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Sample records for kak obraz zhizni

  1. Polyarnye siyaniya sistemy avroral'nogo ovala kak kosmoloficheskij obraz drevnej mifologii %t The northern light of the auroral oval system as a cosmological concept of the archaic mythology

    NASA Astrophysics Data System (ADS)

    Alekseeva, L. M.

    Since archaic epochs people attentively observe the sky. They used to associate the sky phenomena with gods, heroes, spirits, etc. People interpreted the regularities in the motion of celestial objects in terms of their mythological model of the Universe. These observations and interpretations were first steps of the archaeoastronomy. Many remarkable features are inherent in the patterns of northern lights of the auroral oval system. Their manifestations are fairly regular. Did the ancients observe and some how classify these northern light phenomena? If yes, with which mythological personages were they associated? When were studies of the polar lights initiated? The present work is an attempt to answer these questions. We shall see that the ancient people assumed the spirit-world to be situated on the North. If so, it should manifest itself in spectacular polar aurorae. The specifically northern mythic cosmology formed the basis for Slavic fairy tales (theme of the Serpent and Serpent Fighter) and folk-beliefs. Other inhabitants of snowy latitudes should also manifest similar views. Studying the mythological reflections of typical auroral phenomena, it is possible to trace up long-standing ideological trends from the late glaciation epoch to the present time. Our results can help geophysicists in studying paleoauroral phenomena.

  2. Quantitative prediction of molecular clock and ka/ks at short timescales.

    PubMed

    Peterson, Grant I; Masel, Joanna

    2009-11-01

    Recent empirical studies of taxa including humans, fish, and birds have shown elevated rates of molecular evolution between species that diverged recently. Using the Moran model, we calculate expected divergence as a function of time. Our findings suggest that the observed phenomenon of elevated rates at short timescales is consistent with standard population genetics theory. The apparent acceleration of the molecular clock at short timescales can be explained by segregating polymorphisms present at the time of the ancestral population, both neutral and slightly deleterious, and not newly arising slightly deleterious mutations as has been previously hypothesized. Our work also suggests that the duration of the rate elevation depends on the effective population size, providing a method to correct time estimates of recent divergence events. Our model concords with estimates of divergence obtained from African cichlid fish and humans. As an additional application of our model, we calculate that K(a)/K(s) is elevated within a population before decaying slowly to its long-term value. Similar to the molecular clock, the duration and magnitude of K(a)/K(s) elevation depend on the effective population size. Unlike the molecular clock, however, K(a)/K(s) elevation is caused by newly arising slightly deleterious mutations. This elevation, although not as severe in magnitude as had been previously predicted in models neglecting ancestral polymorphism, persists slightly longer.

  3. The great disease enemy, Kak'ke (beriberi) and the Imperial Japanese Army.

    PubMed

    Hawk, Alan

    2006-04-01

    Although Japanese military officials had discovered that an improved diet could prevent beriberi by the late 19th century, their soldiers in the army suffered from beriberi during the Russo-Japanese War and World War II. A change in diet at the end of the Russo-Japanese War solved the problem and the army applied the lesson learned, along with postwar scientific discoveries about nutrition, toward the diet used during World War II. However, beriberi again plagued Japanese soldiers, this time due to poor logistics and unpalatable dietary supplements. PMID:16673750

  4. Application of the Photomodeler software and Matlab environment for analysisof objects movement parameters based on image sequences. (Polish Title: Wykorzystanie pakietu Photomodeler oraz środowiska Matlab, do badania parametrów ruchu obiektów na podstawie obrazów sekwencyjnych)

    NASA Astrophysics Data System (ADS)

    Markowski, T.

    2013-12-01

    Analysis of objects movement parameters is the area of interest of scientists representing many disciplines. Technological progress provides improvement of research methods. One of them is photogrammetry, and more specifically, close-range image sequences processing. Much research on different approaches to this issue are conducted all over the world. Proposed solution is to carry out photogrammetric measurements using one of the standard programs for close-range objects 3D modeling - PhotoModeler software and their mathematical processing using popular computing environment - Matlab software. Application of existing software's functionality, in many cases seems to be less costly than development and then implementation of specialized measuring and computing applications, dedicated to analysis of movement parameters. Considered solution is based primarily on the appropriate transformations of the frame of reference with respect to which the movement takes place. Automatic coded targets measurements and bundle adjustment, carried out using PhotoModeler software, were used in the research. In order to calculate objects movements parameters, there were further repeated isometric coordinates transformations, numerical differentiation in method of difference quotient and orientation by iterative tabulation with intervals narrowing additionally applied by building own Matlab environment functions. A number of experiments were performed using registration in the form of films from JVC GZ-HD5 digital video camera and films and series of photographs from Nikon D5000 digital photographic camera. Accomplished experiments covered different objects of movement parameters analysis and also distinct movement types. There were also three different versions of established frame of reference -movement of the camera in relation to surroundings, movement of the object in relation to the camera and movement of the object in relation to surrounding. Carried out research revealed that there is a very large variation of the computed objects movement parameters accuracies. As the main sources of errors there can be distinguished some problems with identification and measurements of targets, errors in interior and exterior orientations and also the lowering of speed and acceleration accuracies by low time data accuracies. Therefore, positive and negative aspects of applying the discussed method, as well as its limitations and suggestions for possible ways of implementation have been noticed.

  5. Map of land use / land cover changes in Małopolska voivodeship in 1986-2010 created by object based image analysis of. (Polish Title: Mapa zmian pokrycia terenu małwpolski 1986-2011 wykonana w oparciu o klasyfikację obiektową obrazów satelitarnych Landsat oraz RapidEye)

    NASA Astrophysics Data System (ADS)

    Wężyk, P.; Wójtowicz-Nowakowska, A.; Pierzchalski, M.; Mlost, J.; Szafrańska, Beata

    2013-12-01

    Changes in land use / land cover are the result of interaction between natural processes and human activity. Using GIS analysis to estimate the dynamic of these changes we can detect former trends and their simulation in the future. Diagnosed directions of changes can be used e.g. to create local plans of spatial management or region growth policy. Main goal of this study was to diagnose main trends of changes in land use / land cover in Malopolska voivodeship in last 25 years (1986-2010). Results were shown as statistics and map compositions. Project was created based on RapidEye and LANDSAT 5 TM satellite data and aerial imagery from 2009-2010. The best way to process huge amount and various data was to use Object Based Image Analysis (OBIA). As the results of classification we received 10 classes of land use for both terms of analyses (1986-1987 and 2009-2010). Identified classes were: bare soil, grass-covered areas, urban areas, rivers and watercourses, coniferous forest, leaf forest, peatbog, and other areas. Results show, that especially 2 classes arisen much: forest (4.39%) and urban areas (2.40%), mostly at the expanse of agricultural (-3.60%) and grass-covered areas (-1.18%). Based on results we can say, that changes detected in past 25 years in Małopolska region, which we can also notice today, agree with general trends of landscape changes, that we can observe in Poland for the last 3 decades. These general changes are: renewed succession of forest on areas where agricultural production discontinued; also intense development of road infrastructure. Object Based Image Analysis allowed to realize these study for area of more than 15 000 km2for only a few weeks.

  6. Classification of fully polarimetric F-SAR ( X / S ) airborne radar images using decomposition methods. (Polish Title: Klasyfikacja treści polarymetrycznych obrazów radarowych z wykorzystaniem metod dekompozycji na przykładzie systemu F-SAR ( X / S ))

    NASA Astrophysics Data System (ADS)

    Mleczko, M.

    2014-12-01

    Polarimetric SAR data is not widely used in practice, because it is not yet available operationally from the satellites. Currently we can distinguish two approaches in POL - In - SAR technology: alternating polarization imaging (Alt - POL) and fully polarimetric (QuadPol). The first represents a subset of another and is more operational, while the second is experimental because classification of this data requires polarimetric decomposition of scattering matrix in the first stage. In the literature decomposition process is divided in two types: the coherent and incoherent decomposition. In this paper the decomposition methods have been tested using data from the high resolution airborne F - SAR system. Results of classification have been interpreted in the context of the land cover mapping capabilities

  7. Kak Amerikantsy iskali vetra v pole, a nashli radiatsionnyj poyas i kak Russkie iskali radiatsionnyj poyas, a nashli solnechnyj veter Chast' I %t How Americans looked for "a wind in a field" but found a radiation belt, and how Russians looked for a radiation belt but found a solar wind or physical experiments on the first artificial Earth's satellites and a discovery of radiation belts

    NASA Astrophysics Data System (ADS)

    Zavidonov, I. V.

    The history of the most important scientific discovery of the early space era - the discovery of the inner and outer radiation belts of the Earth in 1958 is reconstructed. The paper uses archival records to bring to light the relative contributions of Soviet and American reseachers to the complex process of discovery. It also shows how misuses of science in mass-media political propaganda led to misrepresentations of the real historical portrayal of early space research.

  8. Suppression of Dwarf and irregular xylem Phenotypes Generates Low-Acetylated Biomass Lines in Arabidopsis.

    PubMed

    Bensussan, Matthieu; Lefebvre, Valérie; Ducamp, Aloïse; Trouverie, Jacques; Gineau, Emilie; Fortabat, Marie-Noëlle; Guillebaux, Alexia; Baldy, Aurélie; Naquin, Delphine; Herbette, Stéphane; Lapierre, Catherine; Mouille, Gregory; Horlow, Christine; Durand-Tardif, Mylène

    2015-06-01

    eskimo1-5 (esk1-5) is a dwarf Arabidopsis (Arabidopsis thaliana) mutant that has a constitutive drought syndrome and collapsed xylem vessels, along with low acetylation levels in xylan and mannan. ESK1 has xylan O-acetyltransferase activity in vitro. We used a suppressor strategy on esk1-5 to screen for variants with wild-type growth and low acetylation levels, a favorable combination for ethanol production. We found a recessive mutation in the KAKTUS (KAK) gene that suppressed dwarfism and the collapsed xylem character, the cause of decreased hydraulic conductivity in the esk1-5 mutant. Backcrosses between esk1-5 and two independent knockout kak mutants confirmed suppression of the esk1-5 effect. kak single mutants showed larger stem diameters than the wild type. The KAK promoter fused with a reporter gene showed activity in the vascular cambium, phloem, and primary xylem in the stem and hypocotyl. However, suppression of the collapsed xylem phenotype in esk1 kak double mutants was not associated with the recovery of cell wall O-acetylation or any major cell wall modifications. Therefore, our results indicate that, in addition to its described activity as a repressor of endoreduplication, KAK may play a role in vascular development. Furthermore, orthologous esk1 kak double mutants may hold promise for ethanol production in crop plants.

  9. Suppression of Dwarf and irregular xylem Phenotypes Generates Low-Acetylated Biomass Lines in Arabidopsis1[OPEN

    PubMed Central

    Lefebvre, Valérie; Ducamp, Aloïse; Trouverie, Jacques; Fortabat, Marie-Noëlle; Guillebaux, Alexia; Baldy, Aurélie; Naquin, Delphine; Lapierre, Catherine; Mouille, Gregory; Horlow, Christine; Durand-Tardif, Mylène

    2015-01-01

    eskimo1-5 (esk1-5) is a dwarf Arabidopsis (Arabidopsis thaliana) mutant that has a constitutive drought syndrome and collapsed xylem vessels, along with low acetylation levels in xylan and mannan. ESK1 has xylan O-acetyltransferase activity in vitro. We used a suppressor strategy on esk1-5 to screen for variants with wild-type growth and low acetylation levels, a favorable combination for ethanol production. We found a recessive mutation in the KAKTUS (KAK) gene that suppressed dwarfism and the collapsed xylem character, the cause of decreased hydraulic conductivity in the esk1-5 mutant. Backcrosses between esk1-5 and two independent knockout kak mutants confirmed suppression of the esk1-5 effect. kak single mutants showed larger stem diameters than the wild type. The KAK promoter fused with a reporter gene showed activity in the vascular cambium, phloem, and primary xylem in the stem and hypocotyl. However, suppression of the collapsed xylem phenotype in esk1 kak double mutants was not associated with the recovery of cell wall O-acetylation or any major cell wall modifications. Therefore, our results indicate that, in addition to its described activity as a repressor of endoreduplication, KAK may play a role in vascular development. Furthermore, orthologous esk1 kak double mutants may hold promise for ethanol production in crop plants. PMID:25888614

  10. A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate.

    PubMed

    Wyckoff, Gerald J; Malcom, Christine M; Vallender, Eric J; Lahn, Bruce T

    2005-07-01

    Under prevailing theories, the nonsynonymous-to-synonymous substitution ratio (i.e. K(a)/K(s)), which measures the fixation probability of nonsynonymous mutations, is correlated with the strength of selection. In this article, we report that K(a)/K(s) is also strongly correlated with the mutation rate as measured by K(s), and that this correlation appears to have a similar magnitude as the correlation between K(a)/K(s) and selective strength. This finding cannot be reconciled with current theories. It suggests that we should re-evaluate the current paradigms of coding-sequence evolution, and that the wide use of K(a)/K(s) as a measure of selective strength needs reassessment.

