study, genome-wide analysis of microsatellites in 8 Triticeae species and 9 model plants revealed that microsatellite characteristics were similar among the Triticeae species. Furthermore, genome-wide microsatellite markers were designed in wheat and then used to analyze the evolutionary relationship of wheat and other Triticeae species. Results displayed that Aegilops tauschii was found to be the closest species to Triticum aestivum, followed by Triticum urartu, Triticum turgidum and Aegilops speltoides, while Triticum monococcum, Aegilops sharonensis and Hordeum vulgare showed a relatively lower PCR amplification effectivity. Additionally, a significantly higher PCR amplification effectivity was found in chromosomes at the same subgenome than its homoeologous when these markers were subjected to search against different chromosomes in wheat. After a rigorous screening process, a total of 20,666 markers showed high amplification and polymorphic potential in wheat and its relatives, which were integrated with the public available wheat markers and then anchored to the genome of wheat (CS). This study not only provided the useful resource for SSR markers development in Triticeae species, but also shed light on the evolution of polyploid wheat from the perspective of microsatellites. PMID:27561724

  20. Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species

    PubMed Central

    Asaf, Sajjad; Khan, Abdul L.; Khan, Abdur R.; Waqas, Muhammad; Kang, Sang-Mo; Khan, Muhammad A.; Lee, Seok-Min; Lee, In-Jung

    2016-01-01

    Nicotiana otophora is a wild parental species of Nicotiana tabacum, an interspecific hybrid of Nicotiana tomentosiformis and Nicotiana sylvestris. However, N. otophora is least understood as an alternative paternal donor. Here, we compared the fully assembled chloroplast (cp) genome of N. otophora and with those of closely related species. The analysis showed a cp genome size of 156,073 bp and exhibited a typical quadripartite structure, which contains a pair of inverted repeats separated by small and large single copies, containing 163 representative genes, with 165 microsatellites distributed unevenly throughout the genome. Comparative analysis of a gene with known function across Nicotiana species revealed 76 protein-coding sequences, 20 tRNA sequences, and 3 rRNA sequence shared between the cp genomes. The analysis revealed that N. otophora is a sister species to N. tomentosiformis within the Nicotiana genus, and Atropha belladonna and Datura stramonium are their closest relatives. These findings provide a valuable analysis of the complete N. otophora cp genome, which can identify species, elucidate taxonomy, and reconstruct the phylogeny of genus Nicotiana. PMID:27379132

  1. The complete chloroplast genome of two Brassica species, Brassica nigra and B. Oleracea.

    PubMed

    Seol, Young-Joo; Kim, Kyunghee; Kang, Sang-Ho; Perumal, Sampath; Lee, Jonghoon; Kim, Chang-Kug

    2017-03-01

    The two Brassica species, Brassica nigra and Brassica oleracea, are important agronomic crops. The chloroplast genome sequences were generated by de novo assembly using whole genome next-generation sequences. The chloroplast genomes of B. nigra and B. oleracea were 153 633 bp and 153 366 bp in size, respectively, and showed conserved typical chloroplast structure. The both chloroplast genomes contained a total of 114 genes including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis revealed that B. oleracea is closely related to B. rapa and B. napus but B. nigra is more diverse than the neighbor species Raphanus sativus.

  2. Genome sequencing supports a multi-vertex model for Brassiceae species.

    PubMed

    Cheng, Feng; Liang, Jianli; Cai, Chengcheng; Cai, Xu; Wu, Jian; Wang, Xiaowu

    2017-02-24

    The economically important Brassica genus is a good system for studying the evolution of polyploids. Brassica genomes have undergone whole genome triplication (WGT). Subgenome dominance phenomena such as biased gene fractionation and dominant gene expression were observed in tripled genomes of Brassica. The genome of radish (Raphanus sativus), another important crop of tribe Brassiceae, was derived from the same WGT event and shows similar subgenome dominance. These findings and molecular dating indicate that radish occupies a similar evolutionary origin as that of Brassica species. Here, we extended the Brassica "triangle of U" to a multi-vertex model. This model describes the relationships or the potential of using more Brassiceae mesohexaploids in the creation of new allotetraploid oil or vegetable crop species.

  3. Comparison and correlation of Simple Sequence Repeats distribution in genomes of Brucella species

    PubMed Central

    Kiran, Jangampalli Adi Pradeep; Chakravarthi, Veeraraghavulu Praveen; Kumar, Yellapu Nanda; Rekha, Somesula Swapna; Kruti, Srinivasan Shanthi; Bhaskar, Matcha

    2011-01-01

    Computational genomics is one of the important tools to understand the distribution of closely related genomes including simple sequence repeats (SSRs) in an organism, which gives valuable information regarding genetic variations. The central objective of the present study was to screen the SSRs distributed in coding and non-coding regions among different human Brucella species which are involved in a range of pathological disorders. Computational analysis of the SSRs in the Brucella indicates few deviations from expected random models. Statistical analysis also reveals that tri-nucleotide SSRs are overrepresented and tetranucleotide SSRs underrepresented in Brucella genomes. From the data, it can be suggested that over expressed tri-nucleotide SSRs in genomic and coding regions might be responsible in the generation of functional variation of proteins expressed which in turn may lead to different pathogenicity, virulence determinants, stress response genes, transcription regulators and host adaptation proteins of Brucella genomes. Abbreviations SSRs - Simple Sequence Repeats, ORFs - Open Reading Frames. PMID:21738309

  4. Constraints on Genome Dynamics Revealed from Gene Distribution among the Ralstonia solanacearum Species

    PubMed Central

    Lefeuvre, Pierre; Cellier, Gilles; Remenant, Benoît; Chiroleu, Frédéric; Prior, Philippe

    2013-01-01

    Because it is suspected that gene content may partly explain host adaptation and ecology of pathogenic bacteria, it is important to study factors affecting genome composition and its evolution. While recent genomic advances have revealed extremely large pan-genomes for some bacterial species, it remains difficult to predict to what extent gene pool is accessible within or transferable between populations. As genomes bear imprints of the history of the organisms, gene distribution pattern analyses should provide insights into the forces and factors at play in the shaping and maintaining of bacterial genomes. In this study, we revisited the data obtained from a previous CGH microarrays analysis in order to assess the genomic plasticity of the R. solanacearum species complex. Gene distribution analyses demonstrated the remarkably dispersed genome of R. solanacearum with more than half of the genes being accessory. From the reconstruction of the ancestral genomes compositions, we were able to infer the number of gene gain and loss events along the phylogeny. Analyses of gene movement patterns reveal that factors associated with gene function, genomic localization and ecology delineate gene flow patterns. While the chromosome displayed lower rates of movement, the megaplasmid was clearly associated with hot-spots of gene gain and loss. Gene function was also confirmed to be an essential factor in gene gain and loss dynamics with significant differences in movement patterns between different COG categories. Finally, analyses of gene distribution highlighted possible highways of horizontal gene transfer. Due to sampling and design bias, we can only speculate on factors at play in this gene movement dynamic. Further studies examining precise conditions that favor gene transfer would provide invaluable insights in the fate of bacteria, species delineation and the emergence of successful pathogens. PMID:23723974

  5. Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content

    PubMed Central

    2009-01-01

    Background Streptococcus mutans is the major pathogen of dental caries, and it occasionally causes infective endocarditis. While the pathogenicity of this species is distinct from other human pathogenic streptococci, the species-specific evolution of the genus Streptococcus and its genomic diversity are poorly understood. Results We have sequenced the complete genome of S. mutans serotype c strain NN2025, and compared it with the genome of UA159. The NN2025 genome is composed of 2,013,587 bp, and the two strains show highly conserved core-genome. However, comparison of the two S. mutans strains showed a large genomic inversion across the replication axis producing an X-shaped symmetrical DNA dot plot. This phenomenon was also observed between other streptococcal species, indicating that streptococcal genetic rearrangements across the replication axis play an important role in Streptococcus genetic shuffling. We further confirmed the genomic diversity among 95 clinical isolates using long-PCR analysis. Genomic diversity in S. mutans appears to occur frequently between insertion sequence (IS) elements and transposons, and these diversity regions consist of restriction/modification systems, antimicrobial peptide synthesis systems, and transporters. S. mutans may preferentially reject the phage infection by clustered regularly interspaced short palindromic repeats (CRISPRs). In particular, the CRISPR-2 region, which is highly divergent between strains, in NN2025 has long repeated spacer sequences corresponding to the streptococcal phage genome. Conclusion These observations suggest that S. mutans strains evolve through chromosomal shuffling and that phage infection is not needed for gene acquisition. In contrast, S. pyogenes tolerates phage infection for acquisition of virulence determinants for niche adaptation. PMID:19656368

  6. Acinetobacter sp. isolates from emergency departments in two hospitals of South Korea.

    PubMed

    Choi, Ji-Young; Ko, Eun Ah; Kwon, Ki Tae; Lee, Shinwon; Kang, Choel In; Chung, Doo-Ryeon; Peck, Kyong Ran; Song, Jae-Hoon; Ko, Kwan Soo

    2014-10-01

    A total of 114 Acinetobacter sp. isolates were collected from patients in the emergency departments (EDs) of two Korean hospitals. Most isolates belonged to the Acinetobacter baumannii complex (105 isolates, 92.1 %). Imipenem resistance was found in 39 isolates (34.2 %) of the Acinetobacter sp. isolates, and 6 colistin-resistant isolates were also identified. Species distribution and antimicrobial-resistance rates were different between the two hospitals. In addition, two main clones were identified in the imipenem-resistant A. baumannii isolates from hospital B, but very diverse and novel genotypes were found in those from hospital A. Many Acinetobacter sp. isolates, including the imipenem-resistant A. baumannii, are considered to be associated with the community. The evidence of high antimicrobial resistance and different features in these Acinetobacter sp. isolates between the two EDs suggests the need for continuous testing to monitor changes in epidemiology.

  7. Whole-Genome Sequencing and Intraspecific Analysis of the Yeast Species Lachancea quebecensis

    PubMed Central

    Freel, Kelle C.; Friedrich, Anne; Sarilar, Véronique; Devillers, Hugo; Neuvéglise, Cécile; Schacherer, Joseph

    2016-01-01

    The gold standard in yeast population genomics has been the model organism Saccharomyces cerevisiae. However, the exploration of yeast species outside the Saccharomyces genus is essential to broaden the understanding of genome evolution. Here, we report the analyses of whole-genome sequences of nineisolates from the recently described yeast species Lachancea quebecensis. The genome of one isolate was assembled and annotated, and the intraspecific variability within L. quebecensis was surveyed by comparing the sequences from the eight other isolates to this reference sequence. Our study revealed that these strains harbor genomes with an average nucleotide diversity of π = 2 × 10−3 which is slightly lower, although on the same order of magnitude, as that previously determined for S. cerevisiae (π = 4 × 10−3). Our results show that even though these isolates were all obtained from a relatively isolated geographic location, the same ecological source, and represent a smaller sample size than is available for S. cerevisiae, the levels of divergence are similar to those observed in this model species. This divergence is essentially linked to the presence of two distinct clusters delineated according to geographic location. However, even with relatively similar ranges of genome divergence, L. quebecensis has an extremely low global phenotypic variance of 0.062 compared with 0.59 previously determined in S. cerevisiae. PMID:26733577

  8. Genome-wide microsatellite characterization and marker development in the sequenced Brassica crop species.

    PubMed

    Shi, Jiaqin; Huang, Shunmou; Zhan, Jiepeng; Yu, Jingyin; Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong

    2014-02-01

    Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with public Brassica SSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequenced Brassica species to genetic study/breeding in different Brassica species.

  9. Plastid genomics in horticultural species: importance and applications for plant population genetics, evolution, and biotechnology.

    PubMed

    Rogalski, Marcelo; do Nascimento Vieira, Leila; Fraga, Hugo P; Guerra, Miguel P

    2015-01-01

    During the evolution of the eukaryotic cell, plastids, and mitochondria arose from an endosymbiotic process, which determined the presence of three genetic compartments into the incipient plant cell. After that, these three genetic materials from host and symbiont suffered several rearrangements, bringing on a complex interaction between nuclear and organellar gene products. Nowadays, plastids harbor a small genome with ∼130 genes in a 100-220 kb sequence in higher plants. Plastid genes are mostly highly conserved between plant species, being useful for phylogenetic analysis in higher taxa. However, intergenic spacers have a relatively higher mutation rate and are important markers to phylogeographical and plant population genetics analyses. The predominant uniparental inheritance of plastids is like a highly desirable feature for phylogeny studies. Moreover, the gene content and genome rearrangements are efficient tools to capture and understand evolutionary events between different plant species. Currently, genetic engineering of the plastid genome (plastome) offers a number of attractive advantages as high-level of foreign protein expression, marker gene excision, gene expression in operon and transgene containment because of maternal inheritance of plastid genome in most crops. Therefore, plastid genome can be used for adding new characteristics related to synthesis of metabolic compounds, biopharmaceutical, and tolerance to biotic and abiotic stresses. Here, we describe the importance and applications of plastid genome as tools for genetic and evolutionary studies, and plastid transformation focusing on increasing the performance of horticultural species in the field.

  10. Plastid genomics in horticultural species: importance and applications for plant population genetics, evolution, and biotechnology

    PubMed Central

    Rogalski, Marcelo; do Nascimento Vieira, Leila; Fraga, Hugo P.; Guerra, Miguel P.

    2015-01-01

    During the evolution of the eukaryotic cell, plastids, and mitochondria arose from an endosymbiotic process, which determined the presence of three genetic compartments into the incipient plant cell. After that, these three genetic materials from host and symbiont suffered several rearrangements, bringing on a complex interaction between nuclear and organellar gene products. Nowadays, plastids harbor a small genome with ∼130 genes in a 100–220 kb sequence in higher plants. Plastid genes are mostly highly conserved between plant species, being useful for phylogenetic analysis in higher taxa. However, intergenic spacers have a relatively higher mutation rate and are important markers to phylogeographical and plant population genetics analyses. The predominant uniparental inheritance of plastids is like a highly desirable feature for phylogeny studies. Moreover, the gene content and genome rearrangements are efficient tools to capture and understand evolutionary events between different plant species. Currently, genetic engineering of the plastid genome (plastome) offers a number of attractive advantages as high-level of foreign protein expression, marker gene excision, gene expression in operon and transgene containment because of maternal inheritance of plastid genome in most crops. Therefore, plastid genome can be used for adding new characteristics related to synthesis of metabolic compounds, biopharmaceutical, and tolerance to biotic and abiotic stresses. Here, we describe the importance and applications of plastid genome as tools for genetic and evolutionary studies, and plastid transformation focusing on increasing the performance of horticultural species in the field. PMID:26284102

  11. Complete Plastid Genome Sequencing of Four Tilia Species (Malvaceae): A Comparative Analysis and Phylogenetic Implications

    PubMed Central

    Cai, Jie; Ma, Peng-Fei; Li, Hong-Tao; Li, De-Zhu

    2015-01-01

    Tilia is an ecologically and economically important genus in the family Malvaceae. However, there is no complete plastid genome of Tilia sequenced to date, and the taxonomy of Tilia is difficult owing to frequent hybridization and polyploidization. A well-supported interspecific relationships of this genus is not available due to limited informative sites from the commonly used molecular markers. We report here the complete plastid genome sequences of four Tilia species determined by the Illumina technology. The Tilia plastid genome is 162,653 bp to 162,796 bp in length, encoding 113 unique genes and a total number of 130 genes. The gene order and organization of the Tilia plastid genome exhibits the general structure of angiosperms and is very similar to other published plastid genomes of Malvaceae. As other long-lived tree genera, the sequence divergence among the four Tilia plastid genomes is very low. And we analyzed the nucleotide substitution patterns and the evolution of insertions and deletions in the Tilia plastid genomes. Finally, we build a phylogeny of the four sampled Tilia species with high supports using plastid phylogenomics, suggesting that it is an efficient way to resolve the phylogenetic relationships of this genus. PMID:26566230

  12. Complete Plastid Genome Sequencing of Four Tilia Species (Malvaceae): A Comparative Analysis and Phylogenetic Implications.

    PubMed

    Cai, Jie; Ma, Peng-Fei; Li, Hong-Tao; Li, De-Zhu

    2015-01-01

    Tilia is an ecologically and economically important genus in the family Malvaceae. However, there is no complete plastid genome of Tilia sequenced to date, and the taxonomy of Tilia is difficult owing to frequent hybridization and polyploidization. A well-supported interspecific relationships of this genus is not available due to limited informative sites from the commonly used molecular markers. We report here the complete plastid genome sequences of four Tilia species determined by the Illumina technology. The Tilia plastid genome is 162,653 bp to 162,796 bp in length, encoding 113 unique genes and a total number of 130 genes. The gene order and organization of the Tilia plastid genome exhibits the general structure of angiosperms and is very similar to other published plastid genomes of Malvaceae. As other long-lived tree genera, the sequence divergence among the four Tilia plastid genomes is very low. And we analyzed the nucleotide substitution patterns and the evolution of insertions and deletions in the Tilia plastid genomes. Finally, we build a phylogeny of the four sampled Tilia species with high supports using plastid phylogenomics, suggesting that it is an efficient way to resolve the phylogenetic relationships of this genus.

  13. Mitochondrial Genome Analysis of Wild Rice (Oryza minuta) and Its Comparison with Other Related Species

    PubMed Central

    Asaf, Sajjad; Khan, Abdul Latif; Khan, Abdur Rahim; Waqas, Muhammad; Kang, Sang-Mo; Khan, Muhammad Aaqil; Shahzad, Raheem; Seo, Chang-Woo; Shin, Jae-Ho; Lee, In-Jung

    2016-01-01

    Oryza minuta (Poaceae family) is a tetraploid wild relative of cultivated rice with a BBCC genome. O. minuta has the potential to resist against various pathogenic diseases such as bacterial blight (BB), white backed planthopper (WBPH) and brown plant hopper (BPH). Here, we sequenced and annotated the complete mitochondrial genome of O. minuta. The mtDNA genome is 515,022 bp, containing 60 protein coding genes, 31 tRNA genes and two rRNA genes. The mitochondrial genome organization and the gene content at the nucleotide level are highly similar (89%) to that of O. rufipogon. Comparison with other related species revealed that most of the genes with known function are conserved among the Poaceae members. Similarly, O. minuta mt genome shared 24 protein-coding genes, 15 tRNA genes and 1 ribosomal RNA gene with other rice species (indica and japonica). The evolutionary relationship and phylogenetic analysis revealed that O. minuta is more closely related to O. rufipogon than to any other related species. Such studies are essential to understand the evolutionary divergence among species and analyze common gene pools to combat risks in the current scenario of a changing environment. PMID:27045847

  14. A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species

    PubMed Central

    Nyerges, Ákos; Csörgő, Bálint; Nagy, István; Bálint, Balázs; Bihari, Péter; Lázár, Viktória; Apjok, Gábor; Umenhoffer, Kinga; Bogos, Balázs; Pósfai, György; Pál, Csaba

    2016-01-01

    Currently available tools for multiplex bacterial genome engineering are optimized for a few laboratory model strains, demand extensive prior modification of the host strain, and lead to the accumulation of numerous off-target modifications. Building on prior development of multiplex automated genome engineering (MAGE), our work addresses these problems in a single framework. Using a dominant-negative mutant protein of the methyl-directed mismatch repair (MMR) system, we achieved a transient suppression of DNA repair in Escherichia coli, which is necessary for efficient oligonucleotide integration. By integrating all necessary components into a broad-host vector, we developed a new workflow we term pORTMAGE. It allows efficient modification of multiple loci, without any observable off-target mutagenesis and prior modification of the host genome. Because of the conserved nature of the bacterial MMR system, pORTMAGE simultaneously allows genome editing and mutant library generation in other biotechnologically and clinically relevant bacterial species. Finally, we applied pORTMAGE to study a set of antibiotic resistance-conferring mutations in Salmonella enterica and E. coli. Despite over 100 million y of divergence between the two species, mutational effects remained generally conserved. In sum, a single transformation of a pORTMAGE plasmid allows bacterial species of interest to become an efficient host for genome engineering. These advances pave the way toward biotechnological and therapeutic applications. Finally, pORTMAGE allows systematic comparison of mutational effects and epistasis across a wide range of bacterial species. PMID:26884157

  15. A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species.

    PubMed

    Nyerges, Ákos; Csörgő, Bálint; Nagy, István; Bálint, Balázs; Bihari, Péter; Lázár, Viktória; Apjok, Gábor; Umenhoffer, Kinga; Bogos, Balázs; Pósfai, György; Pál, Csaba

    2016-03-01

    Currently available tools for multiplex bacterial genome engineering are optimized for a few laboratory model strains, demand extensive prior modification of the host strain, and lead to the accumulation of numerous off-target modifications. Building on prior development of multiplex automated genome engineering (MAGE), our work addresses these problems in a single framework. Using a dominant-negative mutant protein of the methyl-directed mismatch repair (MMR) system, we achieved a transient suppression of DNA repair in Escherichia coli, which is necessary for efficient oligonucleotide integration. By integrating all necessary components into a broad-host vector, we developed a new workflow we term pORTMAGE. It allows efficient modification of multiple loci, without any observable off-target mutagenesis and prior modification of the host genome. Because of the conserved nature of the bacterial MMR system, pORTMAGE simultaneously allows genome editing and mutant library generation in other biotechnologically and clinically relevant bacterial species. Finally, we applied pORTMAGE to study a set of antibiotic resistance-conferring mutations in Salmonella enterica and E. coli. Despite over 100 million y of divergence between the two species, mutational effects remained generally conserved. In sum, a single transformation of a pORTMAGE plasmid allows bacterial species of interest to become an efficient host for genome engineering. These advances pave the way toward biotechnological and therapeutic applications. Finally, pORTMAGE allows systematic comparison of mutational effects and epistasis across a wide range of bacterial species.

  16. Chromosome Numbers and Genome Size Variation in Indian Species of Curcuma (Zingiberaceae)

    PubMed Central

    Leong-Škorničková, Jana; Šída, Otakar; Jarolímová, Vlasta; Sabu, Mamyil; Fér, Tomáš; Trávníček, Pavel; Suda, Jan

    2007-01-01

    Background and Aims Genome size and chromosome numbers are important cytological characters that significantly influence various organismal traits. However, geographical representation of these data is seriously unbalanced, with tropical and subtropical regions being largely neglected. In the present study, an investigation was made of chromosomal and genome size variation in the majority of Curcuma species from the Indian subcontinent, and an assessment was made of the value of these data for taxonomic purposes. Methods Genome size of 161 homogeneously cultivated plant samples classified into 51 taxonomic entities was determined by propidium iodide flow cytometry. Chromosome numbers were counted in actively growing root tips using conventional rapid squash techniques. Key Results Six different chromosome counts (2n = 22, 42, 63, >70, 77 and 105) were found, the last two representing new generic records. The 2C-values varied from 1·66 pg in C. vamana to 4·76 pg in C. oligantha, representing a 2·87-fold range. Three groups of taxa with significantly different homoploid genome sizes (Cx-values) and distinct geographical distribution were identified. Five species exhibited intraspecific variation in nuclear DNA content, reaching up to 15·1 % in cultivated C. longa. Chromosome counts and genome sizes of three Curcuma-like species (Hitchenia caulina, Kaempferia scaposa and Paracautleya bhatii) corresponded well with typical hexaploid (2n = 6x = 42) Curcuma spp. Conclusions The basic chromosome number in the majority of Indian taxa (belonging to subgenus Curcuma) is x = 7; published counts correspond to 6x, 9x, 11x, 12x and 15x ploidy levels. Only a few species-specific C-values were found, but karyological and/or flow cytometric data may support taxonomic decisions in some species alliances with morphological similarities. Close evolutionary relationships among some cytotypes are suggested based on the similarity in homoploid genome sizes and geographical grouping

  17. Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features.

    PubMed

    Coutinho, F H; Dutilh, B E; Thompson, C C; Thompson, F L

    2016-12-01

    Members of the recently proposed genus Parasynechococcus (Cyanobacteria) are extremely abundant throughout the global ocean and contribute significantly to global primary productivity. However, the taxonomy of these organisms remains poorly characterized. The aim of this study was to propose a new taxonomic framework for Parasynechococcus based on a genomic taxonomy approach that incorporates genomic, physiological and ecological data. Through in silico DNA-DNA hybridization, average amino acid identity, dinucleotide signatures and phylogenetic reconstruction, a total of 15 species of Parasynechococcus could be delineated. Each species was then described on the basis of their gene content, light and nutrient utilization strategies, geographical distribution patterns throughout the oceans and response to environmental parameters.

  18. Intron Derived Size Polymorphism in the Mitochondrial Genomes of Closely Related Chrysoporthe Species

    PubMed Central

    Kanzi, Aquillah Mumo; Wingfield, Brenda Diana; Steenkamp, Emma Theodora; Naidoo, Sanushka; van der Merwe, Nicolaas Albertus

    2016-01-01

    In this study, the complete mitochondrial (mt) genomes of Chrysoporthe austroafricana (190,834 bp), C. cubensis (89,084 bp) and C. deuterocubensis (124,412 bp) were determined. Additionally, the mitochondrial genome of another member of the Cryphonectriaceae, namely Cryphonectria parasitica (158,902 bp), was retrieved and annotated for comparative purposes. These genomes showed high levels of synteny, especially in regions including genes involved in oxidative phosphorylation and electron transfer, unique open reading frames (uORFs), ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), as well as intron positions. Comparative analyses revealed signatures of duplication events, intron number and length variation, and varying intronic ORFs which highlighted the genetic diversity of mt genomes among the Cryphonectriaceae. These mt genomes showed remarkable size polymorphism. The size polymorphism in the mt genomes of these closely related Chrysoporthe species was attributed to the varying number and length of introns, coding sequences and to a lesser extent, intergenic sequences. Compared to publicly available fungal mt genomes, the C. austroafricana mt genome is the second largest in the Ascomycetes thus far. PMID:27272523

  19. Attenuated Virulence and Genomic Reductive Evolution in the Entomopathogenic Bacterial Symbiont Species, Xenorhabdus poinarii

    PubMed Central

    Ogier, Jean-Claude; Pagès, Sylvie; Bisch, Gaëlle; Chiapello, Hélène; Médigue, Claudine; Rouy, Zoé; Teyssier, Corinne; Vincent, Stéphanie; Tailliez, Patrick; Givaudan, Alain; Gaudriault, Sophie

    2014-01-01

    Bacteria of the genus Xenorhabdus are symbionts of soil entomopathogenic nematodes of the genus Steinernema. This symbiotic association constitutes an insecticidal complex active against a wide range of insect pests. Unlike other Xenorhabdus species, Xenorhabdus poinarii is avirulent when injected into insects in the absence of its nematode host. We sequenced the genome of the X. poinarii strain G6 and the closely related but virulent X. doucetiae strain FRM16. G6 had a smaller genome (500–700 kb smaller) than virulent Xenorhabdus strains and lacked genes encoding potential virulence factors (hemolysins, type 5 secretion systems, enzymes involved in the synthesis of secondary metabolites, and toxin–antitoxin systems). The genomes of all the X. poinarii strains analyzed here had a similar small size. We did not observe the accumulation of pseudogenes, insertion sequences or decrease in coding density usually seen as a sign of genomic erosion driven by genetic drift in host-adapted bacteria. Instead, genome reduction of X. poinarii seems to have been mediated by the excision of genomic blocks from the flexible genome, as reported for the genomes of attenuated free pathogenic bacteria and some facultative mutualistic bacteria growing exclusively within hosts. This evolutionary pathway probably reflects the adaptation of X. poinarii to specific host. PMID:24904010

  20. The BEAF-32 insulator coordinates genome organization and function during the evolution of Drosophila species

    PubMed Central

    Yang, Jingping; Ramos, Edward; Corces, Victor G.