  11. Assessing The Evolutionary Diversity Of Exon Skipping Events In Human, Mouse And Rat

    NASA Astrophysics Data System (ADS)

    Hsu, Fang-Rong; Chen, Chao-Jung; Kuo, Min-Chieh; Chang, Hwan-You; Shia, Wei-Chung

    2008-01-01

    This study is to research on the cross-species comparative analysis of homologous genetic sequence among human, mouse and rat by bioinformatics method, hopefully assessing the evolutionary diversity through exon length, reading frame preservation and KA/KS ratio test of alternative splicing events. Alternative splicing (AS) is an important mechanism in eukaryotic organism. We choose the "exon skipping events" from AS events for research. In the data of "conserved exon skipping events", we get 668 human-mouse conserved events, 179 human-rat conserved events and 266 conserved mouse-rat events. There are some extra data such as "non-conserved exon skipping events" and "species-specific events". We found out that the length of AS exon is shorter in conserved exon skipping event, but the ratio of reading frame preservation is higher. Among them, the minor form is the most special. We even got the same result in non-conserved exon skipping events. We calculated the KA/KS value by KA/KS ratio test and found out that the human-mouse KA/KS ratio is 0.158, the human-rat is 0.182 and the mouse-rat is 0.190. This represents that the human-mouse conserved events have the highest purifying selection pressure. In the end, we adopt KA/KS ratio test to do a further analysis between conserved and non-conserved exon skipping events and evaluate the evolutionary diversity of cross-species comparation.

  12. On the reported magnetic precursor of the 1993 Guam earthquake

    NASA Astrophysics Data System (ADS)

    Thomas, J. N.; Love, J. J.; Johnston, M. J.

    2009-12-01

    Using 1-second magnetometer data recorded 65 km from the epicenter, Hayakawa et al. [1996] and Miyahara et al. [1999] identify changes in ultra-low frequency, magnetic polarization (the ratio of vertical to horizontal field components) occurring prior to and possibly related to the 1993 Mw 7.7 Guam earthquake. We compare these same 1-second Guam data with similar 1-second data from the Kakioka observatory (KAK) in Japan, and the global, magnetic activity index Kp. In analyzing many months of magnetic-polarization data before and after the earthquake, we find (1) analysis problems with both the Hayakawa et al. and the Miyahara et al. results, (2) significant correlation between the Guam and KAK data, and (3) an absence of precursory signals after removing common disturbances using KAK as a reference. We conclude that the observed changes in polarization are part of normal global magnetic activity and are unrelated to the earthquake.

  13. Proceedings of the Annual Meeting of the Association for Education in Journalism and Mass Communication (81st, Baltimore, Maryland, August 5-8, 1998). Advertising.

    ERIC Educational Resources Information Center

    Association for Education in Journalism and Mass Communication.

    The Advertising section of the Proceedings contains the following 18 papers: "The Birth of Adwatches: Political Advertising Becomes Front-Page News" (Jennifer Greer); "A Cross-Cultural Comparison of the Effects of Source Credibility on Attitudes and Behavioral Intentions" (Kak Yoon, Choong Hyun Kim, and Min-Sun Kim); "Perceptions of Japanese…

  14. Land Surface Temperature in Łódź Obtained from Landsat 5TM

    NASA Astrophysics Data System (ADS)

    Jędruszkiewicz, Joanna; Zieliński, Mariusz

    2012-01-01

    The main aim of this paper is to present the spatial differentiation of Land Surface Temperature LST in Łódź based on Landsat 5 Thematic Mapper (L5TM) images. Analysis was performed for all L5TM images from 2011, with clear sky over Łódź. Land surface temperature (LST) play an important role in determination of weather conditions in boundary layer of atmosphere, especially connected with convection. Environmental satellites from Landsat series delivers the high resolution images of Earth's surface and according to the estimations made on the ground of it are precise. LST depends widely on surface emissivity. In this paper the emissivity was estimated from MODIS sensor as well as NDVI index, then both method were compared. The processed images allowed to determine the warmest and the coldest areas in the administrative boundaries of Łódź. The highest LST values has been found in industrial areas and the in the heart of the city. However, there are some places lying in city outskirts, where the LST values are as high, for instance Lodz Airport. On the contrary the lowest LST values occur mostly in terrains covered with vegetation i.e. forests or city parks. Głównym celem tego opracowania było oszacowanie temperatury powierzchni Ziemi w Łodzi, na podstawie obrazów satelitarnych pochodzących z satelity Landsat 5 Thematic Mapper (L5TM). Analizę wykonane dla obrazów wszystkich dostępnych obrazów z 2011 roku, na których zachmurzenie nie wystąpiło nad obszarem Łodzi. Temperatura powierzchni Ziemi odgrywa istotną rolę w kształtowaniu warunków pogodowych w warstwie granicznej, szczególnie związanych z konwekcją. Satelity środowiskowe z serii Landsat dostarczają obrazów w dużej rozdzielczości, dzięki czemu pozwalają na stosunkowo dokładne oszacowanie tego parametru. Wielkość temperatury w dużym stopniu zależy od emisyjności danej powierzchni. W niniejszym opracowaniu porównano temperaturę powierzchniową obliczoną dla emisyjno

  15. On the reported magnetic precursor of the 1993 guam earthquake

    USGS Publications Warehouse

    Thomas, J.N.; Love, J.J.; Johnston, M.J.S.; Yumoto, K.

    2009-01-01

    Using 1-second magnetometer data recorded 67 km from the epicenter of the 1993 Mw 7.7 Guam earthquake, Hayakawa et al. (1996) and Miyahara et al. (1999) identify anomalous precursory changes in ultra-low frequency magnetic polarization (the ratio of vertical to horizontal field components). In a check of their results, we compare their data (GAM) with 1-second data from the Kakioka observatory (KAK) in Japan and the global magnetic activity index Kp. We also examine log books kept by USGS staff working on the Guam magnetic observatory. We find (1) analysis problems with both Hayakawa et al. and Miyahara et al., (2) significant correlation between the GAM, KAK, and Kp data, and (3) an absence of identifiable localized anomalous signals occurring prior to the earthquake. The changes we do find in polarization are part of normal global magnetic activity; they are unrelated to the earthquake. Copyright 2009 by the American Geophysical Union.

  16. On the reported magnetic precursor of the 1993 Guam earthquake

    NASA Astrophysics Data System (ADS)

    Thomas, Jeremy N.; Love, Jeffrey J.; Johnston, Malcolm J. S.; Yumoto, Kiyohumi

    2009-08-01

    Using 1-second magnetometer data recorded 67 km from the epicenter of the 1993 Mw 7.7 Guam earthquake, Hayakawa et al. (1996) and Miyahara et al. (1999) identify anomalous precursory changes in ultra-low frequency magnetic polarization (the ratio of vertical to horizontal field components). In a check of their results, we compare their data (GAM) with 1-second data from the Kakioka observatory (KAK) in Japan and the global magnetic activity index Kp. We also examine log books kept by USGS staff working on the Guam magnetic observatory. We find (1) analysis problems with both Hayakawa et al. and Miyahara et al., (2) significant correlation between the GAM, KAK, and Kp data, and (3) an absence of identifiable localized anomalous signals occurring prior to the earthquake. The changes we do find in polarization are part of normal global magnetic activity; they are unrelated to the earthquake.

  17. Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome.

    PubMed

    Thornton, Kevin; Long, Manyuan

    2002-06-01

    The recent sequencing of several eukaryotic genomes has generated considerable interest in the study of gene duplication events. The classical model of duplicate gene evolution is that recurrent mutation ultimately results in one copy becoming a pseudogene, and only rarely will a beneficial new function evolve. Here, we study divergence between coding sequence duplications in Drosophila melanogaster as a function of the linkage relationship between paralogs. The mean K(a)/K(s) between all duplicates in the D. melanogaster genome is 0.2803, indicating that purifying selection is maintaining the structure of duplicate coding sequences. However, the mean K(a)/K(s) between duplicates that are both on the X chromosome is 0.4701, significantly higher than the genome average. Further, the distribution of K(a)/K(s) for these X-linked duplicates is significantly shifted toward higher values when compared with the distributions for paralogs in other linkage relationships. Two models of molecular evolution provide qualitative explanations of these observations-relaxation of selective pressure on the duplicate copies and, more likely, positive selection on recessive adaptations. We also show that there is an excess of X-linked duplicates with low K(s), suggesting a larger proportion of relatively young duplicates on the D. melanogaster X chromosome relative to autosomes.

  18. The evolution of cancer-related genes in hominoids.

    PubMed

    Kang, Lin; Michalak, Pawel

    2015-01-01

    The evolution of cancer suppression is essential for the maintenance of multicellularity. The lack of correlation between body size and cancer risk across species, known as Peto's paradox, suggests that genetic variation in cancer resistance is sufficient to compensate for increases of cell numbers in bigger animals. To assess evolutionary dynamics of cancer-related genes, we analyzed Ka, Ks,and Ka/Ks values in 120 oncogenes and tumor suppressor genes (TSG) among seven hominoid species, including two extinct species, Neanderthal and Denisovan. Ka/Ks of tumor suppressor genes tended to be higher relative to that of oncogenes, consistent with relaxed purifying selection acting on the former. Ka/Ks values were positively correlated with TSG scores, but negatively correlated with oncogene scores, suggesting opposing selection pressures operating on the two groups of cancer-related genes. Additionally, we found 108 species-divergent substitutions that were prevalent germline genotypes in some species but in humans appeared only as somatic cancerous mutations. Better understanding the resistance to cancer may lead to new methods of cancer prevention in humans.

  19. Activation of trimeric P2X2 receptors by fewer than three ATP molecules.

    PubMed

    Stelmashenko, Olga; Lalo, Ulyana; Yang, Yue; Bragg, Laricia; North, R Alan; Compan, Vincent

    2012-10-01

    P2X receptors are trimeric membrane proteins. When they bind extracellular ATP, a conformational change occurs that opens a transmembrane ion channel. The ATP-binding pocket is formed in a cleft between two subunits, and a critical amino acid residue for ATP contact is Lys⁶⁹ (P2X2 numbering). In the present work, we sought to determine whether the binding of fewer than three ATP molecules could open the ion channel. We expressed eight concatenated cDNAs in human embryonic kidney cells, which encoded three serially joined, epitope-tagged, subunits with either Lys or Ala at position 69 (denoted as KKK, KKA, KAK, AKK, KAA, AKA, AAK, and AAA). Western blotting of surface-biotinylated proteins indicated that breakdown of concatemers to individual subunits was minimal. Recording of membrane currents in response to ATP (whole cell and excised outside-out patch) showed that all formed functional channels except AAK, AKA, and AAA. There was no difference in the kinetics of activation and deactivation among KKK, KKA, KAK, and AKK channels, and amplitude of the unitary conductances was in all cases not different from that found after expression of a single wild-type subunit. Currents through KKA and KAK receptors were larger than those observed for AKK receptors. The results indicate that trimeric P2X receptors containing only two intact binding sites can be readily activated by ATP.

  20. Species-specific duplications of NBS-encoding genes in Chinese chestnut (Castanea mollissima)

    PubMed Central

    Zhong, Yan; Li, Yingjun; Huang, Kaihui; Cheng, Zong-Ming

    2015-01-01

    The disease resistance (R) genes play an important role in protecting plants from infection by diverse pathogens in the environment. The nucleotide-binding site (NBS)-leucine-rich repeat (LRR) class of genes is one of the largest R gene families. Chinese chestnut (Castanea mollissima) is resistant to Chestnut Blight Disease, but relatively little is known about the resistance mechanism. We identified 519 NBS-encoding genes, including 374 NBS-LRR genes and 145 NBS-only genes. The majority of Ka/Ks were less than 1, suggesting the purifying selection operated during the evolutionary history of NBS-encoding genes. A minority (4/34) of Ka/Ks in non-TIR gene families were greater than 1, showing that some genes were under positive selection pressure. Furthermore, Ks peaked at a range of 0.4 to 0.5, indicating that ancient duplications arose during the evolution. The relationship between Ka/Ks and Ks indicated greater selective pressure on the newer and older genes with the critical value of Ks = 0.4–0.5. Notably, species-specific duplications were detected in NBS-encoding genes. In addition, the group of RPW8-NBS-encoding genes clustered together as an independent clade located at a relatively basal position in the phylogenetic tree. Many cis-acting elements related to plant defense responses were detected in promoters of NBS-encoding genes. PMID:26559332

  1. Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae.

    PubMed

    Mao, Yunrui; Zhang, Yonghua; Xu, Chuan; Qiu, Yingxiong

    2016-01-01

    Dysosma species (Berberidaceae, Podophylloideae) are of great medicinal pharmacogenetic importance and used as model systems to study the drivers and mechanisms of species diversification of temperate plants in East Asia. Recently, we have sequenced the transcriptome of the low-elevation D. versipellis. In this study, we sequenced the transcriptome of the high-elevation D. aurantiocaulis and used comparative genomic approaches to investigate the transcriptome evolution of the two species. We retrieved 53,929 unigenes from D. aurantiocaulis by de novo transcriptome assemblies using the Illumina HiSeq 2000 platform. Comparing the transcriptomes of both species, we identified 4593 orthologs. Estimation of Ka/Ks ratios for 3126 orthologs revealed that none had a Ka/Ks significantly greater than 1, whereas 1273 (Ka/Ks < 0.5, P < 0.05) were inferred to be under purifying selection. A total of 51 primer pairs were successfully designed from 461 EST-SSRs contained in 4593 orthologs. Marker validation assay revealed that 26 (51%) and 41 (80.4%) produced clear fragments with the expected sizes in all Podophylloideae species. Specifically, 19 different sequences of CYP719A were identified from PCR-amplified genomic DNA of all 12 species of Podophylloideae using primers designed from the assembled transcripts. The data further indicated that CYP719A was likely subject to strong selective constraints maintaining only one copy per genome. In Dysosma, there was relaxed purifying selection or more positive selection for high-elevation species. Overall, this study has generated a wealth of molecular resources potentially useful for pharmacogenetic and evolutionary studies in Dysosma and allied taxa.

  2. Sperm proteome of Mytilus galloprovincialis: Insights into the evolution of fertilization proteins in marine mussels.

    PubMed

    Zhang, Yanjie; Mu, Huawei; Lau, Stanley C K; Zhang, Zhifeng; Qiu, Jian-Wen

    2015-12-01

    Cataloging the sperm proteome of an animal can improve our understanding of its sperm-egg interaction and speciation, but such data are available for only a few free-spawning invertebrates. This study aimed to identify the sperm proteome of Mytilus galloprovincialis, a free-spawning marine mussel. We integrated public transcriptome datasets by de novo assembly, and applied SDS-PAGE coupled LC-MS/MS analysis to profile the sperm proteome, resulting in the identification of 550 proteins. Comparing the homologous sperm protein coding genes between M. galloprovincialis and its closely related species M. edulis revealed that fertilization proteins have the highest mean nonsynonymous substitution rate (Ka/Ks = 0.62) among 11 functional groups, consistent with previous reports of positive selection of several fertilization proteins in Mytilus. Moreover, 78 sperm proteins in different functional groups have Ka/Ks values > 0.5, indicating the presence of many candidate sperm proteins for further analysis of rapid interspecific divergence. The MS data are available in ProteomeXchange with the identifier PXD001665.

  3. [Dental abnormalities and orthodontic disorders in Turner's syndrome patients].

    PubMed

    Borkowska, Marzena; Gawlik, Aneta; Hankus, Magdalena; Małecka-Tendera, Ewa

    2016-06-01

    Wśród licznych zaburzeń składających się na obraz zespołu Turnera występują również nieprawidłowości stomatologiczne. Szczególną uwagę należy zwrócić na nieprawidłową budowę zębów i zaburzenia ortodontyczne. Wśród nich występują wady zgryzu, takie jak tyłozgryz czy zgryz krzyżowy, a także zwężenie górnego łuku zębowego i wysokie wysklepienie podniebienia. Istotnym elementem są również zaburzenia kostne w obrębie twarzoczaszki, stwierdzane u niemal wszystkich pacjentek. Okazuje się, że terapia rekombinowanym hormonem wzrostu (rGH) mogłaby mieć wpływ na zapobieganie występowaniu ortodontycznych wad szkieletowych. Konieczne są jednak dalsze badania w tym zakresie. Występujące wady mają bezpośredni wpływ na wygląd twarzy pacjentek i ich samoocenę. Niewątpliwie profesjonalna opieka stomatologiczna powinna być włączona w całość wielodyscyplinarnej terapii, którą objęte są pacjentki z ZT.

  4. Legacy and currently used pesticides in the atmospheric environment of Lake Victoria, East Africa.

    PubMed

    Arinaitwe, Kenneth; Kiremire, Bernard T; Muir, Derek C G; Fellin, Phil; Li, Henrik; Teixeira, Camilla; Mubiru, Drake N

    2016-02-01

    The Lake Victoria watershed has extensive agricultural activity with a long history of pesticide use but there is limited information on historical use or on environmental levels. To address this data gap, high volume air samples were collected from two sites close to the northern shore of Lake Victoria; Kakira (KAK) and Entebbe (EBB). The samples, to be analyzed for pesticides, were collected over various periods between 1999 and 2004 inclusive (KAK 1999-2000, KAK 2003-2004, EBB 2003 and EBB 2004 sample sets) and from 2008 to 2010 inclusive (EBB 2008, EBB 2009 and EBB 2010 sample sets). The latter sample sets (which also included precipitation samples) were also analyzed for currently used pesticides (CUPs) including chlorpyrifos, chlorthalonil, metribuzin, trifluralin, malathion and dacthal. Chlorpyrifos was the predominant CUP in air samples with average concentrations of 93.5, 26.1 and 3.54 ng m(-3) for the EBB 2008, 2009, 2010 sample sets, respectively. Average concentrations of total endosulfan (ΣEndo), total DDT related compounds (ΣDDTs) and hexachlorocyclohexanes (ΣHCHs) ranged from 12.3-282, 22.8-130 and 3.72-81.8 pg m(-3), respectively, for all the sample sets. Atmospheric prevalence of residues of persistent organic pollutants (POPs) increased with fresh emissions of endosulfan, DDT and lindane. Hexachlorobenzene (HCB), pentachlorobenzene (PeCB) and dieldrin were also detected in air samples. Transformation products, pentachloroanisole, 3,4,5-trichloroveratrole and 3,4,5,6-tetrachloroveratrole, were also detected. The five most prevalent compounds in the precipitation samples were in the order chlorpyrifos>chlorothalonil>ΣEndo>ΣDDTs>ΣHCHs with average fluxes of 1123, 396, 130, 41.7 and 41.3 ng m(-2)sample(-1), respectively. PeCB exceeded HCB in precipitation samples. The reverse was true for air samples. Backward air trajectories suggested transboundary and local emission sources of the analytes. The results underscore the need for a concerted

  5. Legacy and currently used pesticides in the atmospheric environment of Lake Victoria, East Africa.

    PubMed

    Arinaitwe, Kenneth; Kiremire, Bernard T; Muir, Derek C G; Fellin, Phil; Li, Henrik; Teixeira, Camilla; Mubiru, Drake N

    2016-02-01

    The Lake Victoria watershed has extensive agricultural activity with a long history of pesticide use but there is limited information on historical use or on environmental levels. To address this data gap, high volume air samples were collected from two sites close to the northern shore of Lake Victoria; Kakira (KAK) and Entebbe (EBB). The samples, to be analyzed for pesticides, were collected over various periods between 1999 and 2004 inclusive (KAK 1999-2000, KAK 2003-2004, EBB 2003 and EBB 2004 sample sets) and from 2008 to 2010 inclusive (EBB 2008, EBB 2009 and EBB 2010 sample sets). The latter sample sets (which also included precipitation samples) were also analyzed for currently used pesticides (CUPs) including chlorpyrifos, chlorthalonil, metribuzin, trifluralin, malathion and dacthal. Chlorpyrifos was the predominant CUP in air samples with average concentrations of 93.5, 26.1 and 3.54 ng m(-3) for the EBB 2008, 2009, 2010 sample sets, respectively. Average concentrations of total endosulfan (ΣEndo), total DDT related compounds (ΣDDTs) and hexachlorocyclohexanes (ΣHCHs) ranged from 12.3-282, 22.8-130 and 3.72-81.8 pg m(-3), respectively, for all the sample sets. Atmospheric prevalence of residues of persistent organic pollutants (POPs) increased with fresh emissions of endosulfan, DDT and lindane. Hexachlorobenzene (HCB), pentachlorobenzene (PeCB) and dieldrin were also detected in air samples. Transformation products, pentachloroanisole, 3,4,5-trichloroveratrole and 3,4,5,6-tetrachloroveratrole, were also detected. The five most prevalent compounds in the precipitation samples were in the order chlorpyrifos>chlorothalonil>ΣEndo>ΣDDTs>ΣHCHs with average fluxes of 1123, 396, 130, 41.7 and 41.3 ng m(-2)sample(-1), respectively. PeCB exceeded HCB in precipitation samples. The reverse was true for air samples. Backward air trajectories suggested transboundary and local emission sources of the analytes. The results underscore the need for a concerted

  6. Myostatin rapid sequence evolution in ruminants predates domestication.

    PubMed

    Tellgren, Asa; Berglund, Ann-Charlotte; Savolainen, Peter; Janis, Christine M; Liberles, David A

    2004-12-01

    Myostatin (GDF-8) is a negative regulator of skeletal muscle development. This gene has previously been implicated in the double muscling phenotype in mice and cattle. A systematic analysis of myostatin sequence evolution in ruminants was performed in a phylogenetic context. The myostatin coding sequence was determined from duiker (Sylvicapra grimmia caffra), eland (Taurotragus derbianus), gaur (Bos gaurus), ibex (Capra ibex), impala (Aepyceros melampus rednilis), pronghorn (Antilocapra americana), and tahr (Hemitragus jemlahicus). Analysis of nonsynonymous to synonymous nucleotide substitution rate ratios (Ka/Ks) indicates that positive selection may have been operating on this gene during the time of divergence of Bovinae and Antilopinae, starting from approximately 23 million years ago, a period that appears to account for most of the sequence difference between myostatin in these groups. These periods of positive selective pressure on myostatin may correlate with changes in skeletal muscle mass during the same period. PMID:15522803

  7. Molecular evolution of the HD-ZIP I gene family in legume genomes.

    PubMed

    Li, Zhen; Jiang, Haiyang; Zhou, Lingyan; Deng, Lin; Lin, Yongxiang; Peng, Xiaojian; Yan, Hanwei; Cheng, Beijiu

    2014-01-01

    Homeodomain leucine zipper I (HD-ZIP I) genes were used to increase the plasticity of plants by mediating external signals and regulating growth in response to environmental conditions. The way genomic histories drove the evolution of the HD-ZIP I family in legume species was described; HD-ZIP I genes were searched in Lotus japonicus, Medicago truncatula, Cajanus cajan and Phaseolus vulgaris, and then divided into five clades through phylogenetic analysis. Microsynteny analysis was made based on genomic segments containing the HD-ZIP I genes. Some pairs turned out to conform with syntenic genome regions, while others corresponded to those that were inverted, expanded, or contracted after the divergence of legumes. Besides, we dated their duplications by Ks analysis and demonstrated that all the blocks were formed after the monocot-dicot split; we observed Ka/Ks ratios representing strong purifying selections in the four legume species which might have been followed by gene loss and rearrangement.

  8. Transitions to asexuality result in excess amino acid substitutions.

    PubMed

    Paland, Susanne; Lynch, Michael

    2006-02-17

    Theory predicts that linkage between genetic loci reduces the efficiency of purifying selection. Because of the permanent linkage of all heritable genetic material, asexual lineages may be exceptionally prone to deleterious-mutation accumulation in both nuclear and organelle genes. Here, we show that the ratio of the rate of amino acid to silent substitution (Ka/Ks) in mitochondrial protein-coding genes is higher in obligately asexual lineages than in sexual lineages of the microcrustacean Daphnia pulex. Using a phylogeny-based approach to quantify the frequency of mutational-effect classes, we estimate that mitochondrial protein-coding genes in asexual lineages accumulate deleterious amino acid substitutions at four times the rate in sexual lineages. These results support the hypothesis that sexual reproduction plays a prominent role in reducing the mutational burden in populations.

  9. Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria

    PubMed Central

    2013-01-01

    Background Actinobacteria have adapted to contrasted ecological niches such as the soil, and among others to plants or animals as pathogens or symbionts. Mycobacterium genus contains mostly pathogens that cause a variety of mammalian diseases, among which the well-known leprosy and tuberculosis, it also has saprophytic relatives. Streptomyces genus is mostly a soil microbe known for its secondary metabolites, it contains also plant pathogens, animal pathogens and symbionts. Frankia, a nitrogen-fixing actinobacterium establishes a root symbiosis with dicotyledonous pionneer plants. Pathogens and symbionts live inside eukaryotic cells and tissues and interact with their cellular environment through secreted proteins and effectors transported through transmembrane systems; nevertheless they also need to avoid triggering host defense reactions. A comparative genome analysis of the secretomes of symbionts and pathogens allows a thorough investigation of selective pressures shaping their evolution. In the present study, the rates of silent mutations to non-silent mutations in secretory proteins were assessed in different strains of Frankia, Streptomyces and Mycobacterium, of which several genomes have recently become publicly available. Results It was found that secreted proteins as a whole have a stronger purifying evolutionary rate (non-synonymous to synonymous substitutions or Ka/Ks ratio) than the non-secretory proteins in most of the studied genomes. This difference becomes statistically significant in cases involving obligate symbionts and pathogens. Amongst the Frankia, secretomes of symbiotic strains were found to have undergone evolutionary trends different from those of the mainly saprophytic strains. Even within the secretory proteins, the signal peptide part has a higher Ka/Ks ratio than the mature part. Two contrasting trends were noticed amongst the Frankia genomes regarding the relation between selection strength (i.e. Ka/Ks ratio) and the codon adaptation

  10. [Nucleotide polymorphism and molecular evolution of the LRR region in potato late blight resistance gene Rpi-blb2].