    2012-01-01

    Understanding the relationship between genome organization and expression is central to understanding genome function. Closely apposed genes in a head-to-head orientation share the same upstream region and are likely to be coregulated. Here we identify the Drosophila BEAF-32 insulator as a cis regulatory element separating close head-to-head genes with different transcription regulation modes. We then compare the binding landscapes of the BEAF-32 insulator protein in four different Drosophila genomes and highlight the evolutionarily conserved presence of this protein between close adjacent genes. We find that changes in binding of BEAF-32 to sites in the genome of different Drosophila species correlate with alterations in genome organization caused by DNA rearrangements or genome size expansion. The cross-talk between BEAF-32 genomic distribution and genome organization contributes to new gene-expression profiles, which in turn translate into specific and distinct phenotypes. The results suggest a mechanism for the establishment of differences in transcription patterns during evolution. PMID:22895281

  1. Blood stream infections caused by Acinetobacter baumannii group in Japan - Epidemiological and clinical investigation.

    PubMed

    Fujikura, Yuji; Yuki, Atsushi; Hamamoto, Takaaki; Kawana, Akihiko; Ohkusu, Kiyofumi; Matsumoto, Tetsuya

    2016-06-01

    Acinetobacter calcoaceticus-Acinetobacter baumannii complex, especially A. baumannii, Acinetobacter pittii and Acinetobacter nosocomialis, constitutes an important group of nosocomial pathogens; however, epidemiological or clinical characteristics and prognosis is limited in Japan. From 2009 to 2013, 47 blood stream infection cases resulting from A. baumannii group were reviewed at the National Defense Medical College, an 800-bed tertiary hospital. To determine the genospecies, further comparative nucleotide sequence analyses of the RNA polymerase b-subunit (rpoB) gene were performed. Sequence analysis of rpoB gene showed that 25 (49.0%), 17 (33.3%) and 5 (9.8%) cases were caused by A. baumannii, A. pittii and A. nosocomialis, respectively. The 30-day and in-hospital mortality rates of A. baumannii were 8.5% and 25.5%, respectively, and there were no significant differences between Acinetobacter species. Clinical characteristics were statistically insignificant. Multidrug-resistant Acinetobacter species were detected in 3 cases (5.9%) with same pulsed-field gel electrophoresis (PFGE) pattern and A. baumannii was less susceptible to amikacin and levofloxacin. In this study, the mortality and clinical characteristics were similar among A. baumannii group isolate cases despite some showing drug resistance. However, identification of Acinetobacter species helps to initiate appropriate antibiotic therapy in earlier treatment phase, because A. baumannii shows some drug resistance.

  2. Genome Size Variation in Central European Species of Cirsium (Compositae) and their Natural Hybrids

    PubMed Central

    BUREŠ, PETR; WANG, YI-FENG; HOROVÁ, LUCIE; SUDA, JAN

    2004-01-01

    • Background and Aims Nuclear DNA amounts of 12 diploid and one tetraploid taxa and 12 natural interspecific hybrids of Cirsium from 102 populations in the Czech Republic, Austria, Slovakia and Hungary were estimated. • Methods DAPI and PI flow cytometry were used. • Key Results 2C-values of diploid (2n = 34) species varied from 2·14 pg in C. heterophyllum to 3·60 pg in C. eriophorum (1·68-fold difference); the 2C value for the tetraploid C. vulgare was estimated at 5·54 pg. The DNA contents of hybrids were located between the values of their putative parents, although usually closer to the species with the smaller genome. Biennial species of Cirsium possessed larger nuclear DNA amounts than their perennial relatives. Genome size was negatively correlated with Ellenberg's indicator values for continentality and moisture and with eastern limits of distribution. A negative relationship was also detected between the genome size and the tendency to form natural interspecific hybrids. On the contrary, C-values positively corresponded with the spinyness (degree of spinosity). AT frequency ranged from 48·38 % in C. eriophorum to 51·75 % in C. arvense. Significant intraspecific DNA content variation in DAPI sessions was detected in C. acaule (probably due to the presence of B-chromosomes), and in tetraploid C. vulgare. Only the diploid level was confirmed for the Pannonian C. brachycephalum, generally considered to be tetraploid. In addition, triploidy was discovered for the first time in C. rivulare. • Conclusions Considerable differences in nuclear DNA content exist among Central European species of Cirsium on the diploid level. Perennial soft spiny Cirsium species of wet habitats and continental distributions generally have smaller genomes. The hybrids of diploid species remain diploid, and their DNA content is smaller than the mean of the parents. Species with smaller genomes produce interspecific hybrids more frequently. PMID:15292040

  3. Development of genomic resources for Nothofagus species using next-generation sequencing data.

    PubMed

    El Mujtar, V A; Gallo, L A; Lang, T; Garnier-Géré, P

    2014-11-01

    Using next-generation sequencing, we developed the first whole-genome resources for two hybridizing Nothofagus species of the Patagonian forests that crucially lack genomic data, despite their ecological and industrial value. A de novo assembly strategy combining base quality control and optimization of the putative chloroplast gene map yielded ~32,000 contigs from 43% of the reads produced. With 12.5% of assembled reads, we covered ~96% of the chloroplast genome and ~70% of the mitochondrial gene content, providing functional and structural annotations for 112 and 52 genes, respectively. Functional annotation was possible on 15% of the contigs, with ~1750 potentially novel nuclear genes identified for Nothofagus species. We estimated that the new resources (13.41 Mb in total) included ~4000 gene regions representing ~6.5% of the expected genic partition of the genome, the remaining contigs potentially being nongenic DNA. A high-quality single nucleotide polymorphisms resource was developed by comparing various filtering methods, and preliminary results indicate a strong conservation of cpDNA genomes in contrast to numerous exclusive nuclear polymorphisms in both species. Finally, we characterized 2274 potential simple sequence repeat (SSR) loci, designed primers for 769 of them and validated nine of 29 loci in 42 individuals per species. Nothofagus obliqua had more alleles (4.89) on average than N. nervosa (2.89), 8 SSRs were efficient to discriminate species, and three were successfully transferred in three other Nothofagus species. These resources will greatly help for future inferences of demographic, adaptive and hybridizing events in Nothofagus species, and for conserving and managing natural populations.

  4. Modified CHROMagar Acinetobacter Medium for Direct Detection of Multidrug-Resistant Acinetobacter Strains in Nasal and Rectal Swab Samples

    PubMed Central

    Lee, Jacob; Kim, Taek-Kyung; Park, Min-Jeong; Kim, Han-Sung; Kim, Jae-Seok

    2013-01-01

    This study aimed to investigate whether CHROMagar Acinetobacter medium (CHROMagar, France) in combination with an antimicrobial supplement (modified CHROMagar Acinetobacter; CHROMagar, France) can be used for detecting and isolating multidrug-resistant Acinetobacter species (MRA) in nasal and rectal surveillance cultures. Nasal and rectal swab samples were collected from patients in an intensive care unit at a teaching hospital. The samples were used to inoculate modified CHROMagar Acinetobacter plates, which were examined after 24 and 48 hr of incubation at 37℃. Their susceptibility against the antimicrobial agents meropenem, imipenem, ciprofloxacin, and amikacin was analyzed using the Etest (bioMerieux, France). A total of 406 paired samples (406 nasal swabs and 406 rectal swabs) were obtained from 226 patients, and 120 samples (28 nasal and 28 rectal cultures, 47 nasal cultures only, and 17 rectal cultures only) yielded MRA. Seventy-five MRA isolates (18.5%) were recovered from the 406 nasal samples, and 45 MRA isolates (11.1%) were recovered from the 406 rectal samples. Of the 120 MRA isolates, 3 (2.5%) were detected only after 48 hr of incubation. The use of modified CHROMagar Acinetobacter together with nasal and rectal swabs and 1-day incubation is an effective surveillance tool for detecting MRA colonization. PMID:23667846

  5. Identification of gadoid species in fish meat by polymerase chain reaction (PCR) on genomic DNA.

    PubMed

    Hubalkova, Zora; Kralik, Petr; Kasalova, Janka; Rencova, Eva

    2008-05-28

    Identification of fish species is significant due to the increasing interest of consumers in the meat of sea fish. Methods focusing on fish species identification help to reveal fraudulent substitution among economically important gadoid species in commercial seafood products. The objective of this work was to develop a conventional PCR method for the differentiation of the following gadoid fish species in fish products: Alaska pollack ( Theragra chalcogramma), blue whiting ( Micromesistius poutassou), hake spp. ( Merluccius spp.), Atlantic cod ( Gadus morhua), saithe ( Pollachius virens), and whiting ( Merlangius merlangus). The species-specific primer pairs for gadoid species determination were based on the partial pantophysin I ( PanI) genomic sequence. Sequence identification was confirmed by cloning and sequencing of the PCR products obtained from the species considered. For the simultaneous detection of Alaska pollack, blue whiting, and hake spp., a quadruplex PCR system was constructed. Other gadoid species were detected in separate PCR reactions. After optimization of the reactions, the developed PCR systems were used for the analysis of codfish samples obtained from the Czech market and the customs' laboratories. This method represents an alternative approach in the use of genomic DNA for the identification of fish species. This method is rapid, simple, and reliable without the need for further confirmative methods. Furthermore, the identification of a mixture of more than one species is possible. The PCR system has been optimized for routine diagnostic purposes.

  6. Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species

    PubMed Central

    Yoshida, Kohta; Makino, Takashi; Yamaguchi, Katsushi; Shigenobu, Shuji; Hasebe, Mitsuyasu; Kawata, Masakado; Kume, Manabu; Mori, Seiichi; Peichel, Catherine L.; Toyoda, Atsushi; Fujiyama, Asao; Kitano, Jun

    2014-01-01

    Sex chromosomes turn over rapidly in some taxonomic groups, where closely related species have different sex chromosomes. Although there are many examples of sex chromosome turnover, we know little about the functional roles of sex chromosome turnover in phenotypic diversification and genomic evolution. The sympatric pair of Japanese threespine stickleback (Gasterosteus aculeatus) provides an excellent system to address these questions: the Japan Sea species has a neo-sex chromosome system resulting from a fusion between an ancestral Y chromosome and an autosome, while the sympatric Pacific Ocean species has a simple XY sex chromosome system. Furthermore, previous quantitative trait locus (QTL) mapping demonstrated that the Japan Sea neo-X chromosome contributes to phenotypic divergence and reproductive isolation between these sympatric species. To investigate the genomic basis for the accumulation of genes important for speciation on the neo-X chromosome, we conducted whole genome sequencing of males and females of both the Japan Sea and the Pacific Ocean species. No substantial degeneration has yet occurred on the neo-Y chromosome, but the nucleotide sequence of the neo-X and the neo-Y has started to diverge, particularly at regions near the fusion. The neo-sex chromosomes also harbor an excess of genes with sex-biased expression. Furthermore, genes on the neo-X chromosome showed higher non-synonymous substitution rates than autosomal genes in the Japan Sea lineage. Genomic regions of higher sequence divergence between species, genes with divergent expression between species, and QTL for inter-species phenotypic differences were found not only at the regions near the fusion site, but also at other regions along the neo-X chromosome. Neo-sex chromosomes can therefore accumulate substitutions causing species differences even in the absence of substantial neo-Y degeneration. PMID:24625862

  7. Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness

    SciTech Connect

    Wu, L.; Liu, X.; Fields, M.W.; Thompson, D.K.; Bagwell, C.E.; Tiedje, J. M.; Hazen, T.C.; Zhou, J.

    2008-01-15

    The definition and delineation of microbial species are of great importance and challenge due to the extent of evolution and diversity. Whole-genome DNA-DNA hybridization is the cornerstone for defining procaryotic species relatedness, but obtaining pairwise DNA-DNA reassociation values for a comprehensive phylogenetic analysis of procaryotes is tedious and time consuming. A previously described microarray format containing whole-genomic DNA (the community genome array or CGA) was rigorously evaluated as a high-throughput alternative to the traditional DNA-DNA reassociation approach for delineating procaryotic species relationships. DNA similarities for multiple bacterial strains obtained with the CGA-based hybridization were comparable to those obtained with various traditional whole-genome hybridization methods (r=0.87, P<0.01). Significant linear relationships were also observed between the CGA-based genome similarities and those derived from small subunit (SSU) rRNA gene sequences (r=0.79, P<0.0001), gyrB sequences (r=0.95, P<0.0001) or REP- and BOX-PCR fingerprinting profiles (r=0.82, P<0.0001). The CGA hybridization-revealed species relationships in several representative genera, including Pseudomonas, Azoarcus and Shewanella, were largely congruent with previous classifications based on various conventional whole-genome DNA-DNA reassociation, SSU rRNA and/or gyrB analyses. These results suggest that CGA-based DNA-DNA hybridization could serve as a powerful, high-throughput format for determining species relatedness among microorganisms.

  8. Genomic relations among 31 species of Mammillaria haworth (Cactaceae) using random amplified polymorphic DNA.

    PubMed

    Mattagajasingh, Ilwola; Mukherjee, Arup Kumar; Das, Premananda

    2006-01-01

    Thirty-one species of Mammillaria were selected to study the molecular phylogeny using random amplified polymorphic DNA (RAPD) markers. High amount of mucilage (gelling polysaccharides) present in Mammillaria was a major obstacle in isolating good quality genomic DNA. The CTAB (cetyl trimethyl ammonium bromide) method was modified to obtain good quality genomic DNA. Twenty-two random decamer primers resulted in 621 bands, all of which were polymorphic. The similarity matrix value varied from 0.109 to 0.622 indicating wide variability among the studied species. The dendrogram obtained from the unweighted pair group method using arithmetic averages (UPGMA) analysis revealed that some of the species did not follow the conventional classification. The present work shows the usefulness of RAPD markers for genetic characterization to establish phylogenetic relations among Mammillaria species.

  9. Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics.

    PubMed

    Fontaine, Michael C; Pease, James B; Steele, Aaron; Waterhouse, Robert M; Neafsey, Daniel E; Sharakhov, Igor V; Jiang, Xiaofang; Hall, Andrew B; Catteruccia, Flaminia; Kakani, Evdoxia; Mitchell, Sara N; Wu, Yi-Chieh; Smith, Hilary A; Love, R Rebecca; Lawniczak, Mara K; Slotman, Michel A; Emrich, Scott J; Hahn, Matthew W; Besansky, Nora J

    2015-01-02

    Introgressive hybridization is now recognized as a widespread phenomenon, but its role in evolution remains contested. Here, we use newly available reference genome assemblies to investigate phylogenetic relationships and introgression in a medically important group of Afrotropical mosquito sibling species. We have identified the correct species branching order to resolve a contentious phylogeny and show that lineages leading to the principal vectors of human malaria were among the first to split. Pervasive autosomal introgression between these malaria vectors means that only a small fraction of the genome, mainly on the X chromosome, has not crossed species boundaries. Our results suggest that traits enhancing vectorial capacity may be gained through interspecific gene flow, including between nonsister species.

  10. Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria.

    PubMed

    Sundararaman, Sesh A; Plenderleith, Lindsey J; Liu, Weimin; Loy, Dorothy E; Learn, Gerald H; Li, Yingying; Shaw, Katharina S; Ayouba, Ahidjo; Peeters, Martine; Speede, Sheri; Shaw, George M; Bushman, Frederic D; Brisson, Dustin; Rayner, Julian C; Sharp, Paul M; Hahn, Beatrice H

    2016-03-22

    African apes harbour at least six Plasmodium species of the subgenus Laverania, one of which gave rise to human Plasmodium falciparum. Here we use a selective amplification strategy to sequence the genome of chimpanzee parasites classified as Plasmodium reichenowi and Plasmodium gaboni based on the subgenomic fragments. Genome-wide analyses show that these parasites indeed represent distinct species, with no evidence of cross-species mating. Both P. reichenowi and P. gaboni are 10-fold more diverse than P. falciparum, indicating a very recent origin of the human parasite. We also find a remarkable Laverania-specific expansion of a multigene family involved in erythrocyte remodelling, and show that a short region on chromosome 4, which encodes two essential invasion genes, was horizontally transferred into a recent P. falciparum ancestor. Our results validate the selective amplification strategy for characterizing cryptic pathogen species, and reveal evolutionary events that likely predisposed the precursor of P. falciparum to colonize humans.

  11. Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria

    PubMed Central

    Sundararaman, Sesh A.; Plenderleith, Lindsey J.; Liu, Weimin; Loy, Dorothy E.; Learn, Gerald H.; Li, Yingying; Shaw, Katharina S.; Ayouba, Ahidjo; Peeters, Martine; Speede, Sheri; Shaw, George M.; Bushman, Frederic D.; Brisson, Dustin; Rayner, Julian C.; Sharp, Paul M.; Hahn, Beatrice H.

    2016-01-01

    African apes harbour at least six Plasmodium species of the subgenus Laverania, one of which gave rise to human Plasmodium falciparum. Here we use a selective amplification strategy to sequence the genome of chimpanzee parasites classified as Plasmodium reichenowi and Plasmodium gaboni based on the subgenomic fragments. Genome-wide analyses show that these parasites indeed represent distinct species, with no evidence of cross-species mating. Both P. reichenowi and P. gaboni are 10-fold more diverse than P. falciparum, indicating a very recent origin of the human parasite. We also find a remarkable Laverania-specific expansion of a multigene family involved in erythrocyte remodelling, and show that a short region on chromosome 4, which encodes two essential invasion genes, was horizontally transferred into a recent P. falciparum ancestor. Our results validate the selective amplification strategy for characterizing cryptic pathogen species, and reveal evolutionary events that likely predisposed the precursor of P. falciparum to colonize humans. PMID:27002652

  12. Overview on the Role of Advance Genomics in Conservation Biology of Endangered Species.

    PubMed

    Khan, Suliman; Nabi, Ghulam; Ullah, Muhammad Wajid; Yousaf, Muhammad; Manan, Sehrish; Siddique, Rabeea; Hou, Hongwei

    2016-01-01

    In the recent era, due to tremendous advancement in industrialization, pollution and other anthropogenic activities have created a serious scenario for biota survival. It has been reported that present biota is entering a "sixth" mass extinction, because of chronic exposure to anthropogenic activities. Various ex situ and in situ measures have been adopted for conservation of threatened and endangered plants and animal species; however, these have been limited due to various discrepancies associated with them. Current advancement in molecular technologies, especially, genomics, is playing a very crucial role in biodiversity conservation. Advance genomics helps in identifying the segments of genome responsible for adaptation. It can also improve our understanding about microevolution through a better understanding of selection, mutation, assertive matting, and recombination. Advance genomics helps in identifying genes that are essential for fitness and ultimately for developing modern and fast monitoring tools for endangered biodiversity. This review article focuses on the applications of advanced genomics mainly demographic, adaptive genetic variations, inbreeding, hybridization and introgression, and disease susceptibilities, in the conservation of threatened biota. In short, it provides the fundamentals for novice readers and advancement in genomics for the experts working for the conservation of endangered plant and animal species.

  13. Recombination produces coherent bacterial species clusters in both core and accessory genomes

    PubMed Central

    Croucher, Nicholas J.; Gutmann, Michael U.; Corander, Jukka; Hanage, William P.

    2015-01-01

    Background: Population samples show bacterial genomes can be divided into a core of ubiquitous genes and accessory genes that are present in a fraction of isolates. The ecological significance of this variation in gene content remains unclear. However, microbiologists agree that a bacterial species should be ‘genomically coherent’, even though there is no consensus on how this should be determined. Results: We use a parsimonious model combining diversification in both the core and accessory genome, including mutation, homologous recombination (HR) and horizontal gene transfer (HGT) introducing new loci, to produce a population of interacting clusters of strains with varying genome content. New loci introduced by HGT may then be transferred on by HR. The model fits well to a systematic population sample of 616 pneumococcal genomes, capturing the major features of the population structure with parameter values that agree well with empirical estimates. Conclusions: The model does not include explicit selection on individual genes, suggesting that crude comparisons of gene content may be a poor predictor of ecological function. We identify a clearly divergent subpopulation of pneumococci that are inconsistent with the model and may be considered genomically incoherent with the rest of the population. These strains have a distinct disease tropism and may be rationally defined as a separate species. We also find deviations from the model that may be explained by recent population bottlenecks or spatial structure.

  14. Overview on the Role of Advance Genomics in Conservation Biology of Endangered Species

    PubMed Central

    Khan, Suliman; Nabi, Ghulam; Ullah, Muhammad Wajid; Yousaf, Muhammad; Manan, Sehrish; Siddique, Rabeea

    2016-01-01

    In the recent era, due to tremendous advancement in industrialization, pollution and other anthropogenic activities have created a serious scenario for biota survival. It has been reported that present biota is entering a “sixth” mass extinction, because of chronic exposure to anthropogenic activities. Various ex situ and in situ measures have been adopted for conservation of threatened and endangered plants and animal species; however, these have been limited due to various discrepancies associated with them. Current advancement in molecular technologies, especially, genomics, is playing a very crucial role in biodiversity conservation. Advance genomics helps in identifying the segments of genome responsible for adaptation. It can also improve our understanding about microevolution through a better understanding of selection, mutation, assertive matting, and recombination. Advance genomics helps in identifying genes that are essential for fitness and ultimately for developing modern and fast monitoring tools for endangered biodiversity. This review article focuses on the applications of advanced genomics mainly demographic, adaptive genetic variations, inbreeding, hybridization and introgression, and disease susceptibilities, in the conservation of threatened biota. In short, it provides the fundamentals for novice readers and advancement in genomics for the experts working for the conservation of endangered plant and animal species. PMID:28025636

  15. Evolutionary Genomics of Genes Involved in Olfactory Behavior in the Drosophila melanogaster Species Group

    PubMed Central

    Lavagnino, Nicolás; Serra, François; Arbiza, Leonardo; Dopazo, Hernán; Hasson, Esteban

    2012-01-01

    Previous comparative genomic studies of genes involved in olfactory behavior in Drosophila focused only on particular gene families such as odorant receptor and/or odorant binding proteins. However, olfactory behavior has a complex genetic architecture that is orchestrated by many interacting genes. In this paper, we present a comparative genomic study of olfactory behavior in Drosophila including an extended set of genes known to affect olfactory behavior. We took advantage of the recent burst of whole genome sequences and the development of powerful statistical tools to analyze genomic data and test evolutionary and functional hypotheses of olfactory genes in the six species of the Drosophila melanogaster species group for which whole genome sequences are available. Our study reveals widespread purifying selection and limited incidence of positive selection on olfactory genes. We show that the pace of evolution of olfactory genes is mostly independent of the life cycle stage, and of the number of life cycle stages, in which they participate in olfaction. However, we detected a relationship between evolutionary rates and the position that the gene products occupy in the olfactory system, genes occupying central positions tend to be more constrained than peripheral genes. Finally, we demonstrate that specialization to one host does not seem to be associated with bursts of adaptive evolution in olfactory genes in D. sechellia and D. erecta, the two specialists species analyzed, but rather different lineages have idiosyncratic evolutionary histories in which both historical and ecological factors have been involved. PMID:22346339

  16. Whole genome sequencing data and de novo draft assemblies for 66 teleost species

    PubMed Central

    Malmstrøm, Martin; Matschiner, Michael; Tørresen, Ole K.; Jakobsen, Kjetill S.; Jentoft, Sissel

    2017-01-01

    Teleost fishes comprise more than half of all vertebrate species, yet genomic data are only available for 0.2% of their diversity. Here, we present whole genome sequencing data for 66 new species of teleosts, vastly expanding the availability of genomic data for this important vertebrate group. We report on de novo assemblies based on low-coverage (9–39×) sequencing and present detailed methodology for all analyses. To facilitate further utilization of this data set, we present statistical analyses of the gene space completeness and verify the expected phylogenetic position of the sequenced genomes in a large mitogenomic context. We further present a nuclear marker set used for phylogenetic inference and evaluate each gene tree in relation to the species tree to test for homogeneity in the phylogenetic signal. Collectively, these analyses illustrate the robustness of this highly diverse data set and enable extensive reuse of the selected phylogenetic markers and the genomic data in general. This data set covers all major teleost lineages and provides unprecedented opportunities for comparative studies of teleosts. PMID:28094797

  17. Complete chloroplast genome sequence of a major economic species, Ziziphus jujuba (Rhamnaceae).

    PubMed

    Ma, Qiuyue; Li, Shuxian; Bi, Changwei; Hao, Zhaodong; Sun, Congrui; Ye, Ning

    2017-02-01

    Ziziphus jujuba is an important woody plant with high economic and medicinal value. Here, we analyzed and characterized the complete chloroplast (cp) genome of Z. jujuba, the first member of the Rhamnaceae family for which the chloroplast genome sequence has been reported. We also built a web browser for navigating the cp genome of Z. jujuba ( http://bio.njfu.edu.cn/gb2/gbrowse/Ziziphus_jujuba_cp/ ). Sequence analysis showed that this cp genome is 161,466 bp long and has a typical quadripartite structure of large (LSC, 89,120 bp) and small (SSC, 19,348 bp) single-copy regions separated by a pair of inverted repeats (IRs, 26,499 bp). The sequence contained 112 unique genes, including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The genome structure, gene order, GC content, and codon usage are similar to other typical angiosperm cp genomes. A total of 38 tandem repeats, two forward repeats, and three palindromic repeats were detected in the Z. jujuba cp genome. Simple sequence repeat (SSR) analysis revealed that most SSRs were AT-rich. The homopolymer regions in the cp genome of Z. jujuba were verified and manually corrected by Sanger sequencing. One-third of mononucleotide repeats were found to be erroneously sequenced by the 454 pyrosequencing, which resulted in sequences of 1-4 bases shorter than that by the Sanger sequencing. Analyzing the cp genome of Z. jujuba revealed that the IR contraction and expansion events resulted in ycf1 and rps19 pseudogenes. A phylogenetic analysis based on 64 protein-coding genes showed that Z. jujuba was closely related to members of the Elaeagnaceae family, which will be helpful for phylogenetic studies of other Rosales species. The complete cp genome sequence of Z. jujuba will facilitate population, phylogenetic, and cp genetic engineering studies of this economic plant.