    PubMed

    You, Lu-Peng; Miao, Jing; Zou, Ai-Lan; Qi, Jin-Liang; Yang, Yong-Hua

    2012-04-01

    Rpi-blb2, which is originally derived from Solanum bulbocastanum, is a broad-spectrum potato late blight resistance gene and belongs to the NBS-LRR family. Here, the LRR homologues of Rpi-blb2 were cloned with PCR method from 40 potato cultivars (including 20 resistant potato cultivars and 20 susceptible ones) and 7 wild potato populations. Then, the similarities of the sequences, polymorphic (segregating) sites, and nucleotide diversities were estimated by bioinformatic methods. The results showed that high nucleotide polymorphism and some hot-spot mutations existed in the LRR region of Rpi-blb2. The test of Ka/Ks ratio showed that the function of LRR was conserved because of the purifying selection, although different positions of the Rpi-blb2 LRR region were under different selection pressures. Moreover, the LRR region of Rpi-blb2 had no clear differentiation between the cultivated and wild potatoes. PMID:22522166

  11. Time variation of the electromagnetic transfer function of the earth estimated by using wavelet transform.

    PubMed

    Suto, Noriko; Harada, Makoto; Izutsu, Jun; Nagao, Toshiyasu

    2006-07-01

    In order to accurately estimate the geomagnetic transfer functions in the area of the volcano Mt. Iwate (IWT), we applied the interstation transfer function (ISTF) method to the three-component geomagnetic field data observed at Mt. Iwate station (IWT), using the Kakioka Magnetic Observatory, JMA (KAK) as remote reference station. Instead of the conventional Fourier transform, in which temporary transient noises badly degrade the accuracy of long term properties, continuous wavelet transform has been used. The accuracy of the results was as high as that of robust estimations of transfer functions obtained by the Fourier transform method. This would provide us with possibilities for routinely monitoring the transfer functions, without sophisticated statistical procedures, to detect changes in the underground electrical conductivity structure. PMID:25792780

  12. ULF Seismo-electromagnetic Studies in Kanto, Japan: Progress and Challenges

    NASA Astrophysics Data System (ADS)

    Han, P.; Hattori, K.; Zhuang, J.

    2015-12-01

    In order to clarify the ULF seismo-magnetic phenomena, a sensitive geomagnetic network has been installed in Kanto, Japan. In this study, we have analyzed geomagnetic data observed during the past decade in Izu, Boso, and Kakioka (KAK) stations. To verify the relation between ULF geomagnetic anomalies and local seismicity, statistical studies by superposed epoch analysis (SEA) have been carried out. The results have indicated that before a sizeable earthquake there are clearly higher probabilities of ULF anomalies than after the earthquake: for Seikoshi (SKS) station in Izu, about 20~30 days before, one week and few days before, and one day after the event statistical results of daily counts are significant; for Kiyosumi (KYS) station in Boso around two weeks before, few days before, and one day after the event; For KAK station, 30 days before, about 2 weeks before, few days before, and 2 days after the event. To find out the detailed waveform of anomalous magnetic signals, waveform analysis has been performed. The results show that there are mainly two kinds of seismo-magnetic signature. (1) Noise-like signals: Compared with the background, the signals exhibit small increases of amplitudes at a wide frequency range. (2) Transient/quasi-rectangular signals: the signals have transient/quasi-rectangular waveforms with amplitudes of several nT. The noise-like signals usually persist for several days or even a few weeks, and are mainly associated with large earthquakes; the transient/quasi-rectangular signals have durations of few seconds to few ten seconds, and are registered mainly during slow slip events. Finally, we have evaluated the precursory information of ULF geomagnetic signals for local sizeable earthquakes using Molchan's error diagram. The probability gain is around 2-4 against a Poisson model. The above results have indicated that the ULF seismo-magnetic phenomena clearly contain precursory information and have a possibility of improving the forecasting

  13. A tale of two drug targets: the evolutionary history of BACE1 and BACE2

    PubMed Central

    Southan, Christopher; Hancock, John M.

    2013-01-01

    The beta amyloid (APP) cleaving enzyme (BACE1) has been a drug target for Alzheimer's Disease (AD) since 1999 with lead inhibitors now entering clinical trials. In 2011, the paralog, BACE2, became a new target for type II diabetes (T2DM) having been identified as a TMEM27 secretase regulating pancreatic β cell function. However, the normal roles of both enzymes are unclear. This study outlines their evolutionary history and new opportunities for functional genomics. We identified 30 homologs (UrBACEs) in basal phyla including Placozoans, Cnidarians, Choanoflagellates, Porifera, Echinoderms, Annelids, Mollusks and Ascidians (but not Ecdysozoans). UrBACEs are predominantly single copy, show 35–45% protein sequence identity with mammalian BACE1, are ~100 residues longer than cathepsin paralogs with an aspartyl protease domain flanked by a signal peptide and a C-terminal transmembrane domain. While multiple paralogs in Trichoplax and Monosiga pre-date the nervous system, duplication of the UrBACE in fish gave rise to BACE1 and BACE2 in the vertebrate lineage. The latter evolved more rapidly as the former maintained the emergent neuronal role. In mammals, Ka/Ks for BACE2 is higher than BACE1 but low ratios for both suggest purifying selection. The 5' exons show higher Ka/Ks than the catalytic section. Model organism genomes show the absence of certain BACE human substrates when the UrBACE is present. Experiments could thus reveal undiscovered substrates and roles. The human protease double-target status means that evolutionary trajectories and functional shifts associated with different substrates will have implications for the development of clinical candidates for both AD and T2DM. A rational basis for inhibition specificity ratios and assessing target-related side effects will be facilitated by a more complete picture of BACE1 and BACE2 functions informed by their evolutionary context. PMID:24381583

  14. Complete mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus (Crustacea: Decapoda: Caridea): gene rearrangement and phylogeny within Caridea.

    PubMed

    Shen, Xin; Li, Xiao; Sha, Zhongli; Yan, Binlun; Xu, Qihua

    2012-07-01

    The complete sequence of the mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus Miers (Crustacea: Decapoda: Caridea) is presented here. A comparative analysis based on the currently available mitochondrial genomic data revealed many previously unknown characteristics of the mitochondrial genomes of caridean shrimps. The A. japonicus mitochondrial genome is 16487 bp long and contains the typical set of 37 metazoan genes. The gene arrangements in the mitochondrial genomes of four previously studied carideans (Macrobrachium rosenbergii, M. nipponense, M. lanchesteri and Halocaridina rubra) were found to be identical to the pancrustacean ground pattern; thus, it was considered that gene rearrangements probably did not occur in the suborder Caridea. In the present study, a translocation of the trnE gene involving inversion was found in Alpheus mitochondrial genomes. This phenomenon has not been reported in any other crustacean mitochondrial genome that has been studied so far; however, the translocation of one transfer RNA gene (trnP or trnT) was reported in the mitochondrial genome of Exopalaemon carinicauda. When the ratios of the nonsynonymous and synonymous substitutions rates (Ka/Ks) for the 13 protein coding genes from two Alpheus species (A. japonicus and A. distinguendus) and three Macrobrachium species (M. rosenbergii, M. nipponense, M. lanchesteri) were calculated, the Ka/Ks values for all the protein coding genes in Alpheus and Macrobrachium mitochondrial genomes were found to be less than 1 (between 0.0048 and 0.2057), indicating that a strong purification selection had occurred. The phylogenetic tree that was constructed based on the mitochondrial protein coding genes in the genomes of nine related species indicated that Palaemonidae and Alpheidae formed a monophyly and shared a statistically significant relationship, (Palaemonidae+Alpheidae)+Atyidae, at the family level.

  15. Genetic Basis of Differential Heat Resistance between Two Species of Congeneric Freshwater Snails: Insights from Quantitative Proteomics and Base Substitution Rate Analysis.

    PubMed

    Mu, Huawei; Sun, Jin; Fang, Ling; Luan, Tiangang; Williams, Gray A; Cheung, Siu Gin; Wong, Chris K C; Qiu, Jian-Wen

    2015-10-01

    We compared the heat tolerance, proteomic responses to heat stress, and adaptive sequence divergence in the invasive snail Pomacea canaliculata and its noninvasive congener Pomacea diffusa. The LT50 of P. canaliculata was significantly higher than that of P. diffusa. More than 3350 proteins were identified from the hepatopancreas of the snails exposed to acute and chronic thermal stress using iTRAQ-coupled mass spectrometry. Acute exposure (3 h exposure at 37 °C with 25 °C as control) resulted in similar numbers (27 in P. canaliculata and 23 in P. diffusa) of differentially expressed proteins in the two species. Chronic exposure (3 weeks of exposure at 35 °C with 25 °C as control) caused differential expression of more proteins (58 in P. canaliculata and 118 in P. diffusa), with many of them related to restoration of damaged molecules, ubiquitinating dysfunctional molecules, and utilization of energy reserves in both species; but only in P. diffusa was there a shift from carbohydrate to lipid catabolism. Analysis of orthologous genes encoding the differentially expressed proteins revealed two genes having clear evidence of positive selection (Ka/Ks > 1) and seven candidates for more detailed analysis of positive selection (Ka/Ks between 0.5 and 1). These nine genes are related to energy metabolism, cellular oxidative homeostasis, signaling, and binding processes. Overall, the proteomic and base substitution rate analyses indicate genetic basis of differential resistance to heat stress between the two species, and such differences could affect their further range expansion in a warming climate.

  16. 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

  17. A tale of two drug targets: the evolutionary history of BACE1 and BACE2.

    PubMed

    Southan, Christopher; Hancock, John M

    2013-01-01

    The beta amyloid (APP) cleaving enzyme (BACE1) has been a drug target for Alzheimer's Disease (AD) since 1999 with lead inhibitors now entering clinical trials. In 2011, the paralog, BACE2, became a new target for type II diabetes (T2DM) having been identified as a TMEM27 secretase regulating pancreatic β cell function. However, the normal roles of both enzymes are unclear. This study outlines their evolutionary history and new opportunities for functional genomics. We identified 30 homologs (UrBACEs) in basal phyla including Placozoans, Cnidarians, Choanoflagellates, Porifera, Echinoderms, Annelids, Mollusks and Ascidians (but not Ecdysozoans). UrBACEs are predominantly single copy, show 35-45% protein sequence identity with mammalian BACE1, are ~100 residues longer than cathepsin paralogs with an aspartyl protease domain flanked by a signal peptide and a C-terminal transmembrane domain. While multiple paralogs in Trichoplax and Monosiga pre-date the nervous system, duplication of the UrBACE in fish gave rise to BACE1 and BACE2 in the vertebrate lineage. The latter evolved more rapidly as the former maintained the emergent neuronal role. In mammals, Ka/Ks for BACE2 is higher than BACE1 but low ratios for both suggest purifying selection. The 5' exons show higher Ka/Ks than the catalytic section. Model organism genomes show the absence of certain BACE human substrates when the UrBACE is present. Experiments could thus reveal undiscovered substrates and roles. The human protease double-target status means that evolutionary trajectories and functional shifts associated with different substrates will have implications for the development of clinical candidates for both AD and T2DM. A rational basis for inhibition specificity ratios and assessing target-related side effects will be facilitated by a more complete picture of BACE1 and BACE2 functions informed by their evolutionary context.

  18. Cracking in Concrete near Joints in Steelconcrete Composite Slab / Zarysowanie Płyty Żelbetowej W Strefie Przywęzłowej Stropu Zespolonego

    NASA Astrophysics Data System (ADS)

    Niedośpiał, Marcin; Knauff, Michał; Barcewicz, Wioleta

    2015-03-01

    In this paper results of the experimental tests of four full-scale composite steel-concrete elements are reported. In the steel-concrete composite elements, a steel beam was connected with a slab cast on profiled sheeting, by shear studs. The end-plates were (the thickness of 8 mm, 10 mm and 12 mm) thinner than in ordinary design. Joints between the column and the beams have been designed as semi-rigid, i.e. the deformations of endplates affect the distribution of forces in the adjacent parts of the slab. The paper presents the theory of cracking in reinforced concrete and steel-concrete composite members (according to the codes), view of crack pattern on the surface of the slabs and a comparison of the tests results and the code calculations. It was observed, that some factors influencing on crack widths are not taken in Eurocode 4 (which is based on Eurocode 2 with taking into account the phenomenon called "tension stiffening"). W artykule przedstawiono wyniki badań czterech elementów zespolonych. Kształtownik stalowy połączony był z betonowym stropem wykonanym na blasze fałdowej. W modelu zastosowano cienkie blachy czołowe (o grubości 8 mm, 10 mm i 12 mm), cieńsze niż zwykle przyjmowane w praktyce projektowej. Połączenie to zaprojektowano jako podatne tzn. takie, w którym odkształcenia blach czołowych mają istotny wpływ na rozkład sił w połączeniu. Przedstawiono normową teorię dotyczącą zarysowania elementów żelbetowych i zespolonych, obraz zarysowania stropu oraz porównano otrzymane wyniki z obliczeniami wykonanymi wg aktualnych norm. Zauważono, iż nie wszystkie czynniki obliczania szerokości rys w konstrukcjach zespolonych są zdefiniowane w normie projektowania konstrukcji zespolonych (która w tej kwestii odwołuje się do normy projektowania konstrukcji żelbetowych z uwzględnieniem zjawiska "tension stiffening").

  19. Functional Characterization of Soybean Glyma04g39610 as a Brassinosteroid Receptor Gene and Evolutionary Analysis of Soybean Brassinosteroid Receptors

    PubMed Central

    Peng, Suna; Tao, Ping; Xu, Feng; Wu, Aiping; Huo, Weige; Wang, Jinxiang

    2016-01-01

    Brassinosteroids (BR) play important roles in plant growth and development. Although BR receptors have been intensively studied in Arabidopsis, the BR receptors in soybean remain largely unknown. Here, in addition to the known receptor gene Glyma06g15270 (GmBRI1a), we identified five putative BR receptor genes in the soybean genome: GmBRI1b, GmBRL1a, GmBRL1b, GmBRL2a, and GmBRL2b. Analysis of their expression patterns by quantitative real-time PCR showed that they are ubiquitously expressed in primary roots, lateral roots, stems, leaves, and hypocotyls. We used rapid amplification of cDNA ends (RACE) to clone GmBRI1b (Glyma04g39160), and found that the predicted amino acid sequence of GmBRI1b showed high similarity to those of AtBRI1 and pea PsBRI1. Structural modeling of the ectodomain also demonstrated similarities between the BR receptors of soybean and Arabidopsis. GFP-fusion experiments verified that GmBRI1b localizes to the cell membrane. We also explored GmBRI1b function in Arabidopsis through complementation experiments. Ectopic over-expression of GmBRI1b in Arabidopsis BR receptor loss-of-function mutant (bri1-5 bak1-1D) restored hypocotyl growth in etiolated seedlings; increased the growth of stems, leaves, and siliques in light; and rescued the developmental defects in leaves of the bri1-6 mutant, and complemented the responses of BR biosynthesis-related genes in the bri1-5 bak1-D mutant grown in light. Bioinformatics analysis demonstrated that the six BR receptor genes in soybean resulted from three gene duplication events during evolution. Phylogenetic analysis classified the BR receptors in dicots and monocots into three subclades. Estimation of the synonymous (Ks) and the nonsynonymous substitution rate (Ka) and selection pressure (Ka/Ks) revealed that the Ka/Ks of BR receptor genes from dicots and monocots were less than 1.0, indicating that BR receptor genes in plants experienced purifying selection during evolution. PMID:27338344

  20. Functional Characterization of Soybean Glyma04g39610 as a Brassinosteroid Receptor Gene and Evolutionary Analysis of Soybean Brassinosteroid Receptors.

    PubMed

    Peng, Suna; Tao, Ping; Xu, Feng; Wu, Aiping; Huo, Weige; Wang, Jinxiang

    2016-01-01

    Brassinosteroids (BR) play important roles in plant growth and development. Although BR receptors have been intensively studied in Arabidopsis, the BR receptors in soybean remain largely unknown. Here, in addition to the known receptor gene Glyma06g15270 (GmBRI1a), we identified five putative BR receptor genes in the soybean genome: GmBRI1b, GmBRL1a, GmBRL1b, GmBRL2a, and GmBRL2b. Analysis of their expression patterns by quantitative real-time PCR showed that they are ubiquitously expressed in primary roots, lateral roots, stems, leaves, and hypocotyls. We used rapid amplification of cDNA ends (RACE) to clone GmBRI1b (Glyma04g39160), and found that the predicted amino acid sequence of GmBRI1b showed high similarity to those of AtBRI1 and pea PsBRI1. Structural modeling of the ectodomain also demonstrated similarities between the BR receptors of soybean and Arabidopsis. GFP-fusion experiments verified that GmBRI1b localizes to the cell membrane. We also explored GmBRI1b function in Arabidopsis through complementation experiments. Ectopic over-expression of GmBRI1b in Arabidopsis BR receptor loss-of-function mutant (bri1-5 bak1-1D) restored hypocotyl growth in etiolated seedlings; increased the growth of stems, leaves, and siliques in light; and rescued the developmental defects in leaves of the bri1-6 mutant, and complemented the responses of BR biosynthesis-related genes in the bri1-5 bak1-D mutant grown in light. Bioinformatics analysis demonstrated that the six BR receptor genes in soybean resulted from three gene duplication events during evolution. Phylogenetic analysis classified the BR receptors in dicots and monocots into three subclades. Estimation of the synonymous (Ks) and the nonsynonymous substitution rate (Ka) and selection pressure (Ka/Ks) revealed that the Ka/Ks of BR receptor genes from dicots and monocots were less than 1.0, indicating that BR receptor genes in plants experienced purifying selection during evolution. PMID:27338344

  1. Species-specific expansion and molecular evolution of the 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) gene family in plants.

    PubMed

    Li, Wei; Liu, Wei; Wei, Hengling; He, Qiuling; Chen, Jinhong; Zhang, Baohong; Zhu, Shuijin

    2014-01-01

    The terpene compounds represent the largest and most diverse class of plant secondary metabolites which are important in plant growth and development. The 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR; EC 1.1.1.34) is one of the key enzymes contributed to terpene biosynthesis. To better understand the basic characteristics and evolutionary history of the HMGR gene family in plants, a genome-wide analysis of HMGR genes from 20 representative species was carried out. A total of 56 HMGR genes in the 14 land plant genomes were identified, but no genes were found in all 6 algal genomes. The gene structure and protein architecture of all plant HMGR genes were highly conserved. The phylogenetic analysis revealed that the plant HMGRs were derived from one ancestor gene and finally developed into four distinct groups, two in the monocot plants and two in dicot plants. Species-specific gene duplications, caused mainly by segmental duplication, led to the limited expansion of HMGR genes in Zea mays, Gossypium raimondii, Populus trichocarpa and Glycine max after the species diverged. The analysis of Ka/Ks ratios and expression profiles indicated that functional divergence after the gene duplications was restricted. The results suggested that the function and evolution of HMGR gene family were dramatically conserved throughout the plant kingdom. PMID:24722776

  2. Local adaptation of Gymnocypris przewalskii (Cyprinidae) on the Tibetan Plateau.

    PubMed

    Zhang, Renyi; Ludwig, Arne; Zhang, Cunfang; Tong, Chao; Li, Guogang; Tang, Yongtao; Peng, Zuogang; Zhao, Kai

    2015-05-06

    Divergent selection among environments affects species distributions and can lead to speciation. In this article, we investigated the transcriptomes of two ecotypes of scaleless carp (Gymnocypris przewalskii przewalskii and G. p. ganzihonensis) from the Tibetan Plateau. We used a transcriptome sequencing approach to screen approximately 250,000 expressed sequence tags (ESTs) from the gill and kidney tissues of twelve individuals from the Ganzi River and Lake Qinghai to understand how this freshwater fish has adapted to an ecological niche shift from saline to freshwater. We identified 9,429 loci in the gill transcriptome and 12,034 loci in the kidney transcriptome with significant differences in their expression, of which 242 protein-coding genes exhibited strong positive selection (Ka/Ks > 1). Many of the genes are involved in ion channel functions (e.g., Ca(2+)-binding proteins), immune responses (e.g., nephrosin) or cellular water absorption functions (e.g., aquaporins). These results have potentially broad importance in understanding shifts from saline to freshwater habitats. Furthermore, this study provides the first transcriptome of G. przewalskii, which will facilitate future ecological genomics studies and aid in the identification of genes underlying adaptation and incipient ecological speciation.

  3. Comparative transcriptome analysis highlights the crucial roles of photosynthetic system in drought stress adaptation in upland rice

    PubMed Central

    Zhang, Zheng-Feng; Li, Yuan-Yuan; Xiao, Ben-Ze

    2016-01-01

    Drought stress is one of the major adverse environmental factors reducing plant growth. With the aim to elucidate the underlying molecular basis of rice response to drought stress, comparative transcriptome analysis was conducted between drought susceptible rice cultivar Zhenshan97 and tolerant cultivar IRAT109 at the seedling stage. 436 genes showed differential expression and mainly enriched in the Gene Ontology (GO) terms of stress defence. A large number of variations exist between these two genotypes including 2564 high-quality insertion and deletions (INDELs) and 70,264 single nucleotide polymorphism (SNPs). 1041 orthologous gene pairs show the ratio of nonsynonymous nucleotide substitution rate to synonymous nucleotide substitutions rate (Ka/Ks) larger than 1.5, indicating the rapid adaptation to different environments during domestication. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of positive selection genes suggested that photosynthesis represents the most significant category. The collocation of positively selected genes with the QTLs of photosynthesis and the different photosynthesis performance of these two cultivars further illuminate the crucial function of photosynthesis in rice adaptation to drought stress. Our results also provide fruitful functional markers and candidate genes for future genetic research and improvement of drought tolerance in rice. PMID:26777777

  4. Molecular evolution of the HD-ZIP I gene family in legume genomes.

    PubMed

    Li, Zhen; Jiang, Haiyang; Zhou, Lingyan; Deng, Lin; Lin, Yongxiang; Peng, Xiaojian; Yan, Hanwei; Cheng, Beijiu

    2014-01-01

    Homeodomain leucine zipper I (HD-ZIP I) genes were used to increase the plasticity of plants by mediating external signals and regulating growth in response to environmental conditions. The way genomic histories drove the evolution of the HD-ZIP I family in legume species was described; HD-ZIP I genes were searched in Lotus japonicus, Medicago truncatula, Cajanus cajan and Phaseolus vulgaris, and then divided into five clades through phylogenetic analysis. Microsynteny analysis was made based on genomic segments containing the HD-ZIP I genes. Some pairs turned out to conform with syntenic genome regions, while others corresponded to those that were inverted, expanded, or contracted after the divergence of legumes. Besides, we dated their duplications by Ks analysis and demonstrated that all the blocks were formed after the monocot-dicot split; we observed Ka/Ks ratios representing strong purifying selections in the four legume species which might have been followed by gene loss and rearrangement. PMID:24095777

  5. Selection on rapidly evolving proteins in the Arabidopsis genome.

    PubMed Central

    Barrier, Marianne; Bustamante, Carlos D; Yu, Jiaye; Purugganan, Michael D

    2003-01-01

    Genes that have undergone positive or diversifying selection are likely to be associated with adaptive divergence between species. One indicator of adaptive selection at the molecular level is an excess of amino acid replacement fixed differences per replacement site relative to the number of synonymous fixed differences per synonymous site (omega = K(a)/K(s)). We used an evolutionary expressed sequence tag (EST) approach to estimate the distribution of omega among 304 orthologous loci between Arabidopsis thaliana and A. lyrata to identify genes potentially involved in the adaptive divergence between these two Brassicaceae species. We find that 14 of 304 genes (approximately 5%) have an estimated omega > 1 and are candidates for genes with increased selection intensities. Molecular population genetic analyses of 6 of these rapidly evolving protein loci indicate that, despite their high levels of between-species nonsynonymous divergence, these genes do not have elevated levels of intraspecific replacement polymorphisms compared to previously studied genes. A hierarchical Bayesian analysis of protein-coding region evolution within and between species also indicates that the selection intensities of these genes are elevated compared to previously studied A. thaliana nuclear loci. PMID:12618409

  6. Turning gold into 'junk': transposable elements utilize central proteins of cellular networks.

    PubMed

    Abrusán, György; Szilágyi, András; Zhang, Yang; Papp, Balázs

    2013-03-01

    The numerous discovered cases of domesticated transposable element (TE) proteins led to the recognition that TEs are a significant source of evolutionary innovation. However, much less is known about the reverse process, whether and to what degree the evolution of TEs is influenced by the genome of their hosts. We addressed this issue by searching for cases of incorporation of host genes into the sequence of TEs and examined the systems-level properties of these genes using the Saccharomyces cerevisiae and Drosophila melanogaster genomes. We identified 51 cases where the evolutionary scenario was the incorporation of a host gene fragment into a TE consensus sequence, and we show that both the yeast and fly homologues of the incorporated protein sequences have central positions in the cellular networks. An analysis of selective pressure (Ka/Ks ratio) detected significant selection in 37% of the cases. Recent research on retrovirus-host interactions shows that virus proteins preferentially target hubs of the host interaction networks enabling them to take over the host cell using only a few proteins. We propose that TEs face a similar evolutionary pressure to evolve proteins with high interacting capacities and take some of the necessary protein domains directly from their hosts.