  18. The evolution of microbial species - a view through the genomic lens

    SciTech Connect

    Varghese, Neha; Mukherjee, Supratim; ivanova, Natalia; Mavromatis, Konstantinos; Konstantinidis, Konstantinos; Kyrpides, Nikos; Pati, Amrita

    2014-03-17

    For a long time prokaryotic species definition has been under debate and a constant source of turmoil in microbiology. This has recently prompted the ASM to call for a scalable and reproducible technique, which uses meaningful commonalities to cluster microorganisms into groups corresponding to prokaryotic species. Whole-genome Average Nucleotide Identity (gANI) was previously suggested as a measure of genetic distance that generally agrees with prokaryotic species assignments based on the accepted best practices (DNA-DNA hybridization and 16S rDNA similarity). In this work, we prove that gANI is indeed the meaningful commonality based on which microorganisms can be grouped into the aforementioned clusters. By analyzing 1.76 million pairs of genomes we find that identification of the closest relatives of an organism via gANI is precise, scalable, reproducible, and reflects the evolutionary dynamics of microbes. We model the previously unexplored statistical properties of gANI using 6,000 microbial genomes and apply species-specific gANI cutoffs to reveal anomalies in the current taxonomic species definitions for almost 50percent of the species with multiple genome sequences. We also provide evidence of speciation events and genetic continuums in 17.8percent of those species. We consider disagreements between gANI-based groupings and named species and demonstrate that the former have all the desired features to serve as the much-needed natural groups for moving forward with taxonomy. Further, the groupings identified are presented in detail at http://ani.jgi-psf.org to facilitate comprehensive downstream analysis for researchers across different disciplines

  19. Partitiviruses of a fungal forest pathogen have species-specific quantities of genome segments and transcripts.

    PubMed

    Jurvansuu, Jaana; Kashif, Muhammad; Vaario, Leo; Vainio, Eeva; Hantula, Jarkko

    2014-08-01

    Heterobasidion partitiviruses infect forest pathogenic fungi of the genus Heterobasidion. We have studied the amounts of genomes and transcripts of four partitiviruses isolated from four different Heterobasidion strains infecting different host trees in Greece, Poland, Finland, and China. Heterobasidion partitiviruses have bisegmented genomes encoding coat protein and RNA-dependent RNA polymerase. Our results show that the coat protein genome segment is generally more abundant in infected mycelia than the RNA-dependent RNA polymerase segment and that this bias persists also at transcript levels. The different virus species all have unique ratios of the genome segments and the ratio is generally stable over different temperatures and hosts. The amounts of transcripts of each virus respond to host growth temperatures in a distinctive and consistent manner. The Heterobasidion partitiviruses studied here affect only rarely the growth of their natural hosts but do influence the growth of a new host more frequently.

  20. Complete mitochondrial genome of the versicoloured emerald hummingbird Amazilia versicolor, a polymorphic species.

    PubMed

    Prosdocimi, Francisco; Souto, Helena Magarinos; Ruschi, Piero Angeli; Furtado, Carolina; Jennings, W Bryan

    2016-09-01

    The genome of the versicoloured emerald hummingbird (Amazilia versicolor) was partially sequenced in one-sixth of an Illumina HiSeq lane. The mitochondrial genome was assembled using MIRA and MITObim software, yielding a circular molecule of 16,861 bp in length and deposited in GenBank under the accession number KF624601. The mitogenome contained 13 protein-coding genes, 22 transfer tRNAs, 2 ribosomal RNAs and 1 non-coding control region. The molecule was assembled using 21,927 sequencing reads of 100 bp each, resulting in ∼130 × coverage of uniformly distributed reads along the genome. This is the forth mitochondrial genome described for this highly diverse family of birds and may benefit further phylogenetic, phylogeographic, population genetic and species delimitation studies of hummingbirds.

  1. An Efficient Method for Genomic DNA Extraction from Different Molluscs Species

    PubMed Central

    Pereira, Jorge C.; Chaves, Raquel; Bastos, Estela; Leitão, Alexandra; Guedes-Pinto, Henrique

    2011-01-01

    The selection of a DNA extraction method is a critical step when subsequent analysis depends on the DNA quality and quantity. Unlike mammals, for which several capable DNA extraction methods have been developed, for molluscs the availability of optimized genomic DNA extraction protocols is clearly insufficient. Several aspects such as animal physiology, the type (e.g., adductor muscle or gills) or quantity of tissue, can explain the lack of efficiency (quality and yield) in molluscs genomic DNA extraction procedure. In an attempt to overcome these aspects, this work describes an efficient method for molluscs genomic DNA extraction that was tested in several species from different orders: Veneridae, Ostreidae, Anomiidae, Cardiidae (Bivalvia) and Muricidae (Gastropoda), with different weight sample tissues. The isolated DNA was of high molecular weight with high yield and purity, even with reduced quantities of tissue. Moreover, the genomic DNA isolated, demonstrated to be suitable for several downstream molecular techniques, such as PCR sequencing among others. PMID:22174651

  2. Echinochloa Chloroplast Genomes: Insights into the Evolution and Taxonomic Identification of Two Weedy Species

    PubMed Central

    Li, Gengmi; Wang, Ying-Ying; Qiu, Jie; Fu, Fei; Zhang, Haiqiang; Chen, Li; Ye, Sisi; Song, Weijie; Jin, Gulei; Zhu, Jinwen; Lu, Yongliang; Guo, Longbiao; Fan, Longjiang

    2014-01-01

    The genus Echinochloa (Poaceae) includes numerous problematic weeds that cause the reduction of crop yield worldwide. To date, DNA sequence information is still limited in the genus Echinochloa. In this study, we completed the entire chloroplast genomes of two Echinochloa species (Echinochloa oryzicola and Echinochloa crus-galli) based on high-throughput sequencing data from their fresh green leaves. The two Echinochloa chloroplast genomes are 139,891 and 139,800 base pairs in length, respectively, and contain 131 protein-coding genes, 79 indels and 466 substitutions helpful for discrimination of the two species. The divergence between the genus Echinochloa and Panicum occurred about 21.6 million years ago, whereas the divergence between E. oryzicola and E. crus-galli chloroplast genes occurred about 3.3 million years ago. The two reported Echinochloa chloroplast genome sequences contribute to better understanding of the diversification of this genus. PMID:25427255

  3. Genome Sequences of Three Species of Hanseniaspora Isolated from Spontaneous Wine Fermentations

    PubMed Central

    Sternes, Peter R.; Lee, Danna; Kutyna, Dariusz R.

    2016-01-01

    Members of the genus Hanseniaspora represent a significant proportion of the normal flora of grape berries and play a significant role in wine fermentation. Here, we present genome sequences for three species of Hanseniaspora, H. opuntiae, H. osmophila, and H. uvarum, which were isolated from spontaneous Chardonnay wine fermentation. PMID:27856586

  4. Clade- and species-specific features of genome evolution in the Saccharomycetaceae

    PubMed Central

    Wolfe, Kenneth H.; Armisén, David; Proux-Wera, Estelle; ÓhÉigeartaigh, Seán S.; Azam, Haleema; Gordon, Jonathan L.; Byrne, Kevin P.

    2015-01-01

    Many aspects of the genomes of yeast species in the family Saccharomycetaceae have been well conserved during evolution. They have similar genome sizes, genome contents, and extensive collinearity of gene order along chromosomes. Gene functions can often be inferred reliably by using information from Saccharomyces cerevisiae. Beyond this conservative picture however, there are many instances where a species or a clade diverges substantially from the S. cerevisiae paradigm—for example, by the amplification of a gene family, or by the absence of a biochemical pathway or a protein complex. Here, we review clade-specific features, focusing on genomes sequenced in our laboratory from the post-WGD genera Naumovozyma, Kazachstania and Tetrapisispora, and from the non-WGD species Torulaspora delbrueckii. Examples include the loss of the pathway for histidine synthesis in the cockroach-associated species Tetrapisispora blattae; the presence of a large telomeric GAL gene cluster in To. delbrueckii; losses of the dynein and dynactin complexes in several independent yeast lineages; fragmentation of the MAT locus and loss of the HO gene in Kazachstania africana; and the patchy phylogenetic distribution of RNAi pathway components. PMID:26066552

  5. Genomics and introgression: discovery and mapping of thousands of species-diagnostic SNPs using RAD sequencing

    USGS Publications Warehouse

    Hand, Brian K; Hether, Tyler D; Kovach, Ryan P.; Muhlfeld, Clint C.; Amish, Stephen J.; Boyer, Matthew C.; O’Rourke, Sean M.; Miller, Michael R.; Lowe, Winsor H.; Hohenlohe, Paul A.; Luikart, Gordon

    2015-01-01

    Invasive hybridization and introgression pose a serious threat to the persistence of many native species. Understanding the effects of hybridization on native populations (e.g., fitness consequences) requires numerous species-diagnostic loci distributed genome-wide. Here we used RAD sequencing to discover thousands of single-nucleotide polymorphisms (SNPs) that are diagnostic between rainbow trout (RBT, Oncorhynchus mykiss), the world’s most widely introduced fish, and native westslope cutthroat trout (WCT, O. clarkii lewisi) in the northern Rocky Mountains, USA. We advanced previous work that identified 4,914 species-diagnostic loci by using longer sequence reads (100 bp vs. 60 bp) and a larger set of individuals (n = 84). We sequenced RAD libraries for individuals from diverse sampling sources, including native populations of WCT and hatchery broodstocks of WCT and RBT. We also took advantage of a newly released reference genome assembly for RBT to align our RAD loci. In total, we discovered 16,788 putatively diagnostic SNPs, 10,267 of which we mapped to anchored chromosome locations on the RBT genome. A small portion of previously discovered putative diagnostic loci (325 of 4,914) were no longer diagnostic (i.e., fixed between species) based on our wider survey of non-hybridized RBT and WCT individuals. Our study suggests that RAD loci mapped to a draft genome assembly could provide the marker density required to identify genes and chromosomal regions influencing selection in admixed populations of conservation concern and evolutionary interest.

  6. Whole-Genome Shotgun Sequence of Rhodococcus Species Strain JVH1

    PubMed Central

    Brooks, Shannon L.

    2012-01-01

    Here we present a whole-genome shotgun sequence of Rhodococcus species strain JVH1, an organism capable of degrading a variety of organosulfur compounds. In particular, JVH1 is able to selectively cleave carbon-sulfur bonds within alkyl chains. A large number of oxygenases were identified, consistent with other members of the genus. PMID:22965106

  7. Multiple Genome Sequences of the Important Beer-Spoiling Species Lactobacillus backii

    PubMed Central

    Geissler, Andreas J.; Vogel, Rudi F.

    2016-01-01

    Lactobacillus backii is an important beer-spoiling species. Five strains isolated from four different breweries were sequenced using single-molecule real-time sequencing. Five complete genomes were generated, which will help to understand niche adaptation to beer and provide the basis for consecutive analyses. PMID:27563041

  8. The complete mitochondrial genomes of three cestode species of Taenia infecting animals and humans.

    PubMed

    Liu, Guo-Hua; Lin, Rui-Qing; Li, Ming-Wei; Liu, Wei; Liu, Yi; Yuan, Zi-Guo; Song, Hui-Qun; Zhao, Guang-Hui; Zhang, Kou-Xing; Zhu, Xing-Quan

    2011-04-01

    Mitochondrial (mt) genome sequences provide useful markers for investigating population genetic structures, systematics and phylogenetics of organisms. Although Taenia multiceps, T. hydatigena, and T. taeniaeformis are common taeniid tapeworms of ruminants, pigs, dogs, or cats, causing significant economic losses, no published study on their mt genomes is available. The complete mt genomes of T. multiceps, T. hydatigena, and T. taeniaeformis were amplified in two overlapping fragments and then sequenced. The sizes of the entire mt genome were 13700 bp for T. multiceps, 13489 bp for T. hydatigena, and 13647 bp for T. taeniaeformis. Each of the three genomes contains 36 genes, consisting of 12 genes for proteins, 2 genes for rRNA, and 22 genes for tRNA, which are the same as the mt genomes of all other cestode species studied to date. All genes are transcribed in the same direction and have a nucleotide composition high in A and T. The contents of A+T of the complete genomes are 71.3% for T. multiceps, 70.8% for T. hydatigena, and 73.0% for T. taeniaeformis. The AT bias had a significant effect on both the codon usage pattern and amino acid composition of proteins. T. multiceps and T. hydatigena had two noncoding regions, but T. taeniaeformis had only one. Phylogenetic analyses based on concatenated amino acid sequences of 12 protein-coding genes revealed that T. multiceps, T. hydatigena, and T. taeniaeformis were more closely related to the other members of the Taenia genus, consistent with results of previous morphological and molecular studies. The present study determined the complete mt genome sequences for three Taenia species of animal and human health significance, providing useful markers for studying the systematics, population genetics, and molecular epidemiology of these cestode parasites of animals and humans.

  9. Comparative Transcriptome and Chloroplast Genome Analyses of Two Related Dipteronia Species

    PubMed Central

    Zhou, Tao; Chen, Chen; Wei, Yue; Chang, Yongxia; Bai, Guoqing; Li, Zhonghu; Kanwal, Nazish; Zhao, Guifang

    2016-01-01

    Dipteronia (order Sapindales) is an endangered genus endemic to China and has two living species, D.sinensis and D. dyeriana. The plants are closely related to the genus Acer, which is also classified in the order Sapindales. Evolutionary studies on Dipteronia have been hindered by the paucity of information on their genomes and plastids. Here, we used next generation sequencing to characterize the transcriptomes and complete chloroplast genomes of both Dipteronia species. A comparison of the transcriptomes of both species identified a total of 7814 orthologs. Estimation of selection pressures using Ka/Ks ratios showed that only 30 of 5435 orthologous pairs had a ratio significantly >1, i.e., showing positive selection. However, 4041 orthologs had a Ka/Ks < 0.5 (p < 0.05), suggesting that most genes had likely undergone purifying selection. Based on orthologous unigenes, 314 single copy nuclear genes (SCNGs) were identified. Through a combination of de novo and reference guided assembly, plastid genomes were obtained; that of D. sinensis was 157,080 bp and that of D. dyeriana was 157,071 bp. Both plastid genomes encoded 87 protein coding genes, 40 tRNAs, and 8 rRNAs; no significant differences were detected in the size, gene content, and organization of the two plastomes. We used the whole chloroplast genomes to determine the phylogeny of D. sinensis and D. dyeriana and confirmed that the two species were highly divergent. Overall, our study provides comprehensive transcriptomic and chloroplast genomic resources, which will be valuable for future evolutionary studies of Dipteronia. PMID:27790228

  10. Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers.

    PubMed

    Wang, Nian; Thomson, Marian; Bodles, William J A; Crawford, Robert M M; Hunt, Harriet V; Featherstone, Alan Watson; Pellicer, Jaume; Buggs, Richard J A

    2013-06-01

    New sequencing technologies allow development of genome-wide markers for any genus of ecological interest, including plant genera such as Betula (birch) that have previously proved difficult to study due to widespread polyploidy and hybridization. We present a de novo reference genome sequence assembly, from 66× short read coverage, of Betula nana (dwarf birch) - a diploid that is the keystone woody species of subarctic scrub communities but of conservation concern in Britain. We also present 100 bp PstI RAD markers for B. nana and closely related Betula tree species. Assembly of RAD markers in 15 individuals by alignment to the reference B. nana genome yielded 44-86k RAD loci per individual, whereas de novo RAD assembly yielded 64-121k loci per individual. Of the loci assembled by the de novo method, 3k homologous loci were found in all 15 individuals studied, and 35k in 10 or more individuals. Matching of RAD loci to RAD locus catalogues from the B. nana individual used for the reference genome showed similar numbers of matches from both methods of RAD locus assembly but indicated that the de novo RAD assembly method may overassemble some paralogous loci. In 12 individuals hetero-specific to B. nana 37-47k RAD loci matched a catalogue of RAD loci from the B. nana individual used for the reference genome, whereas 44-60k RAD loci aligned to the B. nana reference genome itself. We present a preliminary study of allele sharing among species, demonstrating the utility of the data for introgression studies and for the identification of species-specific alleles.

  11. Minipig and beagle animal model genomes aid species selection in pharmaceutical discovery and development

    SciTech Connect

    Vamathevan, Jessica J.; Hall, Matthew D.; Hasan, Samiul; Woollard, Peter M.; Xu, Meng; Yang, Yulan; Li, Xin; Wang, Xiaoli; Kenny, Steve; Brown, James R.; Huxley-Jones, Julie; Lyon, Jon; Haselden, John; Min, Jiumeng; Sanseau, Philippe

    2013-07-15

    Improving drug attrition remains a challenge in pharmaceutical discovery and development. A major cause of early attrition is the demonstration of safety signals which can negate any therapeutic index previously established. Safety attrition needs to be put in context of clinical translation (i.e. human relevance) and is negatively impacted by differences between animal models and human. In order to minimize such an impact, an earlier assessment of pharmacological target homology across animal model species will enhance understanding of the context of animal safety signals and aid species selection during later regulatory toxicology studies. Here we sequenced the genomes of the Sus scrofa Göttingen minipig and the Canis familiaris beagle, two widely used animal species in regulatory safety studies. Comparative analyses of these new genomes with other key model organisms, namely mouse, rat, cynomolgus macaque, rhesus macaque, two related breeds (S. scrofa Duroc and C. familiaris boxer) and human reveal considerable variation in gene content. Key genes in toxicology and metabolism studies, such as the UGT2 family, CYP2D6, and SLCO1A2, displayed unique duplication patterns. Comparisons of 317 known human drug targets revealed surprising variation such as species-specific positive selection, duplication and higher occurrences of pseudogenized targets in beagle (41 genes) relative to minipig (19 genes). These data will facilitate the more effective use of animals in biomedical research. - Highlights: • Genomes of the minipig and beagle dog, two species used in pharmaceutical studies. • First systematic comparative genome analysis of human and six experimental animals. • Key drug toxicology genes display unique duplication patterns across species. • Comparison of 317 drug targets show species-specific evolutionary patterns.

  12. Mediterranean Species of Caulerpa Are Polyploid with Smaller Genomes in the Invasive Ones

    PubMed Central

    Varela-Álvarez, Elena; Gómez Garreta, Amelia; Rull Lluch, Jordi; Salvador Soler, Noemi; Serrao, Ester A.; Siguán, María Antonia Ribera

    2012-01-01

    Caulerpa species are marine green algae, which often act as invasive species with rapid clonal proliferation when growing outside their native biogeographical borders. Despite many publications on the genetics and ecology of Caulerpa species, their life history and ploidy levels are still to be resolved and are the subject of large controversy. While some authors claimed that the thallus found in nature has a haplodiplobiontic life cycle with heteromorphic alternation of generations, other authors claimed a diploid or haploid life cycle with only one generation involved. DAPI-staining with image analysis and microspectrophotometry were used to estimate relative nuclear DNA contents in three species of Caulerpa from the Mediterranean, at individual, population and species levels. Results show that ploidy levels and genome size vary in these three Caulerpa species, with a reduction in genome size for the invasive ones. Caulerpa species in the Mediterranean are polyploids in different life history phases; all sampled C. taxifolia and C. racemosa var. cylindracea were in haplophasic phase, but in C. prolifera, the native species, individuals were found in both diplophasic and haplophasic phases. Different levels of endopolyploidy were found in both C. prolifera and C. racemosa var. cylindracea. Life history is elucidated for the Mediterranean C. prolifera and it is hypothesized that haplophasic dominance in C. racemosa var. cylindracea and C. taxifolia is a beneficial trait for their invasive strategies. PMID:23110095

  13. A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis

    PubMed Central

    2014-01-01

    Background A novel Gram-negative, non-haemolytic, non-motile, rod-shaped bacterium was discovered in the lungs of a dead parakeet (Melopsittacus undulatus) that was kept in captivity in a petshop in Basel, Switzerland. The organism is described with a chemotaxonomic profile and the nearly complete genome sequence obtained through the assembly of short sequence reads. Results Genome sequence analysis and characterization of respiratory quinones, fatty acids, polar lipids, and biochemical phenotype is presented here. Comparison of gene sequences revealed that the most similar species is Pelistega europaea, with BLAST identities of only 93% to the 16S rDNA gene, 76% identity to the rpoB gene, and a similar GC content (~43%) as the organism isolated from the parakeet, DSM 24701 (40%). The closest full genome sequences are those of Bordetella spp. and Taylorella spp. High-throughput sequencing reads from the Illumina-Solexa platform were assembled with the Edena de novo assembler to form 195 contigs comprising the ~2 Mb genome. Genome annotation with RAST, construction of phylogenetic trees with the 16S rDNA (rrs) gene sequence and the rpoB gene, and phylogenetic placement using other highly conserved marker genes with ML Tree all suggest that the bacterial species belongs to the Alcaligenaceae family. Analysis of samples from cages with healthy parakeets suggested that the newly discovered bacterial species is not widespread in parakeet living quarters. Conclusions Classification of this organism in the current taxonomy system requires the formation of a new genus and species. We designate the new genus Basilea and the new species psittacipulmonis. The type strain of Basilea psittacipulmonis is DSM 24701 (= CIP 110308 T, 16S rDNA gene sequence Genbank accession number JX412111 and GI 406042063). PMID:24581117

  14. Genome-wide in silico screening for microRNA genetic variability in livestock species.

    PubMed

    Jevsinek Skok, D; Godnic, I; Zorc, M; Horvat, S; Dovc, P; Kovac, M; Kunej, T

    2013-12-01

    MicroRNAs are a class of non-coding RNAs that post-transcriptionally regulate target gene expression. Previous studies have shown that microRNA gene variability can interfere with its function, resulting in phenotypic variation. Polymorphisms within microRNA genes present a source of novel biomarkers for phenotypic traits in animal breeding. However, little is known about microRNA genetic variability in livestock species, which is also due to incomplete data in genomic resource databases. Therefore, the aim of this study was to perform a genome-wide in silico screening of genomic sources and determine the genetic variability of microRNA genes in livestock species using mirna sniper 3.0 (http://www.integratomics-time.com/miRNA-SNiPer/), a new version of our previously developed tool. By examining Ensembl and miRBase genome builds, it was possible to design a tool-based generated search of 16 genomes including four livestock species: pig, horse, cattle and chicken. The analysis revealed 65 polymorphisms located within mature microRNA regions in these four species, including 28% within the seed region in cattle and chicken. Polymorphic microRNA genes in cattle and chicken were further examined for mapping to quantitative trait loci regions associated with production and health traits. The developed bioinformatics tool enables the analysis of polymorphic microRNA genes and prioritization of potential regulatory polymorphisms and therefore contributes to the development of microRNA-based biomarkers in livestock species. The assembled catalog and the developed tool can serve the animal science community to efficiently select microRNA SNPs for further quantitative and molecular genetic evaluations of their phenotypic effects and causal associations with livestock production traits.

  15. Genomic patterns of diversity and divergence of two introduced salmonid species in Patagonia, South America.

    PubMed

    Narum, Shawn R; Gallardo, Pablo; Correa, Cristian; Matala, Amanda; Hasselman, Daniel; Sutherland, Ben J G; Bernatchez, Louis

    2017-04-01

    Invasive species have become widespread in aquatic environments throughout the world, yet there are few studies that have examined genomic variation of multiple introduced species in newly colonized environments. In this study, we contrast genomic variation in two salmonid species (anadromous Chinook Salmon, Oncorhynchus tshawytscha, 11,579 SNPs and resident Brook Charr Salvelinus fontinalis, 13,522 SNPs) with differing invasion success after introduction to new environments in South America relative to populations from their native range in North America. Estimates of genetic diversity were not significantly different between introduced and source populations for either species, indicative of propagule pressure that has been shown to maintain diversity in founding populations relative to their native range. Introduced populations also demonstrated higher connectivity and gene flow than those in their native range. Evidence for candidate loci under divergent selection was observed, but was limited to specific introduced populations and was not widely evident. Patterns of genomic variation were consistent with general dispersal potential of each species and therefore also the notion that life history variation may contribute to both invasion success and subsequent genetic structure of these two salmonids in Patagonia.

  16. Genome-wide analyses of recombination suggest that Giardia intestinalis assemblages represent different species.

    PubMed

    Xu, Feifei; Jerlström-Hultqvist, Jon; Andersson, Jan O

    2012-10-01

    Giardia intestinalis is a major cause of waterborne enteric disease in humans. The species is divided into eight assemblages suggested to represent separate Giardia species based on host specificities and the genetic divergence of marker genes. We have investigated whether genome-wide recombination occurs between assemblages using the three available G. intestinalis genomes. First, the relative nonsynonymous substitution rates of the homologs were compared for 4,009 positional homologs. The vast majority of these comparisons indicate genetic isolation without interassemblage recombinations. Only a region of 6 kbp suggests genetic exchange between assemblages A and E, followed by gene conversion events. Second, recombination-detecting software fails to identify within-gene recombination between the different assemblages for most of the homologs. Our results indicate very low frequency of recombination between the syntenic core genes, suggesting that G. intestinalis assemblages are genetically isolated lineages and thus should be viewed as separated Giardia species.

  17. "Controlled, cross-species dataset for exploring biases in genome annotation and modification profiles".

    PubMed

    McAfee, Alison; Michaud, Sarah; Foster, Leonard J

    2015-12-01

    Since the sequencing of the honey bee genome, proteomics by mass spectrometry has become increasingly popular for biological analyses of this insect; but we have observed that the number of honey bee protein identifications is consistently low compared to other organisms [1]. In this dataset, we use nanoelectrospray ionization-coupled liquid chromatography-tandem mass spectrometry (nLC-MS/MS) to systematically investigate the root cause of low honey bee proteome coverage. To this end, we present here data from three key experiments: a controlled, cross-species analyses of samples from Apis mellifera, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Mus musculus and Homo sapiens; a proteomic analysis of an individual honey bee whose genome was also sequenced; and a cross-tissue honey bee proteome comparison. The cross-species dataset was interrogated to determine relative proteome coverages between species, and the other two datasets were used to search for polymorphic sequences and to compare protein cleavage profiles, respectively.