  7. Horizontal Gene Acquisition of Liberibacter Plant Pathogens from a Bacteriome-Confined Endosymbiont of Their Psyllid Vector

    PubMed Central

    Oshima, Kenshiro; Inoue, Hiromitsu; Ohkuma, Moriya; Hongoh, Yuichi; Miyagishima, Shin-ya; Hattori, Masahira; Fukatsu, Takema

    2013-01-01

    he Asian citrus psyllid Diaphorina citri is a notorious agricultural pest that transmits the phloem-inhabiting alphaproteobacterial ‘Candidatus Liberibacter asiaticus’ and allied plant pathogens, which cause the devastating citrus disease called Huanglongbing or greening disease. D. citri harbors two distinct bacterial mutualists in the symbiotic organ called bacteriome: the betaproteobacterium ‘Candidatus Profftella armatura’ in the syncytial cytoplasm at the center of the bacteriome, and the gammaproteobacterium ‘Candidatus Carsonella ruddii’ in uninucleate bacteriocytes. Here we report that a putative amino acid transporter LysE of Profftella forms a highly supported clade with proteins of L. asiaticus, L. americanus, and L. solanacearum. L. crescens, the most basal Liberibacter lineage currently known, lacked the corresponding gene. The Profftella-Liberibacter subclade of LysE formed a clade with proteins from betaproteobacteria of the order Burkholderiales, to which Profftella belongs. This phylogenetic pattern favors the hypothesis that the Liberibacter lineage acquired the gene from the Profftella lineage via horizontal gene transfer (HGT) after L. crescens diverged from other Liberibacter lineages. KA/KS analyses further supported the hypothesis that the genes encoded in the Liberibacter genomes are functional. These findings highlight the possible evolutionary importance of HGT between plant pathogens and their insect vector’s symbionts that are confined in the symbiotic organ and seemingly sequestered from external microbial populations. PMID:24349319

  8. Novel Cathelicidins from Pigeon Highlights Evolutionary Convergence in Avain Cathelicidins and Functions in Modulation of Innate Immunity.

    PubMed

    Yu, Haining; Lu, Yiling; Qiao, Xue; Wei, Lin; Fu, Tingting; Cai, Shasha; Wang, Chen; Liu, Xuelian; Zhong, Shijun; Wang, Yipeng

    2015-07-21

    Cathelicidins are short cationic host defense peptides and play a central role in host innate immune system. Here we identified two novel cathelicidins, Cl-CATH2 and 3, from Columba livia. Evolutionary analysis of avian cathelicidins via phylogenetic tree and Ka/Ks calculations supported the positive selection that prompted evolution of CATH2 to CATH1 and 3, which originate from common ancestor and could belong to one superfamily. Cl-CATH2 and 3 both adopt amphipathic α-helical comformations identified by circular dichroism and the 3D structures built by Rosetta. Cl-CATH2 of CATH2 family with the most expression abundance in bird, exhibited relatively weak antimicrobial activity, but acted instead on the innate immune response without showing undesirable toxicities. In macrophages primed by LPS, Cl-CATH2 significantly down-regulated the gene and protein expressions of inducible nitric oxide synthase and pro-inflammatory cytokines while enhancing the anti-inflammatory cytokine, acting through MAPK and NF-κB signaling pathways. Molecular docking shows for the first time that cathelicidin binds to the opening region of LPS-binding pocket on myeloid differentiation factor 2 (MD-2) of toll-like receptor (TLR)4-MD-2 complex, which in turn inhibits the TLR4 pathway. Our results, therefore, provide new insight into the mechanism underlying the blockade of TLR4 signaling by cathelicidins.

  9. Criticality features in ULF magnetic fields prior to the 2011 Tohoku earthquake

    PubMed Central

    HAYAKAWA, Masashi; SCHEKOTOV, Alexander; POTIRAKIS, Stelios; EFTAXIAS, Kostas

    2015-01-01

    The criticality of ULF (Ultra-low-frequency) magnetic variations is investigated for the 2011 March 11 Tohoku earthquake (EQ) by natural time analysis. For this attempt, some ULF parameters were considered: (1) Fh (horizontal magnetic field), (2) Fz (vertical magnetic field), and (3) Dh (inverse of horizontal magnetic field). The first two parameters refer to the ULF radiation, while the last parameter refers to another ULF effect of ionospheric signature. Nighttime (L.T. = 3 am ± 2 hours) data at Kakioka (KAK) were used, and the power of each quantity at a particular frequency band of 0.03–0.05 Hz was averaged for nighttime hours. The analysis results indicate that Fh fulfilled all criticality conditions on March 3–5, 2011, and that the additional parameter, Dh reached also a criticality on March 6 or 7. In conclusion, criticality has reached in the pre-EQ fracture region a few days to one week before the main shock of the Tohoku EQ. PMID:25743063

  10. Genomewide analysis of MATE-type gene family in maize reveals microsynteny and their expression patterns under aluminum treatment.

    PubMed

    Zhu, Huasheng; Wu, Jiandong; Jiang, Yingli; Jin, Jing; Zhou, Wei; Wang, Yu; Han, Guomin; Zhao, Yang; Cheng, Beijiu

    2016-09-01

    Multidrug and toxic compound extrusion (MATE) proteins are a group of secondary active transporters, which widely exist in all living organisms and play important role in the detoxication of endogenous secondary metabolites and exogenous agents. However, to date, no systematic and comprehensive study of this family is reported in maize. Here, a total of 49 MATE genes (ZmMATE) were identified and divided into seven groups by phylogenetic analysis. Conserved intro-exon structures and motif compositions were investigated in these genes. Results by gene locations indicated that these genes were unevenly distributed among all 10 chromosomes. Tandem and segmental duplications appeared to contribute to the expansion and evolution of this gene family. The Ka/Ks ratios suggested that the ZmMATE has undergone large-scale purifying selection on the maize genome. Interspecies microsynteny analysis revealed that there were independent gene duplication events of 10 ZmMATE. In addition, most maize MATE genes exhibited different expression profiles in diverse tissues and developmental stages. Sixteen MATE genes were chosen for further quantitative real-time polymerase chain reaction analysis showed differential expression patterns in response to aluminum treatment. These results provide a useful clue for future studies on the identification of MATE genes and functional analysis of MATE proteins in maize. PMID:27659341

  11. Systematic analysis of maize class III peroxidase gene family reveals a conserved subfamily involved in abiotic stress response.

    PubMed

    Wang, Yu; Wang, Qianqian; Zhao, Yang; Han, Guomin; Zhu, Suwen

    2015-07-15

    Class III peroxidases (PRXs) are plant-specific enzymes that play key roles in the responses to biotic and abiotic stress during plant growth and development. In this study, we identified 119 nonredundant PRX genes (designated ZmPRXs). These PRX genes were divided into 18 groups based on their phylogenetic relationships. We performed systematic bioinformatics analysis of the PRX genes, including analysis of gene structures, conserved motifs, phylogenetic relationships and gene expression profiles. The ZmPRXs are unevenly distributed on the 10 maize chromosomes. In addition, these genes have undergone 16 segmental duplication and 12 tandem duplication events, indicating that both segmental and tandem duplication were the main contributors to the expansion of the maize PRX family. Ka/Ks analysis suggested that most duplicated ZmPRXs experienced purifying selection, with limited functional divergence during the duplication events, and comparative analysis among maize, sorghum and rice revealed that there were independent duplication events besides the whole-genome duplication of the maize genome. Furthermore, microarray analysis indicated that most highly expressed genes might play significant roles in root. We examined the expression of five candidate ZmPRXs under H2O2, SA, NaCl and PEG stress conditions using quantitative real-time PCR (qRT-PCR), revealing differential expression patterns. This study provides useful information for further functional analysis of the PRX gene family in maize.

  12. Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes.

    PubMed

    Elmer, K R; Fan, S; Gunter, H M; Jones, J C; Boekhoff, S; Kuraku, S; Meyer, A

    2010-03-01

    Crater lakes provide a natural laboratory to study speciation of cichlid fishes by ecological divergence. Up to now, there has been a dearth of transcriptomic and genomic information that would aid in understanding the molecular basis of the phenotypic differentiation between young species. We used next-generation sequencing (Roche 454 massively parallel pyrosequencing) to characterize the diversity of expressed sequence tags between ecologically divergent, endemic and sympatric species of cichlid fishes from crater lake Apoyo, Nicaragua: benthic Amphilophus astorquii and limnetic Amphilophus zaliosus. We obtained 24 174 A. astorquii and 21 382 A. zaliosus high-quality expressed sequence tag contigs, of which 13 106 pairs are orthologous between species. Based on the ratio of nonsynonymous to synonymous substitutions, we identified six sequences exhibiting signals of strong diversifying selection (K(a)/K(s) > 1). These included genes involved in biosynthesis, metabolic processes and development. This transcriptome sequence variation may be reflective of natural selection acting on the genomes of these young, sympatric sister species. Based on Ks ratios and p-distances between 3'-untranslated regions (UTRs) calibrated to previously published species divergence times, we estimated a neutral transcriptome-wide substitutional mutation rate of approximately 1.25 x 10(-6) per site per year. We conclude that next-generation sequencing technologies allow us to infer natural selection acting to diversify the genomes of young species, such as crater lake cichlids, with much greater scope than previously possible.

  13. Molecular epidemiology of canine picornavirus in Hong Kong and Dubai and proposal of a novel genus in Picornaviridae.

    PubMed

    Woo, Patrick C Y; Lau, Susanna K P; Choi, Garnet K Y; Huang, Yi; Sivakumar, Saritha; Tsoi, Hoi-Wah; Yip, Cyril C Y; Jose, Shanty V; Bai, Ru; Wong, Emily Y M; Joseph, Marina; Li, Tong; Wernery, Ulrich; Yuen, Kwok-Yung

    2016-07-01

    Previously, we reported the discovery of a novel canine picornavirus (CanPV) in the fecal sample of a dog. In this molecular epidemiology study, CanPV was detected in 15 (1.11%) of 1347 canine fecal samples from Hong Kong and one (0.76%) of 131 canine fecal samples from Dubai, with viral loads 1.06×10(3) to 6.64×10(6) copies/ml. Complete genome sequencing and phylogenetic analysis showed that CanPV was clustered with feline picornavirus (FePV), bat picornavirus (BatPV) 1 to 3, Ia io picornavirus 1 (IaioPV1) and bovine picornavirus (BoPV), and this cluster was most closely related to the genera Enterovirus and Sapelovirus. The Ka/Ks ratios of all the coding regions were <0.1. According to the definition of the Picornavirus Study Group of ICTV, CanPV, FePV, BatPV 1 to 3, IaioPV1 and BoPV should constitute a novel genus in Picornaviridae. BEAST analysis showed that this genus diverged from its most closely related genus, Sapelovirus, about 49 years ago.

  14. Genome-wide analysis of homeobox gene family in legumes: identification, gene duplication and expression profiling.

    PubMed

    Bhattacharjee, Annapurna; Ghangal, Rajesh; Garg, Rohini; Jain, Mukesh

    2015-01-01

    Homeobox genes encode transcription factors that are known to play a major role in different aspects of plant growth and development. In the present study, we identified homeobox genes belonging to 14 different classes in five legume species, including chickpea, soybean, Medicago, Lotus and pigeonpea. The characteristic differences within homeodomain sequences among various classes of homeobox gene family were quite evident. Genome-wide expression analysis using publicly available datasets (RNA-seq and microarray) indicated that homeobox genes are differentially expressed in various tissues/developmental stages and under stress conditions in different legumes. We validated the differential expression of selected chickpea homeobox genes via quantitative reverse transcription polymerase chain reaction. Genome duplication analysis in soybean indicated that segmental duplication has significantly contributed in the expansion of homeobox gene family. The Ka/Ks ratio of duplicated homeobox genes in soybean showed that several members of this family have undergone purifying selection. Moreover, expression profiling indicated that duplicated genes might have been retained due to sub-functionalization. The genome-wide identification and comprehensive gene expression profiling of homeobox gene family members in legumes will provide opportunities for functional analysis to unravel their exact role in plant growth and development.

  15. Genome-wide identification and evolution of HECT genes in soybean.

    PubMed

    Meng, Xianwen; Wang, Chen; Rahman, Siddiq Ur; Wang, Yaxu; Wang, Ailan; Tao, Shiheng

    2015-04-16

    Proteins containing domains homologous to the E6-associated protein (E6-AP) carboxyl terminus (HECT) are an important class of E3 ubiquitin ligases involved in the ubiquitin proteasome pathway. HECT-type E3s play crucial roles in plant growth and development. However, current understanding of plant HECT genes and their evolution is very limited. In this study, we performed a genome-wide analysis of the HECT domain-containing genes in soybean. Using high-quality genome sequences, we identified 19 soybean HECT genes. The predicted HECT genes were distributed unevenly across 15 of 20 chromosomes. Nineteen of these genes were inferred to be segmentally duplicated gene pairs, suggesting that in soybean, segmental duplications have made a significant contribution to the expansion of the HECT gene family. Phylogenetic analysis showed that these HECT genes can be divided into seven groups, among which gene structure and domain architecture was relatively well-conserved. The Ka/Ks ratios show that after the duplication events, duplicated HECT genes underwent purifying selection. Moreover, expression analysis reveals that 15 of the HECT genes in soybean are differentially expressed in 14 tissues, and are often highly expressed in the flowers and roots. In summary, this work provides useful information on which further functional studies of soybean HECT genes can be based.

  16. The NLP toxin family in Phytophthora sojae includes rapidly evolving groups that lack necrosis-inducing activity.

    PubMed

    Dong, Suomeng; Kong, Guanghui; Qutob, Dinah; Yu, Xiaoli; Tang, Junli; Kang, Jixiong; Dai, Tingting; Wang, Hai; Gijzen, Mark; Wang, Yuanchao

    2012-07-01

    Necrosis- and ethylene-inducing-like proteins (NLP) are widely distributed in eukaryotic and prokaryotic plant pathogens and are considered to be important virulence factors. We identified, in total, 70 potential Phytophthora sojae NLP genes but 37 were designated as pseudogenes. Sequence alignment of the remaining 33 NLP delineated six groups. Three of these groups include proteins with an intact heptapeptide (Gly-His-Arg-His-Asp-Trp-Glu) motif, which is important for necrosis-inducing activity, whereas the motif is not conserved in the other groups. In total, 19 representative NLP genes were assessed for necrosis-inducing activity by heterologous expression in Nicotiana benthamiana. Surprisingly, only eight genes triggered cell death. The expression of the NLP genes in P. sojae was examined, distinguishing 20 expressed and 13 nonexpressed NLP genes. Real-time reverse-transcriptase polymerase chain reaction results indicate that most NLP are highly expressed during cyst germination and infection stages. Amino acid substitution ratios (Ka/Ks) of 33 NLP sequences from four different P. sojae strains resulted in identification of positive selection sites in a distinct NLP group. Overall, our study indicates that expansion and pseudogenization of the P. sojae NLP family results from an ongoing birth-and-death process, and that varying patterns of expression, necrosis-inducing activity, and positive selection suggest that NLP have diversified in function.

  17. Differential evolutionary rates of neuronal transcriptome in Aplysia kurodai and Aplysia californica as a tool for gene mining.

    PubMed

    Choi, Sun-Lim; Lee, Yong-Seok; Rim, Young-Soo; Kim, Tae-Hyung; Moroz, Leonid L; Kandel, Eric R; Bhak, Jong; Kaang, Bong-Kiun

    2010-07-01

    The marine mollusk Aplysia is a fascinating model organism for studying molecular mechanisms underlying learning and memory. However, evolutionary studies about Aplysia have been limited by the lack of its genomic information. Recently, large-scale expressed sequence tag (EST) databases have been acquired by sequencing cDNA libraries from A. californica and A. kurodai. The closeness between the two species allowed us to investigate rapidly evolving genes by comparing their orthologs. Using this method, we found that a subset of signal transduction genes in neurons showed rates of protein evolution higher than those of housekeeping genes. Moreover, we were also able to find several candidate genes that may be involved in learning and memory or synaptic plasticity among genes showing relatively higher K(a)/K(s) ratios. We also investigated the relationship between evolutionary rates and tissue distribution of Aplysia genes. They propose that the estimation of evolutionary rates cannot be a good marker to assess neuronal expression; however, it still can be an efficient way to narrow down the pool of candidate genes involved in neuronal functions for the further studies. PMID:20536287

  18. Spatiotemporal characteristics of the geomagnetic diurnal variation anomalies prior to the 2011 Tohoku earthquake (Mw 9.0) and the possible coupling of multiple pre-earthquake phenomena

    NASA Astrophysics Data System (ADS)

    Han, Peng; Hattori, Katsumi; Huang, Qinghua; Hirooka, Shinji; Yoshino, Chie

    2016-11-01

    Xu et al. (2013) and Han et al. (2015) have reported unusual behaviors of geomagnetic diurnal variation (GDV) in the vertical component prior to the 2011 off the Pacific coast of Tohoku earthquake (Mw 9.0). To make a better understanding of this phenomenon, temporal-spatial analyses of GDV have been applied in this study. Geomagnetic data of long-term observations at 17 stations in Japan have been analyzed using the same method in Han et al. (2015). Ratios of diurnal variation range between the reference station KAK and the target stations have been computed. After removing seasonal variations, the 15-day backward running mean values of the ratios in the vertical component shows a clear anomaly exceeding the statistical threshold about 2 months before the mega event at both ESA and MIZ stations in the Tohoku Region. Locations of anomalies in spatial distribution show a good correlation with the epicenter of the Mw 9.0 earthquake. These spatiotemporal results are consistent with those obtained from other independent observations such as groundwater level and GPS displacements. The coupling of multiple pre-earthquake phenomena may help to understand the preparation process of a mega earthquake in the subduction zone.

  19. Criticality features in ULF magnetic fields prior to the 2011 Tohoku earthquake

    NASA Astrophysics Data System (ADS)

    Hayakawa, Masashi; Schekotov, Alexander; Potirakis, Stelios; Eftaxias, Kostas

    2015-01-01

    The criticality of ULF (Ultra-low-frequency) magnetic variations is investigated for the 2011 March 11 Tohoku earthquake (EQ) by natural time analysis. For this attempt, some ULF parameters were considered: (1) Fh (horizontal magnetic field), (2) Fz (vertical magnetic field), and (3) Dh (inverse of horizontal magnetic field). The first two parameters refer to the ULF radiation, while the last parameter refers to another ULF effect of ionospheric signature. Nighttime (L.T. = 3 am ± 2 hours) data at Kakioka (KAK) were used, and the power of each quantity at a particular frequency band of 0.03-0.05 Hz was averaged for nighttime hours. The analysis results indicate that Fh fulfilled all criticality conditions on March 3-5, 2011, and that the additional parameter, Dh reached also a criticality on March 6 or 7. In conclusion, criticality has reached in the pre-EQ fracture region a few days to one week before the main shock of the Tohoku EQ.

  20. Comparative and phylogenetic analysis of the mitochondrial genomes in basal hymenopterans

    PubMed Central

    Song, Sheng-Nan; Tang, Pu; Wei, Shu-Jun; Chen, Xue-Xin

    2016-01-01

    The Symphyta is traditionally accepted as a paraphyletic group located in a basal position of the order Hymenoptera. Herein, we conducted a comparative analysis of the mitochondrial genomes in the Symphyta by describing two newly sequenced ones, from Trichiosoma anthracinum, representing the first mitochondrial genome in family Cimbicidae, and Asiemphytus rufocephalus, from family Tenthredinidae. The sequenced lengths of these two mitochondrial genomes were 15,392 and 14,864 bp, respectively. Within the sequenced region, trnC and trnY were rearranged to the upstream of trnI-nad2 in T. anthracinum, while in A. rufocephalus all sequenced genes were arranged in the putative insect ancestral gene arrangement. Rearrangement of the tRNA genes is common in the Symphyta. The rearranged genes are mainly from trnL1 and two tRNA clusters of trnI-trnQ-trnM and trnW-trnC-trnY. The mitochondrial genomes of Symphyta show a biased usage of A and T rather than G and C. Protein-coding genes in Symphyta species show a lower evolutionary rate than those of Apocrita. The Ka/Ks ratios were all less than 1, indicating purifying selection of Symphyta species. Phylogenetic analyses supported the paraphyly and basal position of Symphyta in Hymenoptera. The well-supported phylogenetic relationship in the study is Tenthredinoidea + (Cephoidea + (Orussoidea + Apocrita)). PMID:26879745

  1. Sequence and gene expression evolution of paralogous genes in willows.

    PubMed

    Harikrishnan, Srilakshmy L; Pucholt, Pascal; Berlin, Sofia

    2015-12-22

    Whole genome duplications (WGD) have had strong impacts on species diversification by triggering evolutionary novelties, however, relatively little is known about the balance between gene loss and forces involved in the retention of duplicated genes originating from a WGD. We analyzed putative Salicoid duplicates in willows, originating from the Salicoid WGD, which took place more than 45 Mya. Contigs were constructed by de novo assembly of RNA-seq data derived from leaves and roots from two genotypes. Among the 48,508 contigs, 3,778 pairs were, based on fourfold synonymous third-codon transversion rates and syntenic positions, predicted to be Salicoid duplicates. Both copies were in most cases expressed in both tissues and 74% were significantly differentially expressed. Mean Ka/Ks was 0.23, suggesting that the Salicoid duplicates are evolving by purifying selection. Gene Ontology enrichment analyses showed that functions related to DNA- and nucleic acid binding were over-represented among the non-differentially expressed Salicoid duplicates, while functions related to biosynthesis and metabolism were over-represented among the differentially expressed Salicoid duplicates. We propose that the differentially expressed Salicoid duplicates are regulatory neo- and/or subfunctionalized, while the non-differentially expressed are dose sensitive, hence, functionally conserved. Multiple evolutionary processes, thus drive the retention of Salicoid duplicates in willows.

  2. Novel Cathelicidins from Pigeon Highlights Evolutionary Convergence in Avain Cathelicidins and Functions in Modulation of Innate Immunity

    PubMed Central

    Yu, Haining; Lu, Yiling; Qiao, Xue; Wei, Lin; Fu, Tingting; Cai, Shasha; Wang, Chen; Liu, Xuelian; Zhong, Shijun; Wang, Yipeng

    2015-01-01

    Cathelicidins are short cationic host defense peptides and play a central role in host innate immune system. Here we identified two novel cathelicidins, Cl-CATH2 and 3, from Columba livia. Evolutionary analysis of avian cathelicidins via phylogenetic tree and Ka/Ks calculations supported the positive selection that prompted evolution of CATH2 to CATH1 and 3, which originate from common ancestor and could belong to one superfamily. Cl-CATH2 and 3 both adopt amphipathic α-helical comformations identified by circular dichroism and the 3D structures built by Rosetta. Cl-CATH2 of CATH2 family with the most expression abundance in bird, exhibited relatively weak antimicrobial activity, but acted instead on the innate immune response without showing undesirable toxicities. In macrophages primed by LPS, Cl-CATH2 significantly down-regulated the gene and protein expressions of inducible nitric oxide synthase and pro-inflammatory cytokines while enhancing the anti-inflammatory cytokine, acting through MAPK and NF-κB signaling pathways. Molecular docking shows for the first time that cathelicidin binds to the opening region of LPS-binding pocket on myeloid differentiation factor 2 (MD-2) of toll-like receptor (TLR)4-MD-2 complex, which in turn inhibits the TLR4 pathway. Our results, therefore, provide new insight into the mechanism underlying the blockade of TLR4 signaling by cathelicidins. PMID:26194630

  3. A unique RPW8-encoding class of genes that originated in early land plants and evolved through domain fission, fusion, and duplication

    PubMed Central

    Zhong, Yan; Cheng, Zong-Ming (Max)

    2016-01-01

    Duplication, lateral gene transfer, domain fusion/fission and de novo domain creation play a key role in formation of initial common ancestral protein. Abundant protein diversities are produced by domain rearrangements, including fusions, fissions, duplications, and terminal domain losses. In this report, we explored the origin of the RPW8 domain and examined the domain rearrangements that have driven the evolution of RPW8-encoding genes in land plants. The RPW8 domain first emerged in the early land plant, Physcomitrella patens, and it likely originated de novo from a non-coding sequence or domain divergence after duplication. It was then incorporated into the NBS-LRR protein to create a main sub-class of RPW8-encoding genes, the RPW8-NBS-encoding genes. They evolved by a series of genetic events of domain fissions, fusions, and duplications. Many species-specific duplication events and tandemly duplicated clusters clearly demonstrated that species-specific and tandem duplications played important roles in expansion of RPW8-encoding genes, especially in gymnosperms and species of the Rosaceae. RPW8 domains with greater Ka/Ks values than those of the NBS domains indicated that they evolved faster than the NBS domains in RPW8-NBSs. PMID:27678195

  4. Population-based resequencing analysis of wild and cultivated barley revealed weak domestication signal of selection and bottleneck in the Rrs2 scald resistance gene region.

    PubMed

    Fu, Yong-Bi

    2012-02-01

    Many plant disease resistance (R) genes have been cloned, but the potential of utilizing these plant R-gene genomic resources for genetic inferences of plant domestication history remains unexplored. A population-based resequencing analysis of the genomic region near the Rrs2 scald resistance gene was made in 51 accessions of wild and cultivated barley from 41 countries. Fifteen primer pairs were designed to sample the genomic region with a total length of 10 406 bp. More nucleotide diversity was found in wild (π = 0.01846) than cultivated (π = 0.01507) barley samples. Three distinct groups of 29 haplotypes were detected for all 51 samples, and they were well mixed with wild and cultivated barley samples from different countries and regions. The neutrality tests by Tajima's D were not significant, but a significant (P < 0.05) case by Fu and Li's D* and F* was found in the barley cultivar samples. The estimate of selection intensity by K(a)/K(s) was 0.691 in wild barley and 0.580 in cultivated barley. The estimate of the minimum recombination events was 16 in wild barley and 19 in cultivated barley. A coalescence simulation revealed a bottleneck intensity of 1.5 to 2 since barley domestication. Together, the domestication signal in the genomic region was weak both in human selection and domestication bottleneck.