  18. Comparative Genomic Analysis Reveals a Possible Novel Non-Tuberculous Mycobacterium Species with High Pathogenic Potential

    PubMed Central

    Choo, Siew Woh; Dutta, Avirup; Wong, Guat Jah; Wee, Wei Yee; Ang, Mia Yang; Siow, Cheuk Chuen

    2016-01-01

    Mycobacteria have been reported to cause a wide range of human diseases. We present the first whole-genome study of a Non-Tuberculous Mycobacterium, Mycobacterium sp. UM_CSW (referred to hereafter as UM_CSW), isolated from a patient diagnosed with bronchiectasis. Our data suggest that this clinical isolate is likely a novel mycobacterial species, supported by clear evidence from molecular phylogenetic, comparative genomic, ANI and AAI analyses. UM_CSW is closely related to the Mycobacterium avium complex. While it has characteristic features of an environmental bacterium, it also shows a high pathogenic potential with the presence of a wide variety of putative genes related to bacterial virulence and shares very similar pathogenomic profiles with the known pathogenic mycobacterial species. Thus, we conclude that this possible novel Mycobacterium species should be tightly monitored for its possible causative role in human infections. PMID:27035710

  19. The Genome of a Southern Hemisphere Seagrass Species (Zostera muelleri)1[OPEN

    PubMed Central

    Golicz, Agnieszka A.; Paterson, Andrew H.; Sablok, Gaurav; Krishnaraj, Rahul R.; Chan, Chon-Kit Kenneth; Batley, Jacqueline; Ralph, Peter J.

    2016-01-01

    Seagrasses are marine angiosperms that evolved from land plants but returned to the sea around 140 million years ago during the early evolution of monocotyledonous plants. They successfully adapted to abiotic stresses associated with growth in the marine environment, and today, seagrasses are distributed in coastal waters worldwide. Seagrass meadows are an important oceanic carbon sink and provide food and breeding grounds for diverse marine species. Here, we report the assembly and characterization of the Zostera muelleri genome, a southern hemisphere temperate species. Multiple genes were lost or modified in Z. muelleri compared with terrestrial or floating aquatic plants that are associated with their adaptation to life in the ocean. These include genes for hormone biosynthesis and signaling and cell wall catabolism. There is evidence of whole-genome duplication in Z. muelleri; however, an ancient pan-commelinid duplication event is absent, highlighting the early divergence of this species from the main monocot lineages. PMID:27373688

  20. Comparative Genomics Revealed Genetic Diversity and Species/Strain-Level Differences in Carbohydrate Metabolism of Three Probiotic Bifidobacterial Species

    PubMed Central

    Odamaki, Toshitaka; Horigome, Ayako; Sugahara, Hirosuke; Hashikura, Nanami; Minami, Junichi; Xiao, Jin-zhong; Abe, Fumiaki

    2015-01-01

    Strains of Bifidobacterium longum, Bifidobacterium breve, and Bifidobacterium animalis are widely used as probiotics in the food industry. Although numerous studies have revealed the properties and functionality of these strains, it is uncertain whether these characteristics are species common or strain specific. To address this issue, we performed a comparative genomic analysis of 49 strains belonging to these three bifidobacterial species to describe their genetic diversity and to evaluate species-level differences. There were 166 common clusters between strains of B. breve and B. longum, whereas there were nine common clusters between strains of B. animalis and B. longum and four common clusters between strains of B. animalis and B. breve. Further analysis focused on carbohydrate metabolism revealed the existence of certain strain-dependent genes, such as those encoding enzymes for host glycan utilisation or certain membrane transporters, and many genes commonly distributed at the species level, as was previously reported in studies with limited strains. As B. longum and B. breve are human-residential bifidobacteria (HRB), whereas B. animalis is a non-HRB species, several of the differences in these species' gene distributions might be the result of their adaptations to the nutrient environment. This information may aid both in selecting probiotic candidates and in understanding their potential function as probiotics. PMID:26236711

  1. The secretome of Acinetobacter baumannii ATCC 17978 type II secretion system reveals a novel plasmid encoded phospholipase that could be implicated in lung colonization.

    PubMed

    Elhosseiny, Noha M; El-Tayeb, Ossama M; Yassin, Aymen S; Lory, Stephen; Attia, Ahmed S

    2016-12-01

    Acinetobacter baumannii infections are compounded with a striking lack of treatment options. In many Gram-negative bacteria, secreted proteins play an important early role in avoiding host defences. Typically, these proteins are targeted to the external environment or into host cells using dedicated transport systems. Despite the fact that medically relevant species of Acinetobacter possess a type II secretion system (T2SS), only recently, its significance as an important pathway for delivering virulence factors has gained attention. Using in silico analysis to characterize the genetic determinants of the T2SS, which are found clustered in other organisms, in Acinetobacter species, they appear to have a unique genetic organization and are distributed throughout the genome. When compared to other T2SS orthologs, individual components of the T2SS apparatus showed the highest similarity to those of Pseudomonas aeruginosa. A mutant of Acinetobacter baumannii strain ATCC 17978 lacking the secretin component of the T2SS (ΔgspD), together with a trans-complemented mutant, were tested in a series of in vitro and in vivo assays to determine the role of T2SS in pathogenicity. The ΔgspD mutant displayed decreased lipolytic activity, associated with attenuated colonization ability in a murine pneumonia model. These phenotypes are linked to LipAN, a novel plasmid-encoded phospholipase, identified through mass spectroscopy as a T2SS substrate. Recombinant LipAN showed specific phospholipase activity in vitro. Proteomics on the T2-dependent secretome of ATCC 17978 strain revealed its potential dedication to the secretion of a number of lipolytic enzymes, among others which could contribute to its virulence. This study highlights the role of T2SS as an active contributor to the virulence of A. baumannii potentially through secretion of a newly identified phospholipase.

  2. The Genetic Analysis of an Acinetobacter johnsonii Clinical Strain Evidenced the Presence of Horizontal Genetic Transfer.

    PubMed

    Montaña, Sabrina; Schramm, Sareda T J; Traglia, German Matías; Chiem, Kevin; Parmeciano Di Noto, Gisela; Almuzara, Marisa; Barberis, Claudia; Vay, Carlos; Quiroga, Cecilia; Tolmasky, Marcelo E; Iriarte, Andrés; Ramírez, María Soledad

    2016-01-01

    Acinetobacter johnsonii rarely causes human infections. While most A. johnsonii isolates are susceptible to virtually all antibiotics, strains harboring a variety of β-lactamases have recently been described. An A. johnsonii Aj2199 clinical strain recovered from a hospital in Buenos Aires produces PER-2 and OXA-58. We decided to delve into its genome by obtaining the whole genome sequence of the Aj2199 strain. Genome comparison studies on Aj2199 revealed 240 unique genes and a close relation to strain WJ10621, isolated from the urine of a patient in China. Genomic analysis showed evidence of horizontal genetic transfer (HGT) events. Forty-five insertion sequences and two intact prophages were found in addition to several resistance determinants such as blaPER-2, blaOXA-58, blaTEM-1, strA, strB, ereA, sul1, aacC2 and a new variant of blaOXA-211, called blaOXA-498. In particular, blaPER-2 and blaTEM-1 are present within the typical contexts previously described in the Enterobacteriaceae family. These results suggest that A. johnsonii actively acquires exogenous DNA from other bacterial species and concomitantly becomes a reservoir of resistance genes.

  3. The Genetic Analysis of an Acinetobacter johnsonii Clinical Strain Evidenced the Presence of Horizontal Genetic Transfer

    PubMed Central

    Montaña, Sabrina; Schramm, Sareda T. J.; Traglia, German Matías; Chiem, Kevin; Parmeciano Di Noto, Gisela; Almuzara, Marisa; Barberis, Claudia; Vay, Carlos; Quiroga, Cecilia; Tolmasky, Marcelo E.; Iriarte, Andrés; Ramírez, María Soledad

    2016-01-01

    Acinetobacter johnsonii rarely causes human infections. While most A. johnsonii isolates are susceptible to virtually all antibiotics, strains harboring a variety of β-lactamases have recently been described. An A. johnsonii Aj2199 clinical strain recovered from a hospital in Buenos Aires produces PER-2 and OXA-58. We decided to delve into its genome by obtaining the whole genome sequence of the Aj2199 strain. Genome comparison studies on Aj2199 revealed 240 unique genes and a close relation to strain WJ10621, isolated from the urine of a patient in China. Genomic analysis showed evidence of horizontal genetic transfer (HGT) events. Forty-five insertion sequences and two intact prophages were found in addition to several resistance determinants such as blaPER-2, blaOXA-58, blaTEM-1, strA, strB, ereA, sul1, aacC2 and a new variant of blaOXA-211, called blaOXA-498. In particular, blaPER-2 and blaTEM-1 are present within the typical contexts previously described in the Enterobacteriaceae family. These results suggest that A. johnsonii actively acquires exogenous DNA from other bacterial species and concomitantly becomes a reservoir of resistance genes. PMID:27548264

  4. Genomic characterization of the Bacillus cereus sensu lato species: backdrop to the evolution of Bacillus anthracis.

    PubMed

    Zwick, Michael E; Joseph, Sandeep J; Didelot, Xavier; Chen, Peter E; Bishop-Lilly, Kimberly A; Stewart, Andrew C; Willner, Kristin; Nolan, Nichole; Lentz, Shannon; Thomason, Maureen K; Sozhamannan, Shanmuga; Mateczun, Alfred J; Du, Lei; Read, Timothy D

    2012-08-01

    The key genes required for Bacillus anthracis to cause anthrax have been acquired recently by horizontal gene transfer. To understand the genetic background for the evolution of B. anthracis virulence, we obtained high-redundancy genome sequences of 45 strains of the Bacillus cereus sensu lato (s.l.) species that were chosen for their genetic diversity within the species based on the existing multilocus sequence typing scheme. From the resulting data, we called more than 324,000 new genes representing more than 12,333 new gene families for this group. The core genome size for the B. cereus s.l. group was ∼1750 genes, with another 2150 genes found in almost every genome constituting the extended core. There was a paucity of genes specific and conserved in any clade. We found no evidence of recent large-scale gene loss in B. anthracis or for unusual accumulation of nonsynonymous DNA substitutions in the chromosome; however, several B. cereus genomes isolated from soil and not previously associated with human disease were degraded to various degrees. Although B. anthracis has undergone an ecological shift within the species, its chromosome does not appear to be exceptional on a macroscopic scale compared with close relatives.

  5. Species Delimitation and Interspecific Relationships of the Genus Orychophragmus (Brassicaceae) Inferred from Whole Chloroplast Genomes

    PubMed Central

    Hu, Huan; Hu, Quanjun; Al-Shehbaz, Ihsan A.; Luo, Xin; Zeng, Tingting; Guo, Xinyi; Liu, Jianquan

    2016-01-01

    Genetic variations from few chloroplast DNA fragments show lower discriminatory power in the delimitation of closely related species and less resolution ability in discerning interspecific relationships than from nrITS. Here we use Orychophragmus (Brassicaceae) as a model system to test the hypothesis that the whole chloroplast genomes (plastomes), with accumulation of more variations despite the slow evolution, can overcome these weaknesses. We used Illumina sequencing technology via a reference-guided assembly to construct complete plastomes of 17 individuals from six putatively assumed species in the genus. All plastomes are highly conserved in genome structure, gene order, and orientation, and they are around 153 kb in length and contain 113 unique genes. However, nucleotide variations are quite substantial to support the delimitation of all sampled species and to resolve interspecific relationships with high statistical supports. As expected, the estimated divergences between major clades and species are lower than those estimated from nrITS probably due to the slow substitution rate of the plastomes. However, the plastome and nrITS phylogenies were contradictory in the placements of most species, thus suggesting that these species may have experienced complex non-bifurcating evolutions with incomplete lineage sorting and/or hybrid introgressions. Overall, our case study highlights the importance of using plastomes to examine species boundaries and establish an independent phylogeny to infer the speciation history of plants. PMID:27999584

  6. Species-wide genome sequence and nucleotide polymorphisms from the model allopolyploid plant Brassica napus.

    PubMed

    Schmutzer, Thomas; Samans, Birgit; Dyrszka, Emmanuelle; Ulpinnis, Chris; Weise, Stephan; Stengel, Doreen; Colmsee, Christian; Lespinasse, Denis; Micic, Zeljko; Abel, Stefan; Duchscherer, Peter; Breuer, Frank; Abbadi, Amine; Leckband, Gunhild; Snowdon, Rod; Scholz, Uwe

    2015-12-08

    Brassica napus (oilseed rape, canola) is one of the world's most important sources of vegetable oil for human nutrition and biofuel, and also a model species for studies investigating the evolutionary consequences of polyploidisation. Strong bottlenecks during its recent origin from interspecific hybridisation, and subsequently through intensive artificial selection, have severely depleted the genetic diversity available for breeding. On the other hand, high-throughput genome profiling technologies today provide unprecedented scope to identify, characterise and utilise genetic diversity in primary and secondary crop gene pools. Such methods also enable implementation of genomic selection strategies to accelerate breeding progress. The key prerequisite is availability of high-quality sequence data and identification of high-quality, genome-wide sequence polymorphisms representing relevant gene pools. We present comprehensive genome resequencing data from a panel of 52 highly diverse natural and synthetic B. napus accessions, along with a stringently selected panel of 4.3 million high-confidence, genome-wide SNPs. The data is of great interest for genomics-assisted breeding and for evolutionary studies on the origins and consequences in allopolyploidisation in plants.

  7. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

    SciTech Connect

    Schmoll, Monika; Dattenböck, Christoph; Carreras-Villaseñor, Nohemí; Mendoza-Mendoza, Artemio; Tisch, Doris; Alemán, Mario Ivan; Baker, Scott E.; Brown, Christopher; Cervantes-Badillo, Mayte Guadalupe; Cetz-Chel, José; Cristobal-Mondragon, Gema Rosa; Delaye, Luis; Esquivel-Naranjo, Edgardo Ulises; Frischmann, Alexa; Gallardo-Negrete, Jose de Jesus; García-Esquivel, Monica; Gomez-Rodriguez, Elida Yazmin; Greenwood, David R.; Hernández-Oñate, Miguel; Kruszewska, Joanna S.; Lawry, Robert; Mora-Montes, Hector M.; Muñoz-Centeno, Tania; Nieto-Jacobo, Maria Fernanda; Nogueira Lopez, Guillermo; Olmedo-Monfil, Vianey; Osorio-Concepcion, Macario; Piłsyk, Sebastian; Pomraning, Kyle R.; Rodriguez-Iglesias, Aroa; Rosales-Saavedra, Maria Teresa; Sánchez-Arreguín, J. Alejandro; Seidl-Seiboth, Verena; Stewart, Alison; Uresti-Rivera, Edith Elena; Wang, Chih-Li; Wang, Ting-Fang; Zeilinger, Susanne; Casas-Flores, Sergio; Herrera-Estrella, Alfredo

    2016-02-10

    SUMMARY

    The genusTrichodermacontains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for “hot topic” research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism inT. reesei,T. atroviride, andT. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of eachTrichodermaspecies discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved inN-linked glycosylation was detected, as were indications for the ability ofTrichodermaspp. to generate hybrid galactose-containingN-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique toTrichoderma, and these warrant further investigation. We found interesting expansions in theThe first cases of human bacteremia caused by Acinetobacter seifertii in Japan.

    PubMed

    Kishii, Kozue; Kikuchi, Ken; Tomida, Junko; Kawamura, Yoshiaki; Yoshida, Atsushi; Okuzumi, Katsuko; Moriya, Kyoji

    2016-05-01

    Acinetobacter seifertii, a novel species of Acinetobacter, was first reported in 2015. A. seifertii strains were isolated from human clinical specimens (blood, respiratory tract, and ulcer) and hospital environments. Here, we report the first cases of bacteremia caused by A. seifertii in patients with catheter-related bloodstream infection in Japan. The patients favorably recovered, without any complications, after removal of the peripheral intravenous catheters and administration of antibiotics. The pathogens were initially identified as Acinetobacter baumannii, using phenotypic methods and the MicroScan Walkaway System; however, rpoB gene sequence analysis indicated 99.54% similarity to A. seifertii. Moreover, antimicrobial susceptibility testing revealed that one of the strains was not susceptible to gentamicin and ceftazidime. Our report shows that Acinetobacter species other than A. baumannii can also cause nosocomial infections and that accurate methods for the identification of causative agents should be developed.

  8. Insight into infrageneric circumscription through complete chloroplast genome sequences of two Trillium species

    PubMed Central

    Kim, Sang-Chul; Kim, Jung Sung; Kim, Joo-Hwan

    2016-01-01

    Genomic events including gene loss, duplication, pseudogenization and rearrangement in plant genomes are valuable sources for exploring and understanding the process of evolution in angiosperms. The family Melanthiaceae is distributed in temperate regions of the Northern Hemisphere and divided into five tribes (Heloniadeae, Chionographideae, Xerophylleae, Melanthieae and Parideae) based on the molecular phylogenetic analyses. At present, complete chloroplast genomes of the Melanthiaceae have been reported from three species. In the previous genomic study of Liliales, a trnI-CAU gene duplication event was reported from Paris verticillata, a member of Parideae. To clarify the significant genomic events of the tribe Parideae, we analysed the complete chloroplast genome sequences of two Trillium species representing two subgenera: Trillium and Phyllantherum. In Trillium tschonoskii (subgenus Trillium), the circular double-stranded cpDNA sequence of 156 852 bp consists of two inverted repeat (IR) regions of 26 501 bp each, a large single-copy (LSC) region of 83 981 bp and a small single-copy (SSC) region of 19 869 bp. The chloroplast genome sequence of T. maculatum (subgenus Phyllantherum) is 157 359 bp in length, consisting of two IRs (25 535 bp), one SSC (19 949 bp) and one LSC (86 340 bp), and is longer than that of T. tschonoskii. The results showed that the cpDNAs of Parideae are highly conserved across genome structure, gene order and contents. However, the chloroplast genome of T. maculatum contained a 3.4-kb inverted sequence between ndhC and rbcL in the LSC region, and it was a unique feature for subgenera Phyllantherum. In addition, we found three different types of gene duplication in the intergenic spacer between rpl23 and ycf2 containing trnI-CAU, which were in agreement with the circumscription of subgenera and sections in Parideae excluding T. govanianum. These genomic features provide informative molecular markers for identifying the infrageneric taxa of

  9. Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires.

    PubMed

    Burstein, David; Amaro, Francisco; Zusman, Tal; Lifshitz, Ziv; Cohen, Ofir; Gilbert, Jack A; Pupko, Tal; Shuman, Howard A; Segal, Gil

    2016-02-01

    Infection by the human pathogen Legionella pneumophila relies on the translocation of ∼ 300 virulence proteins, termed effectors, which manipulate host cell processes. However, almost no information exists regarding effectors in other Legionella pathogens. Here we sequenced, assembled and characterized the genomes of 38 Legionella species and predicted their effector repertoires using a previously validated machine learning approach. This analysis identified 5,885 predicted effectors. The effector repertoires of different Legionella species were found to be largely non-overlapping, and only seven core effectors were shared by all species studied. Species-specific effectors had atypically low GC content, suggesting exogenous acquisition, possibly from the natural protozoan hosts of these species. Furthermore, we detected numerous new conserved effector domains and discovered new domain combinations, which allowed the inference of as yet undescribed effector functions. The effector collection and network of domain architectures described here can serve as a roadmap for future studies of effector function and evolution.

  10. Seroprevalence and genomic divergence of circulating strains of feline immunodeficiency virus among Felidae and Hyaenidae species.

    PubMed

    Troyer, Jennifer L; Pecon-Slattery, Jill; Roelke, Melody E; Johnson, Warren; VandeWoude, Sue; Vazquez-Salat, Nuria; Brown, Meredith; Frank, Laurence; Woodroffe, Rosie; Winterbach, Christiaan; Winterbach, Hanlie; Hemson, Graham; Bush, Mitch; Alexander, Kathleen A; Revilla, Eloy; O'Brien, Stephen J

    2005-07-01

    Feline immunodeficiency virus (FIV) infects numerous wild and domestic feline species and is closely related to human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV). Species-specific strains of FIV have been described for domestic cat (Felis catus), puma (Puma concolor), lion (Panthera leo), leopard (Panthera pardus), and Pallas' cat (Otocolobus manul). Here, we employ a three-antigen Western blot screening (domestic cat, puma, and lion FIV antigens) and PCR analysis to survey worldwide prevalence, distribution, and genomic differentiation of FIV based on 3,055 specimens from 35 Felidae and 3 Hyaenidae species. Although FIV infects a wide variety of host species, it is confirmed to be endemic in free-ranging populations of nine Felidae and one Hyaenidae species. These include the large African carnivores (lion, leopard, cheetah, and spotted hyena), where FIV is widely distributed in multiple populations; most of the South American felids (puma, jaguar, ocelot, margay, Geoffroy's cat, and tigrina), which maintain a lower FIV-positive level throughout their range; and two Asian species, the Pallas' cat, which has a species-specific strain of FIV, and the leopard cat, which has a domestic cat FIV strain in one population. Phylogenetic analysis of FIV proviral sequence demonstrates that most species for which FIV is endemic harbor monophyletic, genetically distinct species-specific FIV strains, suggesting that FIV transfer between cat species has occurred in the past but is quite infrequent today.

  11. Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites

    PubMed Central

    Grijseels, Sietske; Nielsen, Jens Christian; Randelovic, Milica; Nielsen, Jens; Nielsen, Kristian Fog; Workman, Mhairi; Frisvad, Jens Christian

    2016-01-01

    A new soil-borne species belonging to the Penicillium section Canescentia is described, Penicillium arizonense sp. nov. (type strain CBS 141311T = IBT 12289T). The genome was sequenced and assembled into 33.7 Mb containing 12,502 predicted genes. A phylogenetic assessment based on marker genes confirmed the grouping of P. arizonense within section Canescentia. Compared to related species, P. arizonense proved to encode a high number of proteins involved in carbohydrate metabolism, in particular hemicellulases. Mining the genome for genes involved in secondary metabolite biosynthesis resulted in the identification of 62 putative biosynthetic gene clusters. Extracts of P. arizonense were analysed for secondary metabolites and austalides, pyripyropenes, tryptoquivalines, fumagillin, pseurotin A, curvulinic acid and xanthoepocin were detected. A comparative analysis against known pathways enabled the proposal of biosynthetic gene clusters in P. arizonense responsible for the synthesis of all detected compounds except curvulinic acid. The capacity to produce biomass degrading enzymes and the identification of a high chemical diversity in secreted bioactive secondary metabolites, offers a broad range of potential industrial applications for the new species P. arizonense. The description and availability of the genome sequence of P. arizonense, further provides the basis for biotechnological exploitation of this species. PMID:27739446

  12. Gene Duplication, Population Genomics, and Species-Level Differentiation within a Tropical Mountain Shrub

    PubMed Central

    Mastretta-Yanes, Alicia; Zamudio, Sergio; Jorgensen, Tove H.; Arrigo, Nils; Alvarez, Nadir; Piñero, Daniel; Emerson, Brent C.

    2014-01-01

    Gene duplication leads to paralogy, which complicates the de novo assembly of genotyping-by-sequencing (GBS) data. The issue of paralogous genes is exacerbated in plants, because they are particularly prone to gene duplication events. Paralogs are normally filtered from GBS data before undertaking population genomics or phylogenetic analyses. However, gene duplication plays an important role in the functional diversification of genes and it can also lead to the formation of postzygotic barriers. Using populations and closely related species of a tropical mountain shrub, we examine 1) the genomic differentiation produced by putative orthologs, and 2) the distribution of recent gene duplication among lineages and geography. We find high differentiation among populations from isolated mountain peaks and species-level differentiation within what is morphologically described as a single species. The inferred distribution of paralogs among populations is congruent with taxonomy and shows that GBS could be used to examine recent gene duplication as a source of genomic differentiation of nonmodel species. PMID:25223767

  13. Genome-wide Evidence Reveals that African and Eurasian Golden Jackals Are Distinct Species.

    PubMed

    Koepfli, Klaus-Peter; Pollinger, John; Godinho, Raquel; Robinson, Jacqueline; Lea, Amanda; Hendricks, Sarah; Schweizer, Rena M; Thalmann, Olaf; Silva, Pedro; Fan, Zhenxin; Yurchenko, Andrey A; Dobrynin, Pavel; Makunin, Alexey; Cahill, James A; Shapiro, Beth; Álvares, Francisco; Brito, José C; Geffen, Eli; Leonard, Jennifer A; Helgen, Kristofer M; Johnson, Warren E; O'Brien, Stephen J; Van Valkenburgh, Blaire; Wayne, Robert K

    2015-08-17

    The golden jackal of Africa (Canis aureus) has long been considered a conspecific of jackals distributed throughout Eurasia, with the nearest source populations in the Middle East. However, two recent reports found that mitochondrial haplotypes of some African golden jackals aligned more closely to gray wolves (Canis lupus), which is surprising given the absence of gray wolves in Africa and the phenotypic divergence between the two species. Moreover, these results imply the existence of a previously unrecognized phylogenetically distinct species despite a long history of taxonomic work on African canids. To test the distinct-species hypothesis and understand the evolutionary history that would account for this puzzling result, we analyzed extensive genomic data including mitochondrial genome sequences, sequences from 20 autosomal loci (17 introns and 3 exon segments), microsatellite loci, X- and Y-linked zinc-finger protein gene (ZFX and ZFY) sequences, and whole-genome nuclear sequences in African and Eurasian golden jackals and gray wolves. Our results provide consistent and robust evidence that populations of golden jackals from Africa and Eurasia represent distinct monophyletic lineages separated for more than one million years, sufficient to merit formal recognition as different species: C. anthus (African golden wolf) and C. aureus (Eurasian golden jackal). Using morphologic data, we demonstrate a striking morphologic similarity between East African and Eurasian golden jackals, suggesting parallelism, which may have misled taxonomists and likely reflects uniquely intense interspecific competition in the East African carnivore guild. Our study shows how ecology can confound taxonomy if interspecific competition constrains size diversification.

  14. Comparative Genomic Analysis of the Streptococcus dysgalactiae Species Group: Gene Content, Molecular Adaptation, and Promoter Evolution

    PubMed Central

    Suzuki, Haruo; Lefébure, Tristan; Hubisz, Melissa Jane; Pavinski Bitar, Paulina; Lang, Ping; Siepel, Adam; Stanhope, Michael J.

    2011-01-01

    Comparative genomics of closely related bacterial species with different pathogenesis and host preference can provide a means of identifying the specifics of adaptive differences. Streptococcus dysgalactiae (SD) is comprised of two subspecies: S. dysgalactiae subsp. equisimilis is both a human commensal organism and a human pathogen, and S. dysgalactiae subsp. dysgalactiae is strictly an animal pathogen. Here, we present complete genome sequences for both taxa, with analyses involving other species of Streptococcus but focusing on adaptation in the SD species group. We found little evidence for enrichment in biochemical categories of genes carried by each SD strain, however, differences in the virulence gene repertoire were apparent. Some of the differences could be ascribed to prophage and integrative conjugative elements. We identified approximately 9% of the nonrecombinant core genome to be under positive selection, some of which involved known virulence factors in other bacteria. Analyses of proteomes by pooling data across genes, by biochemical category, clade, or branch, provided evidence for increased rates of evolution in several gene categories, as well as external branches of the tree. Promoters were primarily evolving under purifying selection but with certain categories of genes evolving faster. Many of these fast-evolving categories were the same as those associated with rapid evolution in proteins. Overall, these results suggest that adaptation to changing environments and new hosts in the SD species group has involved the acquisition of key virulence genes along with selection of orthologous protein-coding loci and operon promoters. PMID:21282711

  15. The Biofuel Feedstock Genomics Resource: a web-based portal and database to enable functional genomics of plant biofuel feedstock species.

    PubMed

    Childs, Kevin L; Konganti, Kranti; Buell, C Robin

    2012-01-01

    Major feedstock sources for future biofuel production are likely to be high biomass producing plant species such as poplar, pine, switchgrass, sorghum and maize. One active area of research in these species is genome-enabled improvement of lignocellulosic biofuel feedstock quality and yield. To facilitate genomic-based investigations in these species, we developed the Biofuel Feedstock Genomic Resource (BFGR), a database and web-portal that provides high-quality, uniform and integrated functional annotation of gene and transcript assembly sequences from species of interest to lignocellulosic biofuel feedstock researchers. The BFGR includes sequence data from 54 species and permits researchers to view, analyze and obtain annotation at the gene, transcript, protein and genome level. Annotation of biochemical pathways permits the identification of key genes and transcripts central to the improvement of lignocellulosic properties in these species. The integrated nature of the BFGR in terms of annotation methods, orthologous/paralogous relationships and linkage to seven species with complete genome sequences allows comparative analyses for biofuel feedstock species with limited sequence resources. Database URL: http://bfgr.plantbiology.msu.edu.

  16. Analysis of Genomic DNAs from Nine Rosaceae Species Using Surface-Enhanced Raman Scattering.

    PubMed

    Lu, Qiu; Lang, Tao; Fan, Shuguo; Chen, Wen; Zang, Deqing; Chen, Jing; Shi, Minzhen

    2015-12-01

    Surface-enhanced Raman scattering (SERS) of genomic DNA was used to determine genetic relationships and species identification of nine plants from three subfamilies of Rosaceae. Genomic DNA was extracted, and the SERS spectra were obtained by using a nanosilver collosol at an excitation wavelength of 785 nm. Adenine and ribodesose were the active sites of genomic DNAs in the silver surface-enhanced Raman spectra. The strong peak at 714 cm(-1) was assigned to the stretching vibration of adenine, the strong peak at 1011cm(-1) contributed to the stretching vibration of the deoxyribose and the scissoring vibrations of cytosine, and the strong peak at 625 cm(-1) is the stretching vibration of glycosidic bond and the scissoring vibrations of guanine. The three-dimensional plot of the first, second, and third principal components showed that the nine species could be classified into three categories (three subfamilies), consistent with the traditional classification. The model of the hierarchical cluster combined with the principal component of the second derivative was more reasonable. The results of the cluster analysis showed that apricot (Prunus armeniaca L.) and cherry (Prunus seudocerasus Lindl.) were clustered into one category (Prunoideae); firethorn (Firethorn fortuneana Li.), loquat (Eriobotrya japonica Lindl.), apple (Malus pumila Mill.), and crabapple (Malus hallianna Koehne.) were clustered into a second category (Pomoideae); and potentilla (Potentilla fulgens Wall.), rose (Rosa chinensis Jacd.), and strawberry (Fragaria chiloensis Duchesne.) were clustered into a third category (Rosoideae). These classifications were in accordance with the traditional classification with a correction rate of clustering of 100%. The correct rate of species identification was 100%. These five main results indicate that the genetic relationship and species identification of nine Rosaceae species could be determined by using SERS spectra of their genomic DNAs.

  17. Characterization and identification of newly isolated Acinetobacter baumannii strain serdang 1 for phenol removal

    NASA Astrophysics Data System (ADS)

    Yadzir, Z. H. M.; Shukor, M. Y.; Nazir, M. S.; Abdullah, M. A.

    2012-09-01

    A new indigenous bacterial strain from Malaysian soil contaminated with petroleum waste had been successfully isolated, characterized and identified for phenol removal. The gram negative bacteria showed 98% identity with Acinetobacter baumannii based on Biolog{trade mark, serif} Identification System and the determination of a partial 16S ribosomal RNA (rRNA) sequence. The isolate clustered with species belonging to Acinetobacter clade in a 16S rDNA-based neighbour-joining phylogenetic tree.

  18. Draft Genome Sequences of Escherichia coli Isolates from Wounded Military Personnel.

    PubMed

    Arivett, Brock A; Ream, Dave C; Fiester, Steven E; Kidane, Destaalem; Actis, Luis A

    2016-08-11

    Members of the Escherichia coli bacterial family have been grouped as ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens because of their extensive drug resistance phenotypes and increasing threat to human health. The genomes of six extended-spectrum β-lactamase (ESBL)-producing E. coli strains isolated from wounded military personnel were sequenced and annotated.

  19. Cyto-nuclear genomic dissociation and the African elephant species question.

    PubMed

    Roca, Alfred L; Georgiadis, Nicholas; O'Brien, Stephen J

    2007-07-01

    Studies of skull morphology and of nuclear DNA have strongly concluded that African elephants comprise two species. Nonetheless, Debruyne (2005) has suggested a single-species model for Loxodonta based on the polyphyly of a single genetic locus, mitochondrial DNA (mtDNA). Discordant patterns between mitochondrial and nuclear DNA markers were subsequently reported in some African savanna elephant populations, further supporting a two-species model, and prompting us to re-examine here the geographic distribution of different elephant morphotypes and their relationship to nuclear and mtDNA phylogeographic patterns. We used exact tests to compare the distribution of forest elephant-typical and savanna elephant-typical characteristics across eight published datasets containing morphological, mtDNA or nuclear DNA data for African elephants. Among the elephants examined by Debruyne (2005), we found that patterns of forest vs. savanna characteristics were significantly different (p < 10(-5)) between mtDNA and morphology, suggesting the presence of cyto-nuclear genomic dissociation. We show that the eight African elephant continent-wide datasets compared, including that of Debruyne (2005), together support a two-species model with cyto-nuclear genomic dissociation rather than a one-species model, and together indicate that Africa harbors two species of elephant.

  1. Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts

    PubMed Central

    Ma, Liang; Chen, Zehua; Huang, Da Wei; Kutty, Geetha; Ishihara, Mayumi; Wang, Honghui; Abouelleil, Amr; Bishop, Lisa; Davey, Emma; Deng, Rebecca; Deng, Xilong; Fan, Lin; Fantoni, Giovanna; Fitzgerald, Michael; Gogineni, Emile; Goldberg, Jonathan M.; Handley, Grace; Hu, Xiaojun; Huber, Charles; Jiao, Xiaoli; Jones, Kristine; Levin, Joshua Z.; Liu, Yueqin; Macdonald, Pendexter; Melnikov, Alexandre; Raley, Castle; Sassi, Monica; Sherman, Brad T.; Song, Xiaohong; Sykes, Sean; Tran, Bao; Walsh, Laura; Xia, Yun; Yang, Jun; Young, Sarah; Zeng, Qiandong; Zheng, Xin; Stephens, Robert; Nusbaum, Chad; Birren, Bruce W.; Azadi, Parastoo; Lempicki, Richard A.; Cuomo, Christina A.; Kovacs, Joseph A.

    2016-01-01

    Pneumocystis jirovecii is a major cause of life-threatening pneumonia in immunosuppressed patients including transplant recipients and those with HIV/AIDS, yet surprisingly little is known about the biology of this fungal pathogen. Here we report near complete genome assemblies for three Pneumocystis species that infect humans, rats and mice. Pneumocystis genomes are highly compact relative to other fungi, with substantial reductions of ribosomal RNA genes, transporters, transcription factors and many metabolic pathways, but contain expansions of surface proteins, especially a unique and complex surface glycoprotein superfamily, as well as proteases and RNA processing proteins. Unexpectedly, the key fungal cell wall components chitin and outer chain N-mannans are absent, based on genome content and experimental validation. Our findings suggest that Pneumocystis has developed unique mechanisms of adaptation to life exclusively in mammalian hosts, including dependence on the lungs for gas and nutrients and highly efficient strategies to escape both host innate and acquired immune defenses. PMID:26899007

  2. Genome sequence of a pathogenic isolate of monkey B virus (species Macacine herpesvirus 1).

    PubMed

    Ohsawa, Kazutaka; Black, Darla; Ohsawa, Makiko; Eberle, R

    2014-10-01

    The only genome sequence for monkey B virus (BV; species Macacine herpesvirus 1) is that of an attenuated vaccine strain originally isolated from a rhesus monkey (BVrh). Here we report the genome sequence of a virulent BV strain isolated from a cynomolgus macaque (BVcy). The overall genome organization is the same, although sequence differences exist. The greatest sequence divergence is located in non-coding areas of the long and short repeat regions. Like BVrh, BVcy has duplicated Ori elements and lacks an ORF corresponding to the γ34.5 gene of herpes simplex virus. Nine of ten miRNAs and the majority of ORFs are conserved between BVrh and BVcy. The most divergent genes are several membrane-associated proteins and those encoding immediate early proteins.

  3. The Complete Genome of Brucella Suis 019 Provides Insights on Cross-Species Infection

    PubMed Central

    Wang, Yuanzhi; Wang, Zhen; Chen, Xin; Zhang, Hui; Guo, Fei; Zhang, Ke; Feng, Hanping; Gu, Wenyi; Wu, Changxin; Ma, Lei; Li, Tiansen; Chen, Chuangfu; Gao, Shan

    2016-01-01

    Brucella species are the most important zoonotic pathogens worldwide and cause considerable harm to humans and animals. In this study, we presented the complete genome of B. suis 019 isolated from sheep (ovine) with epididymitis. B. suis 019 has a rough phenotype and can infect sheep, rhesus monkeys and possibly humans. The comparative genome analysis demonstrated that B. suis 019 is closest to the vaccine strain B. suis bv. 1 str. S2. Further analysis associated the rsh gene to the pathogenicity of B. suis 019, and the WbkA gene to the rough phenotype of B. suis 019. The 019 complete genome data was deposited in the GenBank database with ID PRJNA308608. PMID:26821047

  4. Genomic distribution of AFLP markers relative to gene locations for different eukaryotic species

    PubMed Central

    2013-01-01

    Background Amplified fragment length polymorphism (AFLP) markers are frequently used for a wide range of studies, such as genome-wide mapping, population genetic diversity estimation, hybridization and introgression studies, phylogenetic analyses, and detection of signatures of selection. An important issue to be addressed for some of these fields is the distribution of the markers across the genome, particularly in relation to gene sequences. Results Using in-silico restriction fragment analysis of the genomes of nine eukaryotic species we characterise the distribution of AFLP fragments across the genome and, particularly, in relation to gene locations. First, we identify the physical position of markers across the chromosomes of all species. An observed accumulation of fragments around (peri) centromeric regions in some species is produced by repeated sequences, and this accumulation disappears when AFLP bands rather than fragments are considered. Second, we calculate the percentage of AFLP markers positioned within gene sequences. For the typical EcoRI/MseI enzyme pair, this ranges between 28 and 87% and is usually larger than that expected by chance because of the higher GC content of gene sequences relative to intergenic ones. In agreement with this, the use of enzyme pairs with GC-rich restriction sites substantially increases the above percentages. For example, using the enzyme system SacI/HpaII, 86% of AFLP markers are located within gene sequences in A. thaliana, and 100% of markers in Plasmodium falciparun. We further find that for a typical trait controlled by 50 genes of average size, if 1000 AFLPs are used in a study, the number of those within 1 kb distance from any of the genes would be only about 1–2, and only about 50% of the genes would have markers within that distance. Conclusions The high coverage of AFLP markers across the genomes and the high proportion of markers within or close to gene sequences make them suitable for genome scans and

  5. Genomic architecture of phenotypic divergence between two hybridizing plant species along an elevational gradient.

    PubMed

    Brennan, Adrian C; Hiscock, Simon J; Abbott, Richard J

    2016-01-01

    Knowledge of the genetic basis of phenotypic divergence between species and how such divergence is caused and maintained is crucial to an understanding of speciation and the generation of biodiversity. The hybrid zone between Senecio aethnensis and S. chrysanthemifolius on Mount Etna, Sicily, provides a well-studied example of species divergence in response to conditions at different elevations, despite hybridization and gene flow. Here, we investigate the genetic architecture of divergence between these two species using a combination of quantitative trait locus (QTL) mapping and genetic differentiation measures based on genetic marker analysis. A QTL architecture characterized by physical QTL clustering, epistatic interactions between QTLs, and pleiotropy was identified, and is consistent with the presence of divergent QTL complexes resistant to gene flow. A role for divergent selection between species was indicated by significant negative associations between levels of interspecific genetic differentiation at mapped marker gene loci and map distance from QTLs and hybrid incompatibility loci. Within-species selection contributing to interspecific differentiation was evidenced by negative associations between interspecific genetic differentiation and genetic diversity within species. These results show that the two Senecio species, while subject to gene flow, maintain divergent genomic regions consistent with local selection within species and selection against hybrids between species which, in turn, contribute to the maintenance of their distinct phenotypic differences.

  6. Genomic architecture of phenotypic divergence between two hybridizing plant species along an elevational gradient

    PubMed Central

    Brennan, Adrian C.; Hiscock, Simon J.; Abbott, Richard J.

    2016-01-01

    Knowledge of the genetic basis of phenotypic divergence between species and how such divergence is caused and maintained is crucial to an understanding of speciation and the generation of biodiversity. The hybrid zone between Senecio aethnensis and S. chrysanthemifolius on Mount Etna, Sicily, provides a well-studied example of species divergence in response to conditions at different elevations, despite hybridization and gene flow. Here, we investigate the genetic architecture of divergence between these two species using a combination of quantitative trait locus (QTL) mapping and genetic differentiation measures based on genetic marker analysis. A QTL architecture characterized by physical QTL clustering, epistatic interactions between QTLs, and pleiotropy was identified, and is consistent with the presence of divergent QTL complexes resistant to gene flow. A role for divergent selection between species was indicated by significant negative associations between levels of interspecific genetic differentiation at mapped marker gene loci and map distance from QTLs and hybrid incompatibility loci. Within-species selection contributing to interspecific differentiation was evidenced by negative associations between interspecific genetic differentiation and genetic diversity within species. These results show that the two Senecio species, while subject to gene flow, maintain divergent genomic regions consistent with local selection within species and selection against hybrids between species which, in turn, contribute to the maintenance of their distinct phenotypic differences. PMID:27083198

  7. Comparative genomics of two jute species and insight into fibre biogenesis.

    PubMed

    Islam, Md Shahidul; Saito, Jennifer A; Emdad, Emdadul Mannan; Ahmed, Borhan; Islam, Mohammad Moinul; Halim, Abdul; Hossen, Quazi Md Mosaddeque; Hossain, Md Zakir; Ahmed, Rasel; Hossain, Md Sabbir; Kabir, Shah Md Tamim; Khan, Md Sarwar Alam; Khan, Md Mursalin; Hasan, Rajnee; Aktar, Nasima; Honi, Ummay; Islam, Rahin; Rashid, Md Mamunur; Wan, Xuehua; Hou, Shaobin; Haque, Taslima; Azam, Muhammad Shafiul; Moosa, Mahdi Muhammad; Elias, Sabrina M; Hasan, A M Mahedi; Mahmood, Niaz; Shafiuddin, Md; Shahid, Saima; Shommu, Nusrat Sharmeen; Jahan, Sharmin; Roy, Saroj; Chowdhury, Amlan; Akhand, Ashikul Islam; Nisho, Golam Morshad; Uddin, Khaled Salah; Rabeya, Taposhi; Hoque, S M Ekramul; Snigdha, Afsana Rahman; Mortoza, Sarowar; Matin, Syed Abdul; Islam, Md Kamrul; Lashkar, M Z H; Zaman, Mahboob; Yuryev, Anton; Uddin, Md Kamal; Rahman, Md Sharifur; Haque, Md Samiul; Alam, Md Monjurul; Khan, Haseena; Alam, Maqsudul

    2017-01-30

    Jute (Corchorus sp.) is one of the most important sources of natural fibre, covering ∼80% of global bast fibre production(1). Only Corchorus olitorius and Corchorus capsularis are commercially cultivated, though there are more than 100 Corchorus species(2) in the Malvaceae family. Here we describe high-quality draft genomes of these two species and their comparisons at the functional genomics level to support tailor-designed breeding. The assemblies cover 91.6% and 82.2% of the estimated genome sizes for C. olitorius and C. capsularis, respectively. In total, 37,031 C. olitorius and 30,096 C. capsularis genes are identified, and most of the genes are validated by cDNA and RNA-seq data. Analyses of clustered gene families and gene collinearity show that jute underwent shared whole-genome duplication ∼18.66 million years (Myr) ago prior to speciation. RNA expression analysis from isolated fibre cells reveals the key regulatory and structural genes involved in fibre formation. This work expands our understanding of the molecular basis of fibre formation laying the foundation for the genetic improvement of jute.

  8. Two recently sequenced vertebrate genomes are contaminated with apicomplexan species of the Sarcocystidae family.

    PubMed

    Orosz, Ferenc

    2015-11-01

    This paper highlights a general problem, namely that host genome sequences can easily be contaminated with parasite sequences, thus careful isolation of genetic material and careful bioinformatics analysis are needed in all cases. Two recently published genomes are shown here to be contaminated with sequences of apicomplexan parasites which belong to the Sarcocystidae family. Sequences of the characteristic apicomplexan organelle, the apicoplast, were used as queries in BLASTN searches against nucleotide sequences of various animal groups looking for possible contamination. Draft genomes of a bird, Colinus virginianus (Halley et al., 2014), and a bat, Myotis davidii (Zhang et al., 2013) were found to contain at least six and 17 contigs, respectively, originating from the apicoplast of an apicomplexan species, and other genes specific to this phylum can also be found in the published genomes. Obviously, the sources of the genetic material, the muscle and the kidney of the animals, respectively, contained the parasitic cysts. Phylogenetic analyses using 18S rRNA and internal transcribed spacer 1 genes show that the parasite contaminating C. virginianus is a species of Sarcocystis related to ones known to cycle between avian and mammalian hosts. In the case of M. davidii it belongs to the Nephroisospora genus, the only member of which, Nephroisospora eptesici, has been recently identified from the kidney of big brown bats (Eptesicus fuscus).

  9. Studies on genome relationship and species-specific PCR marker for Dasypyrum breviaristatum in Triticeae.

    PubMed

    Yang, Zu-Jun; Liu, Cheng; Feng, Juan; Li, Guang-Rong; Zhou, Jian-Ping; Deng, Ke-Jun; Ren, Zheng-Long

    2006-12-01

    Dasypyrum breviaristatum and nine related species in Triticeae were analyzed using the random amplified polymorphic DNA (RAPD) technique, in order to understand the genetic relationship and to develop species specific markers. The genome relationship dendrogram shows that D. breviaristatum and D. villosum could not be grouped together, indicating that D. breviaristatum was unlikely to be directly derived from D. villosum, while D. breviaristatum was closest to Thinopyrum intermedium, which implied that they might have similar breeding behaviors when introducing their chromatins into wheat. A D. breviaristatum genome specific RAPD product of 1182bp, was cloned and designated as pDb12H. Sequence analysis revealed that pDb12H was strongly homologuos to a long terminal repeat (LTR) Sabrina retrotransposon newly reported in Hordeum. The pDb12H was converted into a PCR based marker, which allows effectively monitoring the D. breviaristatum chromatin introgression into wheat. Fluorescence in situ hybridization (FISH) suggested that pDb12H was specifically hybridized throughout all D. breviaristatum chromosomes arms except for the terminal and centromeric regions, which can be used to characterize wheat -D. breviaristatum chromosome translocation. The genomes repetitive element will also be useful to study gene interactions between the wheat and alien genomes after the polyploidization.

  10. The complete mitochondrial genomes of five Eimeria species infecting domestic rabbits.

    PubMed

    Liu, Guo-Hua; Tian, Si-Qin; Cui, Ping; Fang, Su-Fang; Wang, Chun-Ren; Zhu, Xing-Quan

    2015-12-01

    Rabbit coccidiosis caused by members of the genus Eimeria can cause enormous economic impact worldwide, but the genetics, epidemiology and biology of these parasites remain poorly understood. In the present study, we sequenced and annotated the complete mitochondrial (mt) genomes of five Eimeria species that commonly infect the domestic rabbits. The complete mt genomes of Eimeria intestinalis, Eimeria flavescens, Eimeria media, Eimeria vejdovskyi and Eimeria irresidua were 6261bp, 6258bp, 6168bp, 6254bp, 6259bp in length, respectively. All of the mt genomes consist of 3 genes for proteins (cytb, cox1, and cox3), 14 gene fragments for the large subunit (LSU) rRNA and 11 gene fragments for the small subunit (SSU) rRNA, but no transfer RNA (tRNA) genes. The gene order of the mt genomes is similar to that of Plasmodium, but distinct from Haemosporida and Theileria. Phylogenetic analyses based on full nucleotide sequences using Bayesian analysis revealed that the monophyly of the Eimeria of rabbits was strongly statistically supported with a Bayesian posterior probabilities. These data provide novel mtDNA markers for studying the population genetics and molecular epidemiology of the Eimeria species, and should have implications for the molecular diagnosis, prevention and control of coccidiosis in rabbits.

  11. miReader: Discovering Novel miRNAs in Species without Sequenced Genome

    PubMed Central

    2013-01-01

    Along with computational approaches, NGS led technologies have caused a major impact upon the discoveries made in the area of miRNA biology, including novel miRNAs identification. However, to this date all microRNA discovery tools compulsorily depend upon the availability of reference or genomic sequences. Here, for the first time a novel approach, miReader, has been introduced which could discover novel miRNAs without any dependence upon genomic/reference sequences. The approach used NGS read data to build highly accurate miRNA models, molded through a Multi-boosting algorithm with Best-First Tree as its base classifier. It was comprehensively tested over large amount of experimental data from wide range of species including human, plants, nematode, zebrafish and fruit fly, performing consistently with >90% accuracy. Using the same tool over Illumina read data for Miscanthus, a plant whose genome is not sequenced; the study reported 21 novel mature miRNA duplex candidates. Considering the fact that miRNA discovery requires handling of high throughput data, the entire approach has been implemented in a standalone parallel architecture. This work is expected to cause a positive impact over the area of miRNA discovery in majority of species, where genomic sequence availability would not be a compulsion any more. PMID:23805282

  12. Genome sequencing reveals widespread virulence gene exchange among human Neisseria species.

    PubMed

    Marri, Pradeep Reddy; Paniscus, Mary; Weyand, Nathan J; Rendón, María A; Calton, Christine M; Hernández, Diana R; Higashi, Dustin L; Sodergren, Erica; Weinstock, George M; Rounsley, Steven D; So, Magdalene

    2010-07-28

    Commensal bacteria comprise a large part of the microbial world, playing important roles in human development, health and disease. However, little is known about the genomic content of commensals or how related they are to their pathogenic counterparts. The genus Neisseria, containing both commensal and pathogenic species, provides an excellent opportunity to study these issues. We undertook a comprehensive sequencing and analysis of human commensal and pathogenic Neisseria genomes. Commensals have an extensive repertoire of virulence alleles, a large fraction of which has been exchanged among Neisseria species. Commensals also have the genetic capacity to donate DNA to, and take up DNA from, other Neisseria. Our findings strongly suggest that commensal Neisseria serve as reservoirs of virulence alleles, and that they engage extensively in genetic exchange.

  13. Genome Sequencing Reveals Widespread Virulence Gene Exchange among Human Neisseria Species

    PubMed Central

    Marri, Pradeep Reddy; Paniscus, Mary; Hernández, Diana R.; Higashi, Dustin L.; Sodergren, Erica; Weinstock, George M.; Rounsley, Steven D.; So, Magdalene

    2010-01-01

    Commensal bacteria comprise a large part of the microbial world, playing important roles in human development, health and disease. However, little is known about the genomic content of commensals or how related they are to their pathogenic counterparts. The genus Neisseria, containing both commensal and pathogenic species, provides an excellent opportunity to study these issues. We undertook a comprehensive sequencing and analysis of human commensal and pathogenic Neisseria genomes. Commensals have an extensive repertoire of virulence alleles, a large fraction of which has been exchanged among Neisseria species. Commensals also have the genetic capacity to donate DNA to, and take up DNA from, other Neisseria. Our findings strongly suggest that commensal Neisseria serve as reservoirs of virulence alleles, and that they engage extensively in genetic exchange. PMID:20676376

  14. Morphological and Genomic Characterization of Filobasidiella depauperata: A Homothallic Sibling Species of the Pathogenic Cryptococcus Species Complex

    PubMed Central

    Rodriguez-Carres, Marianela; Findley, Keisha; Sun, Sheng; Dietrich, Fred S.; Heitman, Joseph

    2010-01-01

    The fungal species Cryptococcus neoformans and Cryptococcus gattii cause respiratory and neurological disease in animals and humans following inhalation of basidiospores or desiccated yeast cells from the environment. Sexual reproduction in C. neoformans and C. gattii is controlled by a bipolar system in which a single mating type locus (MAT) specifies compatibility. These two species are dimorphic, growing as yeast in the asexual stage, and producing hyphae, basidia, and basidiospores during the sexual stage. In contrast, Filobasidiella depauperata, one of the closest related species, grows exclusively as hyphae and it is found in association with decaying insects. Examination of two available strains of F. depauperata showed that the life cycle of this fungal species shares features associated with the unisexual or same-sex mating cycle in C. neoformans. Therefore, F. depauperata may represent a homothallic and possibly an obligately sexual fungal species. RAPD genotyping of 39 randomly isolated progeny from isolate CBS7855 revealed a new genotype pattern in one of the isolated basidiospores progeny, therefore suggesting that the homothallic cycle in F. depauperata could lead to the emergence of new genotypes. Phylogenetic analyses of genes linked to MAT in C. neoformans indicated that two of these genes in F. depauperata, MYO2 and STE20, appear to form a monophyletic clade with the MATa alleles of C. neoformans and C. gattii, and thus these genes may have been recruited to the MAT locus before F. depauperata diverged. Furthermore, the ancestral MATa locus may have undergone accelerated evolution prior to the divergence of the pathogenic Cryptococcus species since several of the genes linked to the MATa locus appear to have a higher number of changes and substitutions than their MATα counterparts. Synteny analyses between C. neoformans and F. depauperata showed that genomic regions on other chromosomes displayed conserved gene order. In contrast, the genes

  15. CG dinucleotide clustering is a species-specific property of the genome.

    PubMed

    Glass, Jacob L; Thompson, Reid F; Khulan, Batbayar; Figueroa, Maria E; Olivier, Emmanuel N; Oakley, Erin J; Van Zant, Gary; Bouhassira, Eric E; Melnick, Ari; Golden, Aaron; Fazzari, Melissa J; Greally, John M

    2007-01-01

    Cytosines at cytosine-guanine (CG) dinucleotides are the near-exclusive target of DNA methyltransferases in mammalian genomes. Spontaneous deamination of methylcytosine to thymine makes methylated cytosines unusually susceptible to mutation and consequent depletion. The loci where CG dinucleotides remain relatively enriched, presumably due to their unmethylated status during the germ cell cycle, have been referred to as CpG islands. Currently, CpG islands are solely defined by base compositional criteria, allowing annotation of any sequenced genome. Using a novel bioinformatic approach, we show that CG clusters can be identified as an inherent property of genomic sequence without imposing a base compositional a priori assumption. We also show that the CG clusters co-localize in the human genome with hypomethylated loci and annotated transcription start sites to a greater extent than annotations produced by prior CpG island definitions. Moreover, this new approach allows CG clusters to be identified in a species-specific manner, revealing a degree of orthologous conservation that is not revealed by current base compositional approaches. Finally, our approach is able to identify methylating genomes (such as Takifugu rubripes) that lack CG clustering entirely, in which it is inappropriate to annotate CpG islands or CG clusters.

  16. The Complete Chloroplast Genome Sequences of Three Veroniceae Species (Plantaginaceae): Comparative Analysis and Highly Divergent Regions

    PubMed Central

    Choi, Kyoung Su; Chung, Myong Gi; Park, SeonJoo

    2016-01-01

    Previous studies of Veronica and related genera were weakly supported by molecular and paraphyletic taxa. Here, we report the complete chloroplast genome sequence of Veronica nakaiana and the related species Veronica persica and Veronicastrum sibiricum. The chloroplast genome length of V. nakaiana, V. persica, and V. sibiricum ranged from 150,198 bp to 152,930 bp. A total of 112 genes comprising 79 protein coding genes, 29 tRNA genes, and 4 rRNA genes were observed in three chloroplast genomes. The total number of SSRs was 48, 51, and 53 in V. nakaiana, V. persica, and V. sibiricum, respectively. Two SSRs (10 bp of AT and 12 bp of AATA) were observed in the same regions (rpoC2 and ndhD) in three chloroplast genomes. A comparison of coding genes and non-coding regions between V. nakaiana and V. persica revealed divergent sites, with the greatest variation occurring petD-rpoA region. The complete chloroplast genome sequence information regarding the three Veroniceae will be helpful for elucidating Veroniceae phylogenetic relationships. PMID:27047524

  17. Comparative Genomics between Two Xenorhabdus bovienii Strains Highlights Differential Evolutionary Scenarios within an Entomopathogenic Bacterial Species

    PubMed Central

    Bisch, Gaëlle; Ogier, Jean-Claude; Médigue, Claudine; Rouy, Zoé; Vincent, Stéphanie; Tailliez, Patrick; Givaudan, Alain; Gaudriault, Sophie

    2016-01-01

    Bacteria of the genus Xenorhabdus are symbionts of soil entomopathogenic nematodes of the genus Steinernema. This symbiotic association constitutes an insecticidal complex active against a wide range of insect pests. Within Xenorhabdus bovienii species, the X. bovienii CS03 strain (Xb CS03) is nonvirulent when directly injected into lepidopteran insects, and displays a low virulence when associated with its Steinernema symbiont. The genome of Xb CS03 was sequenced and compared with the genome of a virulent strain, X. bovienii SS-2004 (Xb SS-2004). The genome size and content widely differed between the two strains. Indeed, Xb CS03 had a large genome containing several specific loci involved in the inhibition of competitors, including a few NRPS-PKS loci (nonribosomal peptide synthetases and polyketide synthases) producing antimicrobial molecules. Consistently, Xb CS03 had a greater antimicrobial activity than Xb SS-2004. The Xb CS03 strain contained more pseudogenes than Xb SS-2004. Decay of genes involved in the host invasion and exploitation (toxins, invasins, or extracellular enzymes) was particularly important in Xb CS03. This may provide an explanation for the nonvirulence of the strain when injected into an insect host. We suggest that Xb CS03 and Xb SS-2004 followed divergent evolutionary scenarios to cope with their peculiar life cycle. The fitness strategy of Xb CS03 would involve competitor inhibition, whereas Xb SS-2004 would quickly and efficiently kill the insect host. Hence, Xenorhabdus strains would have widely divergent host exploitation strategies, which impact their genome structure. PMID:26769959

  18. Complete genome analysis of three novel picornaviruses from diverse bat species.

    PubMed

    Lau, Susanna K P; Woo, Patrick C Y; Lai, Kenneth K Y; Huang, Yi; Yip, Cyril C Y; Shek, Chung-Tong; Lee, Paul; Lam, Carol S F; Chan, Kwok-Hung; Yuen, Kwok-Yung

    2011-09-01

    Although bats are important reservoirs of diverse viruses that can cause human epidemics, little is known about the presence of picornaviruses in these flying mammals. Among 1,108 bats of 18 species studied, three novel picornaviruses (groups 1, 2, and 3) were identified from alimentary specimens of 12 bats from five species and four genera. Two complete genomes, each from the three picornaviruses, were sequenced. Phylogenetic analysis showed that they fell into three distinct clusters in the Picornaviridae family, with low homologies to known picornaviruses, especially in leader and 2A proteins. Moreover, group 1 and 2 viruses are more closely related to each other than to group 3 viruses, which exhibit genome features distinct from those of the former two virus groups. In particular, the group 3 virus genome contains the shortest leader protein within Picornaviridae, a putative type I internal ribosome entry site (IRES) in the 5'-untranslated region instead of the type IV IRES found in group 1 and 2 viruses, one instead of two GXCG motifs in 2A, an L→V substitution in the DDLXQ motif in 2C helicase, and a conserved GXH motif in 3C protease. Group 1 and 2 viruses are unique among picornaviruses in having AMH instead of the GXH motif in 3C(pro). These findings suggest that the three picornaviruses belong to two novel genera in the Picornaviridae family. This report describes the discovery and complete genome analysis of three picornaviruses in bats, and their presence in diverse bat genera/species suggests the ability to cross the species barrier.

  19. A stable hybrid containing haploid genomes of two obligate diploid Candida species.

    PubMed

    Chakraborty, Uttara; Mohamed, Aiyaz; Kakade, Pallavi; Mugasimangalam, Raja C; Sadhale, Parag P; Sanyal, Kaustuv

    2013-08-01

    Candida albicans and Candida dubliniensis are diploid, predominantly asexual human-pathogenic yeasts. In this study, we constructed tetraploid (4n) strains of C. albicans of the same or different lineages by spheroplast fusion. Induction of chromosome loss in the tetraploid C. albicans generated diploid or near-diploid progeny strains but did not produce any haploid progeny. We also constructed stable heterotetraploid somatic hybrid strains (2n + 2n) of C. albicans and C. dubliniensis by spheroplast fusion. Heterodiploid (n + n) progeny hybrids were obtained after inducing chromosome loss in a stable heterotetraploid hybrid. To identify a subset of hybrid heterodiploid progeny strains carrying at least one copy of all chromosomes of both species, unique centromere sequences of various chromosomes of each species were used as markers in PCR analysis. The reduction of chromosome content was confirmed by a comparative genome hybridization (CGH) assay. The hybrid strains were found to be stably propagated. Chromatin immunoprecipitation (ChIP) assays with antibodies against centromere-specific histones (C. albicans Cse4/C. dubliniensis Cse4) revealed that the centromere identity of chromosomes of each species is maintained in the hybrid genomes of the heterotetraploid and heterodiploid strains. Thus, our results suggest that the diploid genome content is not obligatory for the survival of either C. albicans or C. dubliniensis. In keeping with the recent discovery of the existence of haploid C. albicans strains, the heterodiploid strains of our study can be excellent tools for further species-specific genome elimination, yielding true haploid progeny of C. albicans or C. dubliniensis in future.

  20. Acinetobacter plantarum sp. nov. isolated from wheat seedlings plant.

    PubMed

    Du, Juan; Singh, Hina; Yu, Hongshan; Jin, Feng-Xie; Yi, Tae-Hoo

    2016-07-01

    Strain THG-SQM11(T), a Gram-negative, aerobic, non-motile, coccus-shaped bacterium, was isolated from wheat seedlings plant in P. R. China. Strain THG-SQM11(T) was closely related to members of the genus Acinetobacter and showed the highest 16S rRNA sequence similarities with Acinetobacter junii (97.9 %) and Acinetobacter kookii (96.1 %). DNA-DNA hybridization showed 41.3 ± 2.4 % DNA reassociation with A. junii KCTC 12416(T). Chemotaxonomic data revealed that strain THG-SQM11(T) possesses ubiquinone-9 as the predominant respiratory quinone, C18:1 ω9c, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), and C16:0 as the major fatty acids. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylcholine. The DNA G+C content was 41.7 mol %. These data, together with phenotypic characterization, suggest that the isolate represents a novel species, for which the name Acinetobacter plantarum sp. nov. is proposed, with THG-SQM11(T) as the type strain (=CCTCC AB 2015123(T) =KCTC 42611(T)).

  1. Comparative Genomic Analyses of Transport Proteins Encoded Within the Genomes of Leptospira Species

    PubMed Central

    Buyuktimkin, Bora; Saier, Milton H.

    2015-01-01

    Select species of the bacterial genus Leptospira are causative agents of leptospirosis, an emerging global zoonosis affecting nearly one million people worldwide annually. We examined two Leptospira pathogens, L. interrogans serovar Lai str. 56601 and L. borgpetersenii serovar Hardjo-bovis str. L550, as well as the free-living leptospiral saprophyte, L. biflexa serovar Patoc str. ‘Patoc 1 (Ames)’. The transport proteins of these leptospires were identified and compared using bioinformatics to gain an appreciation for which proteins may be related to pathogenesis and saprophytism. L. biflexa possesses a disproportionately high number of secondary carriers for metabolite uptake and environmental adaptability as well as an increased number of inorganic cation transporters providing ionic homeostasis and effective osmoregulation in a rapidly changing environment. L. interrogans and L. borgpetersenii possess far fewer transporters, but those that they have are remarkably similar, with near-equivalent representation in most transporter families. These two Leptospira pathogens also possess intact sphingomyelinases, holins, and virulence-related outer membrane porins. These virulence-related factors, in conjunction with decreased transporter substrate versatility, indicate that pathogenicity was accompanied by progressively narrowing ecological niches and the emergence of a limited set of proteins responsible for host invasion. The variability of host tropism and mortality rates by infectious leptospires suggests that small differences in individual sets of proteins play important physiological and pathological roles. PMID:26247102

  2. Genetic Diversity in Lens Species Revealed by EST and Genomic Simple Sequence Repeat Analysis.

    PubMed

    Dikshit, Harsh Kumar; Singh, Akanksha; Singh, Dharmendra; Aski, Muraleedhar Sidaram; Prakash, Prapti; Jain, Neelu; Meena, Suresh; Kumar, Shiv; Sarker, Ashutosh

    2015-01-01

    Low productivity of pilosae type lentils grown in South Asia is attributed to narrow genetic base of the released cultivars which results in susceptibility to biotic and abiotic stresses. For enhancement of productivity and production, broadening of genetic base is essentially required. The genetic base of released cultivars can be broadened by using diverse types including bold seeded and early maturing lentils from Mediterranean region and related wild species. Genetic diversity in eighty six accessions of three species of genus Lens was assessed based on twelve genomic and thirty one EST-SSR markers. The evaluated set of genotypes included diverse lentil varieties and advanced breeding lines from Indian programme, two early maturing ICARDA lines and five related wild subspecies/species endemic to the Mediterranean region. Genomic SSRs exhibited higher polymorphism in comparison to EST SSRs. GLLC 598 produced 5 alleles with highest gene diversity value of 0.80. Among the studied subspecies/species 43 SSRs detected maximum number of alleles in L. orientalis. Based on Nei's genetic distance cultivated lentil L. culinaris subsp. culinaris was found to be close to its wild progenitor L. culinaris subsp. orientalis. The Prichard's structure of 86 genotypes distinguished different subspecies/species. Higher variability was recorded among individuals within population than among populations.

  3. Genomic linkage of male song and female acoustic preference QTL underlying a rapid species radiation

    PubMed Central

    Shaw, Kerry L.; Lesnick, Sky C.

    2009-01-01

    The genetic coupling hypothesis of signal-preference evolution, whereby the same genes control male signal and female preference for that signal, was first inspired by the evolution of cricket acoustic communication nearly 50 years ago. To examine this hypothesis, we compared the genomic location of quantitative trait loci (QTL) underlying male song and female acoustic preference variation in the Hawaiian cricket genus Laupala. We document a QTL underlying female acoustic preference variation between 2 closely related species (Laupala kohalensis and Laupala paranigra). This preference QTL colocalizes with a song QTL identified previously, providing compelling evidence for a genomic linkage of the genes underlying these traits. We show that both song and preference QTL make small to moderate contributions to the behavioral difference between species, suggesting that divergence in mating behavior among Laupala species is due to the fixation of many genes of minor effect. The diversity of acoustic signaling systems in crickets exemplifies the evolution of elaborate male displays by sexual selection through female choice. Our data reveal genetic conditions that would enable functional coordination between song and acoustic preference divergence during speciation, resulting in a behaviorally coupled mode of signal-preference evolution. Interestingly, Laupala exhibits one of the fastest rates of speciation in animals, concomitant with equally rapid evolution in sexual signaling behaviors. Genomic linkage may facilitate rapid speciation by contributing to genetic correlations between sexual signaling behaviors that eventually cause sexual isolation between diverging populations. PMID:19487670

  4. The Organization of Repetitive DNA in the Genomes of Amazonian Lizard Species in the Family Teiidae.

    PubMed

    Carvalho, Natalia D M; Pinheiro, Vanessa S S; Carmo, Edson J; Goll, Leonardo G; Schneider, Carlos H; Gross, Maria C

    2015-01-01

    Repetitive DNA is the largest fraction of the eukaryote genome and comprises tandem and dispersed sequences. It presents variations in relation to its composition, number of copies, distribution, dynamics, and genome organization, and participates in the evolutionary diversification of different vertebrate species. Repetitive sequences are usually located in the heterochromatin of centromeric and telomeric regions of chromosomes, contributing to chromosomal structures. Therefore, the aim of this study was to physically map repetitive DNA sequences (5S rDNA, telomeric sequences, tropomyosin gene 1, and retroelements Rex1 and SINE) of mitotic chromosomes of Amazonian species of teiids (Ameiva ameiva, Cnemidophorus sp. 1, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin) to understand their genome organization and karyotype evolution. The mapping of repetitive sequences revealed a distinct pattern in Cnemidophorus sp. 1, whereas the other species showed all sequences interspersed in the heterochromatic region. Physical mapping of the tropomyosin 1 gene was performed for the first time in lizards and showed that in addition to being functional, this gene has a structural function similar to the mapped repetitive elements as it is located preferentially in centromeric regions and termini of chromosomes.

  5. Cross-species transferability and mapping of genomic and cDNA SSRs in pines.

    PubMed

    Chagné, D; Chaumeil, P; Ramboer, A; Collada, C; Guevara, A; Cervera, M T; Vendramin, G G; Garcia, V; Frigerio, J-M; Echt, C; Richardson, T; Plomion, C

    2004-10-01

    Two unigene datasets of Pinus taeda and Pinus pinaster were screened to detect di-, tri- and tetranucleotide repeated motifs using the SSRIT script. A total of 419 simple sequence repeats (SSRs) were identified, from which only 12.8% overlapped between the two sets. The position of the SSRs within their coding sequences were predicted using FrameD. Trinucleotides appeared to be the most abundant repeated motif (63 and 51% in P. taeda and P. pinaster, respectively) and tended to be found within translated regions (76% in both species), whereas dinucleotide repeats were preferentially found within the 5'- and 3'-untranslated regions (75 and 65%, respectively). Fifty-three primer pairs amplifying a single PCR fragment in the source species (mainly P. taeda), were tested for amplification in six other pine species. The amplification rate with other pine species was high and corresponded with the phylogenetic distance between species, varying from 64.6% in P. canariensis to 94.2% in P. radiata. Genomic SSRs were found to be less transferable; 58 of the 107 primer pairs (i.e. 54%) derived from P. radiata amplified a single fragment in P. pinaster. Nine cDNA-SSRs were located to their chromosomes in two P. pinaster linkage maps. The level of polymorphism of these cDNA-SSRs was compared to that of previously and newly developed genomic-SSRs. Overall, genomic SSRs tend to perform better in terms of heterozygosity and number of alleles. This study suggests that useful SSR markers can be developed from pine ESTs.

  6. Mitochondrial genomic comparison of Clonorchis sinensis from South Korea with other isolates of this species.

    PubMed

    Wang, Daxi; Young, Neil D; Koehler, Anson V; Tan, Patrick; Sohn, Woon-Mok; Korhonen, Pasi K; Gasser, Robin B

    2017-02-22

    Clonorchiasis is a neglected tropical disease that affects >35 million people mainly in China, Vietnam, South Korea and some parts of Russia. The disease-causing agent, Clonorchis sinensis, is a liver fluke of humans and other piscivorous animals, and has a complex aquatic life cycle involving snails and fish intermediate hosts. Chronic infection in humans causes liver disease and associated complications including malignant bile duct cancer. Central to control and to understanding the epidemiology of this disease is knowledge of the specific identity of the causative agent as well as genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species and that genetic variation within the species is limited, karyotypic variation within C. sinensis among China, Korea (2n=56) and Russian Far East (2n=14) suggests that this taxon might contain sibling species. Here, we assessed and applied a deep sequencing-bioinformatic approach to sequence and define a reference mitochondrial (mt) genome for a particular isolate of C. sinensis from Korea (Cs-k2), to confirm its specific identity, and compared this mt genome with homologous data sets available for this species. Comparative analyses revealed consistency in the number and structure of genes as well as in the lengths of protein-coding genes, and limited genetic variation among isolates of C. sinensis. Phylogenetic analyses of amino acid sequences predicted from mt genes showed that representatives of C. sinensis clustered together, with absolute nodal support, to the exclusion of other liver fluke representatives, but sub-structuring within C. sinensis was not well supported. The plan now is to proceed with the sequencing, assembly and annotation of a high quality draft nuclear genome of this defined isolate (Cs-k2) as a basis for a detailed investigation of molecular variation within C. sinensis from disparate

  7. Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae)

    PubMed Central

    Dong, Wenpan; Xu, Chao; Li, Delu; Jin, Xiaobai; Li, Ruili

    2016-01-01

    The Haloxylon genus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. The small trees or shrubs in this genus are referred to as the King of psammophytic plants, and perform important functions in environmental protection, including wind control and sand fixation in deserts. To better understand these beneficial plants, we sequenced the chloroplast (cp) genomes of Haloxylon ammodendron (HA) and Haloxylon persicum (HP) and conducted comparative genomic analyses on these and two other representative Amaranthaceae species. Similar to other higher plants, we found that the Haloxylon cp genome is a quadripartite, double-stranded, circular DNA molecule of 151,570 bp in HA and 151,586 bp in HP. It contains a pair of inverted repeats (24,171 bp in HA and 24,177 bp in HP) that separate the genome into a large single copy region of 84,214 bp in HA and 84,217 bp in HP, and a small single copy region of 19,014 bp in HA and 19,015 bp in HP. Each Haloxylon cp genome contains 112 genes, including 78 coding, 30 tRNA, and four ribosomal RNA genes. We detected 59 different simple sequence repeat loci, including 44 mono-nucleotide, three di-nucleotide, one tri-nucleotide, and 11 tetra-nucleotide repeats. Comparative analysis revealed only 67 mutations between the two species, including 44 substitutions, 23 insertions/deletions, and two micro-inversions. The two inversions, with lengths of 14 and 3 bp, occur in the petA-psbJ intergenic region and rpl16 intron, respectively, and are predicted to form hairpin structures with repeat sequences of 27 and 19 bp, respectively, at the two ends. The ratio of transitions to transversions was 0.76. These results are valuable for future studies on Haloxylon genetic diversity and will enhance our understanding of the phylogenetic evolution of Amaranthaceae. PMID:27867769

  8. Intraspecies Transfer of the Chromosomal Acinetobacter baumannii blaNDM-1 Carbapenemase Gene

    PubMed Central

    Krahn, Thomas; Wibberg, Daniel; Maus, Irena; Winkler, Anika; Bontron, Séverine; Sczyrba, Alexander; Nordmann, Patrice; Pühler, Alfred; Poirel, Laurent

    2016-01-01

    The species Acinetobacter baumannii is one of the most important multidrug-resistant human pathogens. To determine its virulence and antibiotic resistance determinants, the genome of the nosocomial blaNDM-1-positive A. baumannii strain R2090 originating from Egypt was completely sequenced. Genome analysis revealed that strain R2090 is highly related to the community-acquired Australian A. baumannii strain D1279779. The two strains belong to sequence type 267 (ST267). Isolate R2090 harbored the chromosomally integrated transposon Tn125 carrying the carbapenemase gene blaNDM-1 that is not present in the D1279779 genome. To test the transferability of the metallo-β-lactamase (MBL) gene region, the clinical isolate R2090 was mated with the susceptible A. baumannii recipient CIP 70.10, and the carbapenem-resistant derivative R2091 was obtained. Genome sequencing of the R2091 derivative revealed that it had received an approximately 66-kb region comprising the transposon Tn125 embedding the blaNDM-1 gene. This region had integrated into the chromosome of the recipient strain CIP 70.10. From the four known mechanisms for horizontal gene transfer (conjugation, outer membrane vesicle-mediated transfer, transformation, and transduction), conjugation could be ruled out, since strain R2090 lacks any plasmid, and a type IV secretion system is not encoded in its chromosome. However, strain R2090 possesses three putative prophages, two of which were predicted to be complete and therefore functional. Accordingly, it was supposed that the transfer of the resistance gene region from the clinical isolate R2090 to the recipient occurred by general transduction facilitated by one of the prophages present in the R2090 genome. Hence, phage-mediated transduction has to be taken into account for the dissemination of antibiotic resistance genes within the species A. baumannii. PMID:26953198

  9. Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

    PubMed Central

    Barbe, Valérie; Baeriswyl, Simon; Bidet, Philippe; Bingen, Edouard; Bonacorsi, Stéphane; Bouchier, Christiane; Bouvet, Odile; Calteau, Alexandra; Chiapello, Hélène; Clermont, Olivier; Cruveiller, Stéphane; Danchin, Antoine; Diard, Médéric; Dossat, Carole; Karoui, Meriem El; Frapy, Eric; Garry, Louis; Ghigo, Jean Marc; Gilles, Anne Marie; Johnson, James; Le Bouguénec, Chantal; Lescat, Mathilde; Mangenot, Sophie; Martinez-Jéhanne, Vanessa; Matic, Ivan; Nassif, Xavier; Oztas, Sophie; Petit, Marie Agnès; Pichon, Christophe; Rouy, Zoé; Ruf, Claude Saint; Schneider, Dominique; Tourret, Jérôme; Vacherie, Benoit; Vallenet, David; Médigue, Claudine; Rocha, Eduardo P. C.; Denamur, Erick

    2009-01-01

    The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the ∼18,000 families of orthologous genes, we found ∼2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome. PMID:19165319

  10. Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks

    PubMed Central

    2012-01-01

    Background The study of speciation and maintenance of species barriers is at the core of evolutionary biology. During speciation the genome of one population becomes separated from other populations of the same species, which may lead to genomic incompatibility with time. This separation is complete when no fertile offspring is produced from inter-population matings, which is the basis of the biological species concept. Birds, in particular ducks, are recognised as a challenging and illustrative group of higher vertebrates for speciation studies. There are many sympatric and ecologically similar duck species, among which fertile hybrids occur relatively frequently in nature, yet these species remain distinct. Results We show that the degree of shared single nucleotide polymorphisms (SNPs) between five species of dabbling ducks (genus Anas) is an order of magnitude higher than that previously reported between any pair of eukaryotic species with comparable evolutionary distances. We demonstrate that hybridisation has led to sustained exchange of genetic material between duck species on an evolutionary time scale without disintegrating species boundaries. Even though behavioural, genetic and ecological factors uphold species boundaries in ducks, we detect opposing forces allowing for viable interspecific hybrids, with long-term evolutionary implications. Based on the superspecies concept we here introduce the novel term "supra-population" to explain the persistence of SNPs identical by descent within the studied ducks despite their history as distinct species dating back millions of years. Conclusions By reviewing evidence from speciation theory, palaeogeography and palaeontology we propose a fundamentally new model of speciation to accommodate our genetic findings in dabbling ducks. This model, we argue, may also shed light on longstanding unresolved general speciation and hybridisation patterns in higher organisms, e.g. in other bird groups with unusually high

  11. Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera.

    PubMed

    Meganathan, P R; Pagan, Heidi J T; McCulloch, Eve S; Stevens, Richard D; Ray, David A

    2012-01-15

    Order Chiroptera is a unique group of mammals whose members have attained self-powered flight as their main mode of locomotion. Much speculation persists regarding bat evolution; however, lack of sufficient molecular data hampers evolutionary and conservation studies. Of ~1200 species, complete mitochondrial genome sequences are available for only eleven. Additional sequences should be generated if we are to resolve many questions concerning these fascinating mammals. Herein, we describe the complete mitochondrial genomes of three bats: Corynorhinus rafinesquii, Lasiurus borealis and Artibeus lituratus. We also compare the currently available mitochondrial genomes and analyze codon usage in Chiroptera. C. rafinesquii, L. borealis and A. lituratus mitochondrial genomes are 16438 bp, 17048 bp and 16709 bp, respectively. Genome organization and gene arrangements are similar to other bats. Phylogenetic analyses using complete mitochondrial genome sequences support previously established phylogenetic relationships and suggest utility in future studies focusing on the evolutionary aspects of these species. Comprehensive analyses of available bat mitochondrial genomes reveal distinct nucleotide patterns and synonymous codon preferences corresponding to different chiropteran families. These patterns suggest that mutational and selection forces are acting to different extents within Chiroptera and shape their mitochondrial genomes.

  12. Acinetobacter indicus sp. nov., isolated from a hexachlorocyclohexane dump site.

    PubMed

    Malhotra, Jaya; Anand, Shailly; Jindal, Swati; Rajagopal, Raman; Lal, Rup

    2012-12-01

    The taxonomic position of a Gram-negative, non-motile, oxidase negative and catalase positive strain, A648(T), isolated from a hexachlorocyclohexane (HCH) dump site located in Lucknow, India, was ascertained by using a polyphasic approach. A comparative analysis of a partial sequence of the rpoB gene and the 16S rRNA gene sequence revealed that strain A648(T) belonged to the genus Acinetobacter. DNA-DNA relatedness values between strain A648(T) and other closely related members (16S rRNA gene sequence similarity greater than 97%), namely Acinetobacter radioresistens DSM 6976(T), A. venetianus ATCC 31012(T), A. baumannii LMG 1041(T), A. parvus LMG 21765(T) A. junii LMG 998(T) and A. soli JCM 15062(T), were found to be less than 8%. The major cellular fatty acids of strain A648(T) were 18:1ω9c (19.6%), summed feature 3 (15.9%), 16:0 (10.6%) and 12:0 (6.4%). The DNA G+C content was 40.4 mol%. The polar lipid profile of strain A648(T) indicated the presence of diphosphatidylglycerol, phosphatidylethanolamine, followed by phosphatidylglycerol and phosphatidylcholine. The predominant polyamine of strain A648(T) was 1,3-diaminopropane and moderate amounts of putrescine, spermidine and spermine were also detected. The respiratory quinone consisted of ubiquinone with nine isoprene units (Q-9). On the basis of DNA-DNA hybridization, phenotypic characteristics and chemotaxonomic and phylogenetic comparisons with other members of the genus Acinetobacter, strain A648(T) is found to be a novel species of the genus Acinetobacter, for which the name Acinetobacter indicus sp. nov. is proposed. The type strain is A648(T) ( = DSM 25388(T) = CCM 7832(T)).

  13. Revisiting the reference genomes of human pathogenic Cryptosporidium species: reannotation of C. parvum Iowa and a new C. hominis reference.

    PubMed

    Isaza, Juan P; Galván, Ana Luz; Polanco, Victor; Huang, Bernice; Matveyev, Andrey V; Serrano, Myrna G; Manque, Patricio; Buck, Gregory A; Alzate, Juan F

    2015-11-09

    Cryptosporidium parvum and C. hominis are the most relevant species of this genus for human health. Both cause a self-limiting diarrhea in immunocompetent individuals, but cause potentially life-threatening disease in the immunocompromised. Despite the importance of these pathogens, only one reference genome of each has been analyzed and published. These two reference genomes were sequenced using automated capillary sequencing; as of yet, no next generation sequencing technology has been applied to improve their assemblies and annotations. For C. hominis, the main challenge that prevents a larger number of genomes to be sequenced is its resistance to axenic culture. In the present study, we employed next generation technology to analyse the genomic DNA and RNA to generate a new reference genome sequence of a C. hominis strain isolated directly from human stool and a new genome annotation of the C. parvum Iowa reference genome.

  14. Revisiting the reference genomes of human pathogenic Cryptosporidium species: reannotation of C. parvum Iowa and a new C. hominis reference

    PubMed Central

    Isaza, Juan P.; Galván, Ana Luz; Polanco, Victor; Huang, Bernice; Matveyev, Andrey V.; Serrano, Myrna G.; Manque, Patricio; Buck, Gregory A.; Alzate, Juan F.

    2015-01-01

    Cryptosporidium parvum and C. hominis are the most relevant species of this genus for human health. Both cause a self-limiting diarrhea in immunocompetent individuals, but cause potentially life-threatening disease in the immunocompromised. Despite the importance of these pathogens, only one reference genome of each has been analyzed and published. These two reference genomes were sequenced using automated capillary sequencing; as of yet, no next generation sequencing technology has been applied to improve their assemblies and annotations. For C. hominis, the main challenge that prevents a larger number of genomes to be sequenced is its resistance to axenic culture. In the present study, we employed next generation technology to analyse the genomic DNA and RNA to generate a new reference genome sequence of a C. hominis strain isolated directly from human stool and a new genome annotation of the C. parvum Iowa reference genome. PMID:26549794

  15. Genome Sequencing and Analysis of Catopsilia pomona nucleopolyhedrovirus: A Distinct Species in Group I Alphabaculovirus

    PubMed Central

    Wang, Jun; Zhu, Zheng; Zhang, Lei; Hou, Dianhai; Wang, Manli; Arif, Basil; Kou, Zheng; Wang, Hualin; Deng, Fei; Hu, Zhihong

    2016-01-01

    The genome sequence of Catopsilia pomona nucleopolyhedrovirus (CapoNPV) was determined by the Roche 454 sequencing system. The genome consisted of 128,058 bp and had an overall G+C content of 40%. There were 130 hypothetical open reading frames (ORFs) potentially encoding proteins of more than 50 amino acids and covering 92% of the genome. Among all the hypothetical ORFs, 37 baculovirus core genes, 23 lepidopteran baculovirus conserved genes and 10 genes conserved in Group I alphabaculoviruses were identified. In addition, the genome included regions of 8 typical baculoviral homologous repeat sequences (hrs). Phylogenic analysis showed that CapoNPV was in a distinct branch of clade “a” in Group I alphabaculoviruses. Gene parity plot analysis and overall similarity of ORFs indicated that CapoNPV is more closely related to the Group I alphabaculoviruses than to other baculoviruses. Interesting, CapoNPV lacks the genes encoding the fibroblast growth factor (fgf) and ac30, which are conserved in most lepidopteran and Group I baculoviruses, respectively. Sequence analysis of the F-like protein of CapoNPV showed that some amino acids were inserted into the fusion peptide region and the pre-transmembrane region of the protein. All these unique features imply that CapoNPV represents a member of a new baculovirus species. PMID:27166956

  16. Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species.

    PubMed

    Nazareno, Alison G; Bemmels, Jordan B; Dick, Christopher W; Lohmann, Lúcia G

    2017-01-12

    High-throughput DNA sequencing facilitates the analysis of large portions of the genome in nonmodel organisms, ensuring high accuracy of population genetic parameters. However, empirical studies evaluating the appropriate sample size for these kinds of studies are still scarce. In this study, we use double-digest restriction-associated DNA sequencing (ddRADseq) to recover thousands of single nucleotide polymorphisms (SNPs) for two physically isolated populations of Amphirrhox longifolia (Violaceae), a nonmodel plant species for which no reference genome is available. We used resampling techniques to construct simulated populations with a random subset of individuals and SNPs to determine how many individuals and biallelic markers should be sampled for accurate estimates of intra- and interpopulation genetic diversity. We identified 3646 and 4900 polymorphic SNPs for the two populations of A. longifolia, respectively. Our simulations show that, overall, a sample size greater than eight individuals has little impact on estimates of genetic diversity within A. longifolia populations, when 1000 SNPs or higher are used. Our results also show that even at a very small sample size (i.e. two individuals), accurate estimates of FST can be obtained with a large number of SNPs (≥1500). These results highlight the potential of high-throughput genomic sequencing approaches to address questions related to evolutionary biology in nonmodel organisms. Furthermore, our findings also provide insights into the optimization of sampling strategies in the era of population genomics.

  17. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that i...

  18. Genomic analysis of three Bifidobacterium species isolated from the calf gastrointestinal tract

    PubMed Central

    Kelly, William J.; Cookson, Adrian L.; Altermann, Eric; Lambie, Suzanne C.; Perry, Rechelle; Teh, Koon Hoong; Otter, Don E.; Shapiro, Nicole; Woyke, Tanja; Leahy, Sinead C.

    2016-01-01

    Ruminant animals contribute significantly to the global value of agriculture and rely on a complex microbial community for efficient digestion. However, little is known of how this microbial-host relationship develops and is maintained. To begin to address this, we have determined the ability of three Bifidobacterium species isolated from the faeces of newborn calves to grow on carbohydrates typical of a newborn ruminant diet. Genome sequences have been determined for these bacteria with analysis of the genomes providing insights into the host association and identification of several genes that may mediate interactions with the ruminant gastrointestinal tract. The present study provides a starting point from which we can define the role of potential beneficial microbes in the nutrition of young ruminants and begin to influence the interactions between the microbiota and the host. The differences observed in genomic content hint at niche partitioning among the bifidobacterial species analysed and the different strategies they employ to successfully adapt to this habitat. PMID:27468806

  19. Genome-wide scans detect adaptation to aridity in a widespread forest tree species.

    PubMed

    Steane, Dorothy A; Potts, Brad M; McLean, Elizabeth; Prober, Suzanne M; Stock, William D; Vaillancourt, René E; Byrne, Margaret

    2014-05-01

    Patterns of adaptive variation within plant species are best studied through common garden experiments, but these are costly and time-consuming, especially for trees that have long generation times. We explored whether genome-wide scanning technology combined with outlier marker detection could be used to detect adaptation to climate and provide an alternative to common garden experiments. As a case study, we sampled nine provenances of the widespread forest tree species, Eucalyptus tricarpa, across an aridity gradient in southeastern Australia. Using a Bayesian analysis, we identified a suite of 94 putatively adaptive (outlying) sequence-tagged markers across the genome. Population-level allele frequencies of these outlier markers were strongly correlated with temperature and moisture availability at the site of origin, and with population differences in functional traits measured in two common gardens. Using the output from a canonical analysis of principal coordinates, we devised a metric that provides a holistic measure of genomic adaptation to aridity that could be used to guide assisted migration or genetic augmentation.

  20. Genome-Wide Comparative Analysis of Chemosensory Gene Families in Five Tsetse Fly Species

    PubMed Central

    Macharia, Rosaline; Mireji, Paul; Murungi, Edwin; Murilla, Grace; Christoffels, Alan; Aksoy, Serap; Masiga, Daniel

    2016-01-01

    For decades, odour-baited traps have been used for control of tsetse flies (Diptera; Glossinidae), vectors of African trypanosomes. However, differential responses to known attractants have been reported in different Glossina species, hindering establishment of a universal vector control tool. Availability of full genome sequences of five Glossina species offers an opportunity to compare their chemosensory repertoire and enhance our understanding of their biology in relation to chemosensation. Here, we identified and annotated the major chemosensory gene families in Glossina. We identified a total of 118, 115, 124, and 123 chemosensory genes in Glossina austeni, G. brevipalpis, G. f. fuscipes, G. pallidipes, respectively, relative to 127 reported in G. m. morsitans. Our results show that tsetse fly genomes have fewer chemosensory genes when compared to other dipterans such as Musca domestica (n>393), Drosophila melanogaster (n = 246) and Anopheles gambiae (n>247). We also found that Glossina chemosensory genes are dispersed across distantly located scaffolds in their respective genomes, in contrast to other insects like D. melanogaster whose genes occur in clusters. Further, Glossina appears to be devoid of sugar receptors and to have expanded CO2 associated receptors, potentially reflecting Glossina's obligate hematophagy and the need to detect hosts that may be out of sight. We also identified, in all species, homologs of Ir84a; a Drosophila-specific ionotropic receptor that promotes male courtship suggesting that this is a conserved trait in tsetse flies. Notably, our selection analysis revealed that a total of four gene loci (Gr21a, GluRIIA, Gr28b, and Obp83a) were under positive selection, which confers fitness advantage to species. These findings provide a platform for studies to further define the language of communication of tsetse with their environment, and influence development of novel approaches for control. PMID:26886411

  1. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

    PubMed Central

    Fouts, Derrick E.; Matthias, Michael A.; Adhikarla, Haritha; Adler, Ben; Amorim-Santos, Luciane; Berg, Douglas E.; Bulach, Dieter; Buschiazzo, Alejandro; Chang, Yung-Fu; Galloway, Renee L.; Haake, David A.; Haft, Daniel H.; Hartskeerl, Rudy; Ko, Albert I.; Levett, Paul N.; Matsunaga, James; Mechaly, Ariel E.; Monk, Jonathan M.; Nascimento, Ana L. T.; Nelson, Karen E.; Palsson, Bernhard; Peacock, Sharon J.; Picardeau, Mathieu; Ricaldi, Jessica N.; Thaipandungpanit, Janjira; Wunder, Elsio A.; Yang, X. Frank; Zhang, Jun-Jie; Vinetz, Joseph M.

    2016-01-01

    Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field. Infectious Leptospira, comprised of pathogenic and intermediately pathogenic Leptospira, evolutionarily diverged from non-infectious, saprophytic Leptospira, as demonstrated by the following computational biology analyses: 1) the definitive taxonomy and evolutionary relatedness among all known Leptospira species; 2) genomically-predicted metabolic reconstructions that indicate novel adaptation of infectious Leptospira to mammals, including sialic acid biosynthesis, pathogen-specific porphyrin metabolism and the first-time demonstration of cobalamin (B12) autotrophy as a bacterial virulence factor; 3) CRISPR/Cas systems demonstrated only to be present in pathogenic Leptospira, suggesting a potential mechanism for this clade’s refractoriness to gene targeting; 4) finding Leptospira pathogen-specific specialized protein secretion systems; 5) novel virulence-related genes/gene families such as the Virulence Modifying (VM) (PF07598 paralogs) proteins and pathogen-specific adhesins; 6) discovery of novel, pathogen-specific protein modification and secretion mechanisms including unique lipoprotein signal peptide motifs, Sec-independent twin arginine protein secretion motifs, and the absence of certain canonical signal recognition particle proteins from all Leptospira; and 7) and demonstration of infectious Leptospira-specific signal-responsive gene expression, motility and chemotaxis systems. By identifying large scale changes in infectious (pathogenic and intermediately pathogenic

  2. Membrane proteomes of Pseudomonas aeruginosa and Acinetobacter baumannii.

    PubMed

    Dé, E; Cosette, P; Coquet, L; Siroy, A; Alexandre, S; Duncan, A; Naudin, B; Rihouey, C; Schaumann, A; Junter, G A; Jouenne, T

    2011-12-01

    Acinetobacter baumannii and Pseudomonas aeruginosa are known for their intrinsic resistance to antibiotics. Between mechanisms involved in this resistance, diminished expression of outer membrane proteins and up-regulation of efflux pumps play an important role. The characterization of membrane proteins is consequently necessary because of their importance in the antibiotic resistance but also in virulence. This review presents proteomic investigations aiming to describe the protein content of the membranes of these two bacterial species.

  3. Development and cross-species/genera transferability of microsatellite markers discovered using 454 genome sequencing in chokecherry (Prunus virginiana L.).

    PubMed

    Wang, Hongxia; Walla, James A; Zhong, Shaobin; Huang, Danqiong; Dai, Wenhao

    2012-11-01

    Chokecherry (Prunus virginiana L.) (2n = 4x = 32) is a unique Prunus species for both genetics and disease-resistance research due to its tetraploid nature and X-disease resistance. However, no genetic and genomic information on chokecherry is available. A partial chokecherry genome was sequenced using Roche 454 sequencing technology. A total of 145,094 reads covering 4.8 Mbp of the chokecherry genome were generated and 15,113 contigs were assembled, of which 11,675 contigs were larger than 100 bp in size. A total of 481 SSR loci were identified from 234 (out of 11,675) contigs and 246 polymerase chain reaction (PCR) primer pairs were designed. Of 246 primers, 212 (86.2 %) effectively produced amplification from the genomic DNA of chokecherry. All 212 amplifiable chokecherry primers were used to amplify genomic DNA from 11 other rosaceous species (sour cherry, sweet cherry, black cherry, peach, apricot, plum, apple, crabapple, pear, juneberry, and raspberry). Thus, chokecherry SSR primers can be transferable across Prunus species and other rosaceous species. An average of 63.2 and 58.7 % of amplifiable chokecherry primers amplified DNA from cherry and other Prunus species, respectively, while 47.2 % of amplifiable chokecherry primers amplified DNA from other rosaceous species. Using random genome sequence data generated from next-generation sequencing technology to identify microsatellite loci appears to be rapid and cost-efficient, particularly for species with no sequence information available. Sequence information and confirmed transferability of the identified chokecherry SSRs among species will be valuable for genetic research in Prunus and other rosaceous species. Key message A total of 246 SSR primers were identified from chokecherry genome sequences. Of which, 212 were confirmed amplifiable both in chokecherry and other 11 other rosaceous species.

  4. Acinetobacter baumannii: Emergence of a Successful Pathogen

    PubMed Central

    Peleg, Anton Y.; Seifert, Harald; Paterson, David L.

    2008-01-01

    Acinetobacter baumannii has emerged as a highly troublesome pathogen for many institutions globally. As a consequence of its immense ability to acquire or upregulate antibiotic drug resistance determinants, it has justifiably been propelled to the forefront of scientific attention. Apart from its predilection for the seriously ill within intensive care units, A. baumannii has more recently caused a range of infectious syndromes in military personnel injured in the Iraq and Afghanistan conflicts. This review details the significant advances that have been made in our understanding of this remarkable organism over the last 10 years, including current taxonomy and species identification, issues with susceptibility testing, mechanisms of antibiotic resistance, global epidemiology, clinical impact of infection, host-pathogen interactions, and infection control and therapeutic considerations. PMID:18625687

  5. Description of a species of Fabaeformiscandona (Ostracoda, Crustacea) from Kushiro Marsh, Hokkaido, Japan, with the nearly complete mitochondrial genomic sequence

    PubMed Central

    Hiruta, Shin-ichi

    2015-01-01

    Abstract Background So far, 16 species of non-marine ostracods have been reported from Kushiro Marsh, Kushiro Shitsugen National Park, eastern Hokkaido, Japan (Hiruta and Smith 2001, Smith and Hiruta 2004). Nine of these species are in Candonidae, the second-most diverse family of non-marine ostracods. This family contains ca. 550 species, or around 25% of the total number of non-marine ostracod species (Martens et al. 2008). New information We sampled ostracods in Kushiro Marsh on 27 December 2012 and identified an undescribed species in the family Candonidae, herein described as Fabaeformiscandona kushiroensis sp. nov. This species belongs to the F. acuminata species group and is characterized by the shapes of the elongate, dorsally directed medial and outer lobes on the distal end of each hemipenis. We also determined for this species the sequence of the nearly complete mitochondrial genome, the first record from the order Podocopa. The genome (ca. 17 kbp) contains two ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes, as also found in other arthropods for which the mitochondrial genome has been sequenced. The gene arrangement is similar to the pancrustacean ground pattern, except that in the control region there is an approximately 2 kbp tandem repeat region composed of 220-bp motif sequences. We describe the genetic features of the mitochondrial genome, including nucleotide composition and the secondary structures of tRNAs and rRNAs, and compare them with the genome of Vargula hilgendorfii (Myodocopa, Ostracoda). PMID:26751633

  6. Genome sequences of six Phytophthora species associated with forests in New Zealand.

    PubMed

    Studholme, D J; McDougal, R L; Sambles, C; Hansen, E; Hardy, G; Grant, M; Ganley, R J; Williams, N M

    2016-03-01

    In New Zealand there has been a long association of Phytophthora diseases in forests, nurseries, remnant plantings and horticultural crops. However, new Phytophthora diseases of trees have recently emerged. Genome sequencing has been performed for 12 Phytophthora isolates, from six species: Phytophthora pluvialis, Phytophthora kernoviae, Phytophthora cinnamomi, Phytophthora agathidicida, Phytophthora multivora and Phytophthora taxon Totara. These sequences will enable comparative analyses to identify potential virulence strategies and ultimately facilitate better control strategies. This Whole Genome Shotgun data have been deposited in DDBJ/ENA/GenBank under the accession numbers LGTT00000000, LGTU00000000, JPWV00000000, JPWU00000000, LGSK00000000, LGSJ00000000, LGTR00000000, LGTS00000000, LGSM00000000, LGSL00000000, LGSO00000000, and LGSN00000000.

  7. Genome sequences of six Phytophthora species associated with forests in New Zealand

    PubMed Central

    Studholme, D.J.; McDougal, R.L.; Sambles, C.; Hansen, E.; Hardy, G.; Grant, M.; Ganley, R.J.; Williams, N.M.

    2015-01-01

    In New Zealand there has been a long association of Phytophthora diseases in forests, nurseries, remnant plantings and horticultural crops. However, new Phytophthora diseases of trees have recently emerged. Genome sequencing has been performed for 12 Phytophthora isolates, from six species: Phytophthora pluvialis, Phytophthora kernoviae, Phytophthora cinnamomi, Phytophthora agathidicida, Phytophthora multivora and Phytophthora taxon Totara. These sequences will enable comparative analyses to identify potential virulence strategies and ultimately facilitate better control strategies. This Whole Genome Shotgun data have been deposited in DDBJ/ENA/GenBank under the accession numbers LGTT00000000, LGTU00000000, JPWV00000000, JPWU00000000, LGSK00000000, LGSJ00000000, LGTR00000000, LGTS00000000, LGSM00000000, LGSL00000000, LGSO00000000, and LGSN00000000. PMID:26981359

  8. Cross Species Genomic Analysis Identifies a Mouse Model as Undifferentiated Pleomorphic Sarcoma/Malignant Fibrous Histiocytoma

    PubMed Central

    Mito, Jeffrey K.; Riedel, Richard F.; Dodd, Leslie; Lahat, Guy; Lazar, Alexander J.; Dodd, Rebecca D.; Stangenberg, Lars; Eward, William C.; Hornicek, Francis J.; Yoon, Sam S.; Brigman, Brian E.; Jacks, Tyler; Lev, Dina; Mukherjee, Sayan; Kirsch, David G.

    2009-01-01

    Undifferentiated pleomorphic sarcoma/Malignant Fibrous Histiocytoma (MFH) is one of the most common subtypes of human soft tissue sarcoma. Using cross species genomic analysis, we define a geneset from the LSL-KrasG12D; Trp53Flox/Flox mouse model of soft tissue sarcoma that is highly enriched in human MFH. With this mouse geneset as a filter, we identify expression of the RAS target FOXM1 in human MFH. Expression of Foxm1 is elevated in mouse sarcomas that metastasize to the lung and tissue microarray analysis of human MFH correlates overexpression of FOXM1 with metastasis. These results suggest that genomic alterations present in human MFH are conserved in the LSL-KrasG12D; p53Flox/Flox mouse model of soft tissue sarcoma and demonstrate the utility of this pre-clinical model. PMID:19956606

  9. Genome-wide identification and functional analyses of calmodulin genes in Solanaceous species

    PubMed Central

    2013-01-01

    Background Calmodulin (CaM) is a major calcium sensor in all eukaryotes. It binds calcium and modulates the activity of a wide range of downstream proteins in response to calcium signals. However, little is known about the CaM gene family in Solanaceous species, including the economically important species, tomato (Solanum lycopersicum), and the gene silencing model plant, Nicotiana benthamiana. Moreover, the potential function of CaM in plant disease resistance remains largely unclear. Results We performed genome-wide identification of CaM gene families in Solanaceous species. Employing bioinformatics approaches, multiple full-length CaM genes were identified from tomato, N. benthamiana and potato (S. tuberosum) genomes, with tomato having 6 CaM genes, N. benthamiana having 7 CaM genes, and potato having 4 CaM genes. Sequence comparison analyses showed that three tomato genes, SlCaM3/4/5, two potato genes StCaM2/3, and two sets of N. benthamiana genes, NbCaM1/2/3/4 and NbCaM5/6, encode identical CaM proteins, yet the genes contain different intron/exon organization and are located on different chromosomes. Further sequence comparisons and gene structural and phylogenetic analyses reveal that Solanaceous species gained a new group of CaM genes during evolution. These new CaM genes are unusual in that they contain three introns in contrast to only a single intron typical of known CaM genes in plants. The tomato CaM (SlCaM) genes were found to be expressed in all organs. Prediction of cis-acting elements in 5' upstream sequences and expression analyses demonstrated that SlCaM genes have potential to be highly responsive to a variety of biotic and abiotic stimuli. Additionally, silencing of SlCaM2 and SlCaM6 altered expression of a set of signaling and defense-related genes and resulted in significantly lower resistance to Tobacco rattle virus and the oomycete pathogen, Pythium aphanidermatum. Conclusions The CaM gene families in the Solanaceous species tomato, N

  10. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

    PubMed Central

    Dattenböck, Christoph; Carreras-Villaseñor, Nohemí; Mendoza-Mendoza, Artemio; Tisch, Doris; Alemán, Mario Ivan; Baker, Scott E.; Brown, Christopher; Cervantes-Badillo, Mayte Guadalupe; Cetz-Chel, José; Cristobal-Mondragon, Gema Rosa; Delaye, Luis; Esquivel-Naranjo, Edgardo Ulises; Frischmann, Alexa; Gallardo-Negrete, Jose de Jesus; García-Esquivel, Monica; Gomez-Rodriguez, Elida Yazmin; Greenwood, David R.; Hernández-Oñate, Miguel; Kruszewska, Joanna S.; Lawry, Robert; Mora-Montes, Hector M.; Muñoz-Centeno, Tania; Nieto-Jacobo, Maria Fernanda; Nogueira Lopez, Guillermo; Olmedo-Monfil, Vianey; Osorio-Concepcion, Macario; Piłsyk, Sebastian; Pomraning, Kyle R.; Rodriguez-Iglesias, Aroa; Rosales-Saavedra, Maria Teresa; Sánchez-Arreguín, J. Alejandro; Seidl-Seiboth, Verena; Stewart, Alison; Uresti-Rivera, Edith Elena; Wang, Chih-Li; Wang, Ting-Fang; Zeilinger, Susanne; Casas-Flores, Sergio

    2016-01-01

    SUMMARY The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for “hot topic” research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway. PMID:26864432

  11. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species.

    PubMed

    Schmoll, Monika; Dattenböck, Christoph; Carreras-Villaseñor, Nohemí; Mendoza-Mendoza, Artemio; Tisch, Doris; Alemán, Mario Ivan; Baker, Scott E; Brown, Christopher; Cervantes-Badillo, Mayte Guadalupe; Cetz-Chel, José; Cristobal-Mondragon, Gema Rosa; Delaye, Luis; Esquivel-Naranjo, Edgardo Ulises; Frischmann, Alexa; Gallardo-Negrete, Jose de Jesus; García-Esquivel, Monica; Gomez-Rodriguez, Elida Yazmin; Greenwood, David R; Hernández-Oñate, Miguel; Kruszewska, Joanna S; Lawry, Robert; Mora-Montes, Hector M; Muñoz-Centeno, Tania; Nieto-Jacobo, Maria Fernanda; Nogueira Lopez, Guillermo; Olmedo-Monfil, Vianey; Osorio-Concepcion, Macario; Piłsyk, Sebastian; Pomraning, Kyle R; Rodriguez-Iglesias, Aroa; Rosales-Saavedra, Maria Teresa; Sánchez-Arreguín, J Alejandro; Seidl-Seiboth, Verena; Stewart, Alison; Uresti-Rivera, Edith Elena; Wang, Chih-Li; Wang, Ting-Fang; Zeilinger, Susanne; Casas-Flores, Sergio; Herrera-Estrella, Alfredo

    2016-03-01

    The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.

  12. Molecular variability in the Celleporella hyalina (Bryozoa; Cheilostomata) species complex: evidence for cryptic speciation from complete mitochondrial genomes.

    PubMed

    Waeschenbach, Andrea; Porter, Joanne S; Hughes, Roger N

    2012-09-01

    The bryozoan Celleporella has been shown to be composed of multiple, often cryptic, lineages. We sequenced two complete mitochondrial (mt) genomes of the Celleporella hyalina species complex from Wales, UK and Norway (i) to determine genetic divergence at the complete mt genome level, and (ii) to design new molecular markers for examining the interrelationships amongst the major lineages. In addressing (i), we estimated genetic divergence at three levels: (a) nucleotide diversity (π), (b) genome size, and (c) gene order. Genes nad4L, nad6, and atp8 showed the highest levels of divergence, and rrnL, rrnS, and cox1 showed the lowest levels. Inter-genome nucleotide divergence of protein-coding and ribosomal RNA genes, measured as π, was 0.21. The two genomes differed substantially in size, with the Norwegian genome being 2,573 base pairs (bp) longer than the Welsh genome, 17,265 and 14,692 bp, respectively. This difference in size is attributable to long non-coding regions present in the Norwegian genome. Both genomes exhibit similar gene orders, except for the translocation of one transfer RNA (trnA). Considering the high nucleotide diversity, genome size difference and change in gene order, these mt genomes are considered sufficiently divergent to have originated from two distinct species. In addressing (ii) we designed PCR primers that flank the most conserved regions of the genome: 1,300 bp of cox1 and a contiguous 2,000 bp fragment of rrnL + rrnS. The primers have yielded products for tissue from Wales, Norway, New Zealand, Alaska and Chile and should provide useful tools in establishing species- and population-level diversity within the Celleporella complex.

  13. Extrahuman Epidemiology of Acinetobacter baumannii in Lebanon

    PubMed Central

    Rafei, Rayane; Hamze, Monzer; Pailhoriès, Hélène; Eveillard, Matthieu; Marsollier, Laurent; Joly-Guillou, Marie-Laure; Dabboussi, Fouad

    2015-01-01

    The presence of Acinetobacter baumannii outside hospitals is still a controversial issue. The objective of our study was to explore the extrahospital epidemiology of A. baumannii in Lebanon. From February 2012 to October 2013, a total of 73 water samples, 51 soil samples, 37 raw cow milk samples, 50 cow meat samples, 7 raw cheese samples, and 379 animal samples were analyzed by cultural methods for the presence of A. baumannii. Species identification was performed by rpoB gene sequencing. Antibiotic susceptibility was investigated, and the A. baumannii population was studied by two genotyping approaches: multilocus sequence typing (MLST) and blaOXA-51 sequence-based typing (SBT). A. baumannii was detected in 6.9% of water samples, 2.7% of milk samples, 8.0% of meat samples, 14.3% of cheese samples, and 7.7% of animal samples. All isolates showed a susceptible phenotype against most of the antibiotics tested and lacked carbapenemase-encoding genes, except one that harbored a blaOXA-143 gene. MLST analysis revealed the presence of 36 sequence types (STs), among which 24 were novel STs reported for the first time in this study. blaOXA-51 SBT showed the presence of 34 variants, among which 21 were novel and all were isolated from animal origins. Finally, 30 isolates had new partial rpoB sequences and were considered putative new Acinetobacter species. In conclusion, animals can be a potential reservoir for A. baumannii and the dissemination of new emerging carbapenemases. The roles of the novel animal clones identified in community-acquired infections should be investigated. PMID:25616788

  14. Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species.

    PubMed

    Hess, Jon E; Campbell, Nathan R; Close, David A; Docker, Margaret F; Narum, Shawn R

    2013-06-01

    Unlike most anadromous fishes that have evolved strict homing behaviour, Pacific lamprey (Entosphenus tridentatus) seem to lack philopatry as evidenced by minimal population structure across the species range. Yet unexplained findings of within-region population genetic heterogeneity coupled with the morphological and behavioural diversity described for the species suggest that adaptive genetic variation underlying fitness traits may be responsible. We employed restriction site-associated DNA sequencing to genotype 4439 quality filtered single nucleotide polymorphism (SNP) loci for 518 individuals collected across a broad geographical area including British Columbia, Washington, Oregon and California. A subset of putatively neutral markers (N = 4068) identified a significant amount of variation among three broad populations: northern British Columbia, Columbia River/southern coast and 'dwarf' adults (F(CT) = 0.02, P ≪ 0.001). Additionally, 162 SNPs were identified as adaptive through outlier tests, and inclusion of these markers revealed a signal of adaptive variation related to geography and life history. The majority of the 162 adaptive SNPs were not independent and formed four groups of linked loci. Analyses with matsam software found that 42 of these outlier SNPs were significantly associated with geography, run timing and dwarf life history, and 27 of these 42 SNPs aligned with known genes or highly conserved genomic regions using the genome browser available for sea lamprey. This study provides both neutral and adaptive context for observed genetic divergence among collections and thus reconciles previous findings of population genetic heterogeneity within a species that displays extensive gene flow.

  15. De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species

    PubMed Central

    Pootakham, Wirulda; Sonthirod, Chutima; Naktang, Chaiwat; Ruang-Areerate, Panthita; Yoocha, Thippawan; Sangsrakru, Duangjai; Theerawattanasuk, Kanikar; Rattanawong, Ratchanee; Lekawipat, Napawan; Tangphatsornruang, Sithichoke

    2017-01-01

    Para rubber tree (Hevea brasiliensis) is an important economic species as it is the sole commercial producer of high-quality natural rubber. Here, we report a de novo hybrid assembly of BPM24 accession, which exhibits resistance to major fungal pathogens in Southeast Asia. Deep-coverage 454/Illumina short-read and Pacific Biosciences (PacBio) long-read sequence data were acquired to generate a preliminary draft, which was subsequently scaffolded using a long-range “Chicago” technique to obtain a final assembly of 1.26 Gb (N50 = 96.8 kb). The assembled genome contains 69.2% repetitive sequences and has a GC content of 34.31%. Using a high-density SNP-based genetic map, we were able to anchor 28.9% of the genome assembly (363 Mb) associated with over two thirds of the predicted protein-coding genes into rubber tree’s 18 linkage groups. These genetically anchored sequences allowed comparative analyses of the intragenomic homeologous synteny, providing the first concrete evidence to demonstrate the presence of paleotetraploidy in Hevea species. Additionally, the degree of macrosynteny conservation observed between rubber tree and cassava strongly supports the hypothesis that the paleotetraploidization event took place prior to the divergence of the Hevea and Manihot species. PMID:28150702

  16. Differentiating sibling species of Zeugodacus caudatus (Insecta: Tephritidae) by complete mitochondrial genome.

    PubMed

    Yong, Hoi-Sen; Song, Sze-Looi; Lim, Phaik-Eem; Eamsobhana, Praphathip; Suana, I Wayan

    2016-10-01

    Zeugodacus caudatus is a pest of pumpkin flowers. It has a Palearctic and Oriental distribution. We report here the complete mitochondrial genome of the Malaysian and Indonesian samples of Z. caudatus determined by next-generation sequencing of genomic DNA and determine their taxonomic status as sibling species and phylogeny with other taxa of the genus Zeugodacus. The whole mitogenome of both samples possessed 37 genes (13 protein-coding genes-PCGs, 2 rRNA and 22 tRNA genes) and a control region. The mitogenome of the Indonesian sample (15,885 bp) was longer than that of the Malaysian sample (15,866 bp). In both samples, TΨC-loop was absent in trnF and DHU-loop was absent in trnS1. Molecular phylogeny based on 13 PCGs was concordant with 15 mitochondrial genes (13 PCGs and 2 rRNA genes), with the two samples of Z. caudatus forming a sister group and the genus Zeugodacus was monophyletic. The Malaysian and Indonesian samples of Z. caudatus have a genetic distance of p = 7.8 % based on 13 PCGs and p = 7.0 % based on 15 mitochondrial genes, indicating status of sibling species. They are proposed to be accorded specific status as members of a species complex.

  17. Genomic Characterization Reveals Insights Into Patulin Biosynthesis and Pathogenicity in Penicillium Species.

    PubMed

    Li, Boqiang; Zong, Yuanyuan; Du, Zhenglin; Chen, Yong; Zhang, Zhanquan; Qin, Guozheng; Zhao, Wenming; Tian, Shiping

    2015-06-01

    Penicillium species are fungal pathogens that infect crop plants worldwide. P. expansum differs from P. italicum and P. digitatum, all major postharvest pathogens of pome and citrus, in that the former is able to produce the mycotoxin patulin and has a broader host range. The molecular basis of host-specificity of fungal pathogens has now become the focus of recent research. The present report provides the whole genome sequence of P. expansum (33.52 Mb) and P. italicum (28.99 Mb) and identifies differences in genome structure, important pathogenic characters, and secondary metabolite (SM) gene clusters in Penicillium species. We identified a total of 55 gene clusters potentially related to secondary metabolism, including a cluster of 15 genes (named PePatA to PePatO), that may be involved in patulin biosynthesis in P. expansum. Functional studies confirmed that PePatL and PePatK play crucial roles in the biosynthesis of patulin and that patulin production is not related to virulence of P. expansum. Collectively, P. expansum contains more pathogenic genes and SM gene clusters, in particular, an intact patulin cluster, than P. italicum or P. digitatum. These findings provide important information relevant to understanding the molecular network of patulin biosynthesis and mechanisms of host-specificity in Penicillium species.

  18. Homologs of the Acinetobacter baumannii AceI Transporter Represent a New Family of Bacterial Multidrug Efflux Systems

    PubMed Central

    Liu, Qi; Henderson, Peter J. F.

    2015-01-01

    ABSTRACT Multidrug efflux systems are a major cause of resistance to antimicrobials in bacteria, including those pathogenic to humans, animals, and plants. These proteins are ubiquitous in these pathogens, and five families of bacterial multidrug efflux systems have been identified to date. By using transcriptomic and biochemical analyses, we recently identified the novel AceI (Acinetobacter chlorhexidine efflux) protein from Acinetobacter baumannii that conferred resistance to the biocide chlorhexidine, via an active efflux mechanism. Proteins homologous to AceI are encoded in the genomes of many other bacterial species and are particularly prominent within proteobacterial lineages. In this study, we expressed 23 homologs of AceI and examined their resistance and/or transport profiles. MIC analyses demonstrated that, like AceI, many of the homologs conferred resistance to chlorhexidine. Many of the AceI homologs conferred resistance to additional biocides, including benzalkonium, dequalinium, proflavine, and acriflavine. We conducted fluorimetric transport assays using the AceI homolog from Vibrio parahaemolyticus and confirmed that resistance to both proflavine and acriflavine was mediated by an active efflux mechanism. These results show that this group of AceI homologs represent a new family of bacterial multidrug efflux pumps, which we have designated the proteobacterial antimicrobial compound efflux (PACE) family of transport proteins. PMID:25670776

  19. Lettuce and fruits as a source of multidrug resistant Acinetobacter spp.

    PubMed

    Carvalheira, Ana; Silva, Joana; Teixeira, Paula

    2017-06-01

    The role of ready-to-eat products as a reservoir of pathogenic species of Acinetobacter remains unclear. The objective of the present study was to evaluate the presence of Acinetobacter species in lettuces and fruits marketed in Portugal, and their susceptibility to antimicrobials. Acinetobacter spp. were isolated from 77.9% of the samples and these microorganisms were also found as endophytes (i.e. present within the plant tissue) in 12 of 20 samples of lettuces analysed. Among 253 isolates that were identified as belonging to this genus, 181 presented different PFGE profiles, representing different strains. Based on the analysis of the partial sequence of rpoB, 175 strains were identified as members of eighteen distinct species and the remaining six strains may represent five new candidate species since their rpoB sequence similarities with type strains were less than 95%. Acinetobacter calcoaceticus and Acinetobacter johnsonii were the most common species, both with the frequency of 26.5%; and 11% of the strains belong to the Acinetobacter baumannii group (i.e. A. baumannii, Acinetobacter pittii, Acinetobacter seifertii and Acinetobacter nosocomialis), which is most frequently associated with nosocomial infections. Overall, the strains were least susceptible to piperacillin (80.1%), piperacillin-tazobactam (64.1%), ceftazidime (43.1%), ciprofloxacin (16.6%), trimethoprim-sulfamethoxazole (14.9%), imipenem (14.4%) and colistin (13.3%). The most active antimicrobials were minocycline and tetracycline, with 0.6% and 3.9% of strains resistant, respectively. About 29.8% of the strains were classified as multidrug-resistant (MDR), 4.4% as extensively drug-resistant (XDR) and the prevalence of MDR strains within the A. baumannii group (25%) was similar to other species (30.4%). The presence of clinically important species as well as MDR strains in lettuces and fruits may be a threat to public health considering that they may transmit these pathogens to environments

  20. Evolution of the bacterial species Lactobacillus delbrueckii: a partial genomic study with reflections on prokaryotic species concept.

    PubMed

    Germond, Jacques-Edouard; Lapierre, Luciane; Delley, Michèle; Mollet, Beat; Felis, Giovanna E; Dellaglio, Franco

    2003-01-01

    presented evidences. Our results indicate the need for an accurate investigation of internal heterogeneity of bacterial species. This study has consequences on the prokaryotic species concept, since genomic flexibility of prokaryotes collides with a stable classification, necessary from a scientific and applied point of view.

  1. Mitochondrial Genome Analyses Suggest Multiple Trichuris Species in Humans, Baboons, and Pigs from Different Geographical Regions

    PubMed Central

    Hawash, Mohamed B. F.; Andersen, Lee O.; Gasser, Robin B.; Stensvold, Christen Rune; Nejsum, Peter

    2015-01-01

    Background The whipworms Trichuris trichiura and Trichuris suis are two parasitic nematodes of humans and pigs, respectively. Although whipworms in human and non-human primates historically have been referred to as T. trichiura, recent reports suggest that several Trichuris spp. are found in primates. Methods and Findings We sequenced and annotated complete mitochondrial genomes of Trichuris recovered from a human in Uganda, an olive baboon in the US, a hamadryas baboon in Denmark, and two pigs from Denmark and Uganda. Comparative analyses using other published mitochondrial genomes of Trichuris recovered from a human and a porcine host in China and from a françois’ leaf-monkey (China) were performed, including phylogenetic analyses and pairwise genetic and amino acid distances. Genetic and protein distances between human Trichuris in Uganda and China were high (~19% and 15%, respectively) suggesting that they represented different species. Trichuris from the olive baboon in US was genetically related to human Trichuris in China, while the other from the hamadryas baboon in Denmark was nearly identical to human Trichuris from Uganda. Baboon-derived Trichuris was genetically distinct from Trichuris from françois’ leaf monkey, suggesting multiple whipworm species circulating among non-human primates. The genetic and protein distances between pig Trichuris from Denmark and other regions were roughly 9% and 6%, respectively, while Chinese and Ugandan whipworms were more closely related. Conclusion and Significance Our results indicate that Trichuris species infecting humans and pigs are phylogenetically distinct across geographical regions, which might have important implications for the implementation of suitable and effective control strategies in different regions. Moreover, we provide support for the hypothesis that Trichuris infecting primates represents a complex of cryptic species with some species being able to infect both humans and non-human primates

  2. Development of a Rapid Identification Method for the Differentiation of Enterococcus Species Using a Species-Specific Multiplex PCR Based on Comparative Genomics.

    PubMed

    Park, Jongbin; Jin, Gwi-Deuk; Pak, Jae In; Won, Jihyun; Kim, Eun Bae

    2017-04-01

    Enterococci are lactic acid bacteria that are commonly found in food and in animal gut. Since 16 S ribosomal RNA (rRNA) sequences, genetic markers for bacterial identification, are similar among several Enterococcus species, it is very difficult to determine the correct species based on only 16 S rRNA sequences. Therefore, we developed a rapid method for the identification of different Enterococcus species using comparative genomics. We compared 38 genomes of 13 Enterococcus species retrieved from the National Center of Biotechnology Information database and identified 25,623 orthologs. Among the orthologs, four genes were specific to four Enterococcus species (Enterococcus faecalis, Enterococcus faecium, Enterococcus hirae, and Enterococcus durans). We designed species-specific primer sets targeting the genes and developed a multiplex PCR using primer sets that could distinguish the four Enterococcus species among the nine strains of Enterococcus species that were available locally. The multiplex PCR method also distinguished the four species isolated from various environments, such as feces of chicken and cow, meat of chicken, cow, and pigs, and fermented soybeans (Cheonggukjang and Doenjang). These results indicated that our novel multiplex PCR using species-specific primers could identify the four Enterococcus species in a rapid and easy way. This method will be useful to distinguish Enterococcus species in food, feed, and clinical settings.

  3. Comprehensive Phylogenetic Analysis of Bovine Non-aureus Staphylococci Species Based on Whole-Genome Sequencing

    PubMed Central

    Naushad, Sohail; Barkema, Herman W.; Luby, Christopher; Condas, Larissa A. Z.; Nobrega, Diego B.; Carson, Domonique A.; De Buck, Jeroen

    2016-01-01

    Non-aureus staphylococci (NAS), a heterogeneous group of a large number of species and subspecies, are the most frequently isolated pathogens from intramammary infections in dairy cattle. Phylogenetic relationships among bovine NAS species are controversial and have mostly been determined based on single-gene trees. Herein, we analyzed phylogeny of bovine NAS species using whole-genome sequencing (WGS) of 441 distinct isolates. In addition, evolutionary relationships among bovine NAS were estimated from multilocus data of 16S rRNA, hsp60, rpoB, sodA, and tuf genes and sequences from these and numerous other single genes/proteins. All phylogenies were created with FastTree, Maximum-Likelihood, Maximum-Parsimony, and Neighbor-Joining methods. Regardless of methodology, WGS-trees clearly separated bovine NAS species into five monophyletic coherent clades. Furthermore, there were consistent interspecies relationships within clades in all WGS phylogenetic reconstructions. Except for the Maximum-Parsimony tree, multilocus data analysis similarly produced five clades. There were large variations in determining clades and interspecies relationships in single gene/protein trees, under different methods of tree constructions, highlighting limitations of using single genes for determining bovine NAS phylogeny. However, based on WGS data, we established a robust phylogeny of bovine NAS species, unaffected by method or model of evolutionary reconstructions. Therefore, it is now possible to determine associations between phylogeny and many biological traits, such as virulence, antimicrobial resistance, environmental niche, geographical distribution, and host specificity. PMID:28066335

  4. Comprehensive Phylogenetic Analysis of Bovine Non-aureus Staphylococci Species Based on Whole-Genome Sequencing.

    PubMed

    Naushad, Sohail; Barkema, Herman W; Luby, Christopher; Condas, Larissa A Z; Nobrega, Diego B; Carson, Domonique A; De Buck, Jeroen

    2016-01-01

    Non-aureus staphylococci (NAS), a heterogeneous group of a large number of species and subspecies, are the most frequently isolated pathogens from intramammary infections in dairy cattle. Phylogenetic relationships among bovine NAS species are controversial and have mostly been determined based on single-gene trees. Herein, we analyzed phylogeny of bovine NAS species using whole-genome sequencing (WGS) of 441 distinct isolates. In addition, evolutionary relationships among bovine NAS were estimated from multilocus data of 16S rRNA, hsp60, rpoB, sodA, and tuf genes and sequences from these and numerous other single genes/proteins. All phylogenies were created with FastTree, Maximum-Likelihood, Maximum-Parsimony, and Neighbor-Joining methods. Regardless of methodology, WGS-trees clearly separated bovine NAS species into five monophyletic coherent clades. Furthermore, there were consistent interspecies relationships within clades in all WGS phylogenetic reconstructions. Except for the Maximum-Parsimony tree, multilocus data analysis similarly produced five clades. There were large variations in determining clades and interspecies relationships in single gene/protein trees, under different methods of tree constructions, highlighting limitations of using single genes for determining bovine NAS phylogeny. However, based on WGS data, we established a robust phylogeny of bovine NAS species, unaffected by method or model of evolutionary reconstructions. Therefore, it is now possible to determine associations between phylogeny and many biological traits, such as virulence, antimicrobial resistance, environmental niche, geographical distribution, and host specificity.

  5. Ant Species Differences Determined by Epistasis between Brood and Worker Genomes

    PubMed Central

    Linksvayer, Timothy A.

    2007-01-01

    Epistasis arising from physiological interactions between gene products often contributes to species differences, particularly those involved in reproductive isolation. In social organisms, phenotypes are influenced by the genotypes of multiple interacting individuals. In theory, social interactions can give rise to an additional type of epistasis between the genomes of social partners that can contribute to species differences. Using a full-factorial cross-fostering design with three species of closely related Temnothorax ants, I found that adult worker size was determined by an interaction between the genotypes of developing brood and care-giving workers, i.e. intergenomic epistasis. Such intergenomic social epistasis provides a strong signature of coevolution between social partners. These results demonstrate that just as physiologically interacting genes coevolve, diverge, and contribute to species differences, so do socially interacting genes. Coevolution and conflict between social partners, especially relatives such as parents and offspring, has long been recognized as having widespread evolutionary effects. This coevolutionary process may often result in coevolved socially-interacting gene complexes that contribute to species differences. PMID:17912371

  6. Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species.

    PubMed

    Lassiter, Erica S; Russ, Carsten; Nusbaum, Chad; Zeng, Qiandong; Saville, Amanda C; Olarte, Rodrigo A; Carbone, Ignazio; Hu, Chia-Hui; Seguin-Orlando, Andaine; Samaniego, Jose A; Thorne, Jeffrey L; Ristaino, Jean B

    2015-11-01

    Phytophthora infestans is one of the most destructive plant pathogens of potato and tomato globally. The pathogen is closely related to four other Phytophthora species in the 1c clade including P. phaseoli, P. ipomoeae, P. mirabilis and P. andina that are important pathogens of other wild and domesticated hosts. P. andina is an interspecific hybrid between P. infestans and an unknown Phytophthora species. We have sequenced mitochondrial genomes of the sister species of P. infestans and examined the evolutionary relationships within the clade. Phylogenetic analysis indicates that the P. phaseoli mitochondrial lineage is basal within the clade. P. mirabilis and P. ipomoeae are sister lineages and share a common ancestor with the Ic mitochondrial lineage of P. andina. These lineages in turn are sister to the P. infestans and P. andina Ia mitochondrial lineages. The P. andina Ic lineage diverged much earlier than the P. andina Ia mitochondrial lineage and P. infestans. The presence of two mitochondrial lineages in P. andina supports the hybrid nature of this species. The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests that the origin of this species hybrid in nature may occur there.

  7. Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.

    PubMed

    Wang, Jing; Street, Nathaniel R; Scofield, Douglas G; Ingvarsson, Pär K

    2016-03-01

    A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.

  8. [Problem of treatment for pyo-inflammatory complications caused by Acinetobacter].

    PubMed

    Bogomolova, N S; Bol'shakov, L V; Kuznetsova, S M

    2014-01-01

    The article deals with analysis of a detection frequency and antibacterial treatment resistance of Acinetobacter spp.of different species affiliation. Strains of bacteria detected in patients with pyo-inflammatory complications after surgeries (period from 2010 to 2012) were involved in the study 137 strains of Acinetobacter spp. were detected and studied Fraction of Acinetobacter spp. in 2010, 2011 and 2012 was 2.3, 3 and 3.4% respectively. Fraction of P. aeruginosain all non-fermentative Gram-negative bacteria (NFGNB) decreased by 120% and fraction of Acinetobacter spp. increased by 200-250%. Acinetobacter spp. detection frequency was not significantly changed in the period from 2006 to 2012. However the fraction of Acinetobacter spp. in NFGNB increased by 150% and was 29% in 2012. Detection frequency of A. baumanii sharply increased in 2012. A study of antibacterial treatment resistance of Acinetobacter spp. (10 antibacterial medicines) showed that Polymyxin B and E (Colistin) was the most effective medicine for A. baumanii and A. calcoaceticus infection. 85-95% of Acinetobacter spp.strains kept sensitivity to this antibacterial medicine. 66-88.9% of A. baumanii strains, 66.7-81.8% of A. alcoaceticus and 66.6% of other Acinetobacter spp. were sensitive to Tigecycline. Dioxidine effectiveness was close to Tigecycline in 66.7-80% of A. baumanii strains. 85-100% of A. calcoaceticus strains were sensitive to Dioxidine. There is a trend of decreasing of A. baumanii sensitivity to Carbapenems by 200%. Fraction of strains sensitive to Meropenem and Imipenem in 2012 was 21.4% and