  5. Nucleotide variation and identification of novel blast resistance alleles of Pib by allele mining strategy.

    PubMed

    Ramkumar, G; Madhav, M S; Devi, S J S Rama; Prasad, M S; Babu, V Ravindra

    2015-04-01

    Pib is one of significant rice blast resistant genes, which provides resistance to wide range of isolates of rice blast pathogen, Magnaporthe oryzae. Identification and isolation of novel and beneficial alleles help in crop enhancement. Allele mining is one of the best strategies for dissecting the allelic variations at candidate gene and identification of novel alleles. Hence, in the present study, Pib was analyzed by allele mining strategy, and coding and non-coding (upstream and intron) regions were examined to identify novel Pib alleles. Allelic sequences comparison revealed that nucleotide polymorphisms at coding regions affected the amino acid sequences, while the polymorphism at upstream (non-coding) region affected the motifs arrangements. Pib alleles from resistant landraces, Sercher and Krengosa showed better resistance than Pib donor variety, might be due to acquired mutations, especially at LRR region. The evolutionary distance, Ka/Ks and phylogenetic analyzes also supported these results. Transcription factor binding motif analysis revealed that Pib (Sr) had a unique motif (DPBFCOREDCDC3), while five different motifs differentiated the resistance and susceptible Pib alleles. As the Pib is an inducible gene, the identified differential motifs helps to understand the Pib expression mechanism. The identified novel Pib resistant alleles, which showed high resistance to the rice blast, can be used directly in blast resistance breeding program as alternative Pib resistant sources.

  6. Evolutionary analysis of RB/Rpi-blb1 locus in the Solanaceae family.

    PubMed

    Xie, Zhengqing; Si, Weina; Gao, Rongchao; Zhang, Xiaohui; Yang, Sihai

    2015-12-01

    Late blight caused by the oomycete Phytophthora infestans is one of the most severe threats to potato production worldwide. Numerous studies suggest that the most effective protective strategy against the disease would be to provide potato cultivars with durable resistance (R) genes. However, little is known about the origin and evolutional history of these durable R-genes in potato. Addressing this might foster better understanding of the dynamics of these genes in nature and provide clues for identifying potential candidate R-genes. Here, a systematic survey was executed at RB/Rpi-blb1 locus, an exclusive broad-spectrum R-gene locus in potato. As indicated by synteny analysis, RB/Rpi-blb1 homologs were identified in all tested genomes, including potato, tomato, pepper, and Nicotiana, suggesting that the RB/Rpi-blb1 locus has an ancient origin. Two evolutionary patterns, similar to those reported on RGC2 in Lactuca, and Pi2/9 in rice, were detected at this locus. Type I RB/Rpi-blb1 homologs have frequent copy number variations and sequence exchanges, obscured orthologous relationships, considerable nucleotide divergence, and high non-synonymous to synonymous substitutions (Ka/Ks) between or within species, suggesting rapid diversification and balancing selection in response to rapid changes in the oomycete pathogen genomes. These characteristics may serve as signatures for cloning of late blight resistance genes.

  7. Comparative Genome Analysis and Phylogenetic Relationship of Order Liliales Insight from the Complete Plastid Genome Sequences of Two Lilies (Lilium longiflorum and Alstroemeria aurea)

    PubMed Central

    Kim, Jung Sung; Kim, Joo-Hwan

    2013-01-01

    Monocots are one of the most diverse, successful and economically important clades of angiosperms. We attempt to analyse the complete plastid genome sequences of two lilies and their lengths were 152,793bp in Liliumlongiflorum (Liliaceae) and 155,510bp in Alstroemeriaaurea (Alstroemeriaceae). Phylogenetic analyses were performed for 28 taxa including major lineages of monocots using the sequences of 79 plastid genes for clarifying the phylogenetic relationship of the order Liliales. The sister relationship of Liliales and Asparagales-commelinids was improved with high resolution. Comparative analyses of inter-familial and inter-specific sequence variation were also carried out among three families of Liliaceae, Smilacaceae, and Alstroemeriaceae, and between two Lilium species of L. longflorum and L. superbum. Gene content and order were conserved in the order Liliales except infA loss in Smilax and Alstroemeria. IR boundaries were similar in IRa, however, IRb showed different extension patterns as JLB of Smilax and JSB in Alstroemeria. Ka/Ks ratio was high in matK among the pair-wise comparison of three families and the most variable genes were psaJ, ycf1, rpl32, rpl22, matK, and ccsA among the three families and rps15, rpoA, matK, and ndhF between Lilium. PMID:23950788

  8. Identification and expression profiling of DNA methyltransferases during development and stress conditions in Solanaceae.

    PubMed

    Kumar, Rahul; Chauhan, Pankaj Kumar; Khurana, Ashima

    2016-09-01

    DNA methyltransferase (DMTase) enzymes contribute to plant development and stress responses by de novo establishment and subsequent maintenance of DNA methylation during replication. However, the molecular mechanism underlying this activity remains obscure, especially in crop species. Using DMTase homolog complement in six Solanaceae species, we demonstrated here that their number remained conserved in Solanum lineage, whereas it was expanded in both pepper and Nicotiana benthamiana. Non-synonymous vs synonymous (Ka/Ks) substitution ratio revealed that most of the Solanaceous DMTase homologs undergo purifying selection. The genomic sequences of tomato DMT homologs in its wild relative, Solanum pennellii, remained highly conserved in their exons and methyltransferase domains. Structure analysis further revealed highly similar folding of DMTase homologs and conservation in the residues participating in protein-protein interaction in Solanum lineage, whereas a considerable diversification was observed of pepper homologs. Transcript profiling of DMTases highlighted both similar and distinct expression patterns of tomato homologs in other species during fruit development and stress responses. Overall, our analysis provides a strong basis for in-depth exploration of both conserved as well as distinct functions of tomato DMTase homologs in other economically important Solanaceae species. PMID:27380018

  9. Complete mitochondrial genome sequence from an endangered Indian snake, Python molurus molurus (Serpentes, Pythonidae).

    PubMed

    Dubey, Bhawna; Meganathan, P R; Haque, Ikramul

    2012-07-01

    This paper reports the complete mitochondrial genome sequence of an endangered Indian snake, Python molurus molurus (Indian Rock Python). A typical snake mitochondrial (mt) genome of 17258 bp length comprising of 37 genes including the 13 protein coding genes, 22 tRNA genes, and 2 ribosomal RNA genes along with duplicate control regions is described herein. The P. molurus molurus mt. genome is relatively similar to other snake mt. genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases. The nucleotide composition of the genome shows that there are more A-C % than T-G% on the positive strand as revealed by positive AT and CG skews. Comparison of individual protein coding genes, with other snake genomes suggests that ATP8 and NADH3 genes have high divergence rates. Codon usage analysis reveals a preference of NNC codons over NNG codons in the mt. genome of P. molurus. Also, the synonymous and non-synonymous substitution rates (ka/ks) suggest that most of the protein coding genes are under purifying selection pressure. The phylogenetic analyses involving the concatenated 13 protein coding genes of P. molurus molurus conformed to the previously established snake phylogeny.

  10. Finds in Belize document Late Classic Maya salt making and canoe transport

    PubMed Central

    McKillop, Heather

    2005-01-01

    How did people in preIndustrial ancient civilizations produce and distribute bulk items, such as salt, needed for everyday use by their large urban populations? This report focuses on the ancient Maya who obtained quantities of salt at cities in the interior of the Yucatan peninsula of Mexico, Belize, and Guatemala in an area where salt is scarce. I report the discovery of 41 Late Classic Maya saltworks (anno Domini 600–900) in Punta Ycacos Lagoon on the south coast of Belize, including one with the first-known ancient Maya canoe paddle. The discoveries add important empirical information for evaluating the extent of surplus salt production and river transport during the height of Late Classic civilization in the southern Maya lowlands. The discovery of the saltworks indicates that there was extensive production and distribution of goods and resources outside the cities in the interior of the Yucatan. The discovery of a wooden canoe paddle from one of the Punta Ycacos saltworks, Ka'k' Naab', ties the production of salt to its inland transport by rivers and documents the importance of canoe trade between the coast and the interior during the Late Classic. Archaeological discovery of multiple saltworks on the Belizean coast represents surplus production of salt destined largely for the inland Peten Maya during their Late Classic peak, underscoring the importance of non-state-controlled workshop production in preIndustrial societies. PMID:15809426

  11. Evolutionary conservation analysis between the essential and nonessential genes in bacterial genomes.

    PubMed

    Luo, Hao; Gao, Feng; Lin, Yan

    2015-08-14

    Essential genes are thought to be critical for the survival of the organisms under certain circumstances, and the natural selection acting on essential genes is expected to be stricter than on nonessential ones. Up to now, essential genes have been identified in approximately thirty bacterial organisms by experimental methods. In this paper, we performed a comprehensive comparison between the essential and nonessential genes in the genomes of 23 bacterial species based on the Ka/Ks ratio, and found that essential genes are more evolutionarily conserved than nonessential genes in most of the bacteria examined. Furthermore, we also analyzed the conservation by functional clusters with the clusters of orthologous groups (COGs), and found that the essential genes in the functional categories of G (Carbohydrate transport and metabolism), H (Coenzyme transport and metabolism), I (Transcription), J (Translation, ribosomal structure and biogenesis), K (Lipid transport and metabolism) and L (Replication, recombination and repair) tend to be more evolutionarily conserved than the corresponding nonessential genes in bacteria. The results suggest that the essential genes in these subcategories are subject to stronger selective pressure than the nonessential genes, and therefore, provide more insights of the evolutionary conservation for the essential and nonessential genes in complex biological processes.

  12. Molecular evolution and expression divergence of the Populus euphratica Hsf genes provide insight into the stress acclimation of desert poplar

    PubMed Central

    Zhang, Jin; Jia, Huixia; Li, Jianbo; Li, Yu; Lu, Mengzhu; Hu, Jianjun

    2016-01-01

    Heat shock transcription factor (Hsf) family is one of the most important regulators in the plant kingdom. Hsf has been demonstrated to be involved in various processes associated with plant growth, development as well as in response to hormone and abiotic stresses. In this study, we carried out a comprehensive analysis of Hsf family in desert poplar, Populus euphratica. Total of 32 genes encoding Hsf were identified and they were classified into three main classes (A, B, and C). Gene structure and conserved motif analyses indicated that the members in each class were relatively conserved. Total of 10 paralogous pairs were identified in PeuHsf family, in which nine pairs were generated by whole genome duplication events. Ka/Ks analysis showed that PeuHsfs underwent purifying selection pressure. In addition, various cis-acting elements involved in hormone and stress responses located in the promoter regions of PeuHsfs. Gene expression analysis indicated that several PeuHsfs were tissue-specific expression. Compared to Arabidopsis, more PeuHsf genes were significantly induced by heat, drought, and salt stresses (21, 19, and 22 PeuHsfs, respectively). Our findings are helpful in understanding the distinguished adaptability of P. euphratica to extreme environment and providing a basis for functional analysis of PeuHsfs in the future. PMID:27425424

  13. Positively selected genes of the Chinese tree shrew (Tupaia belangeri chinensis) locomotion system

    PubMed Central

    Yu, FAN; Dan-Dan, YU; Yong-Gang, YAO

    2014-01-01

    While the recent release of the Chinese tree shrew (Tupaia belangeri chinensis) genome has made the tree shrew an increasingly viable experimental animal model for biomedical research, further study of the genome may facilitate new insights into the applicability of this model. For example, though the tree shrew has a rapid rate of speed and strong jumping ability, there are limited studies on its locomotion ability. In this study we used the available Chinese tree shrew genome information and compared the evolutionary pattern of 407 locomotion system related orthologs among five mammals (human, rhesus monkey, mouse, rat and dog) and the Chinese tree shrew. Our analyses identified 29 genes with significantly high ω (Ka/Ks ratio) values and 48 amino acid sites in 14 genes showed significant evidence of positive selection in the Chinese tree shrew. Some of these positively selected genes, e.g. HOXA6 (homeobox A6) and AVP (arginine vasopressin), play important roles in muscle contraction or skeletal morphogenesis. These results provide important clues in understanding the genetic bases of locomotor adaptation in the Chinese tree shrew. PMID:24866495

  14. Transcriptome Sequencing and Positive Selected Genes Analysis of Bombyx mandarina

    PubMed Central

    Wu, Yuqian; Long, Renwen; Liu, Chun; Xia, Qingyou

    2015-01-01

    The wild silkworm Bombyx mandarina is widely believed to be an ancestor of the domesticated silkworm, Bombyx mori. Silkworms are often used as a model for studying the mechanism of species domestication. Here, we performed transcriptome sequencing of the wild silkworm using an Illumina HiSeq2000 platform. We produced 100,004,078 high-quality reads and assembled them into 50,773 contigs with an N50 length of 1764 bp and a mean length of 941.62 bp. A total of 33,759 unigenes were identified, with 12,805 annotated in the Nr database, 8273 in the Pfam database, and 9093 in the Swiss-Prot database. Expression profile analysis found significant differential expression of 1308 unigenes between the middle silk gland (MSG) and posterior silk gland (PSG). Three sericin genes (sericin 1, sericin 2, and sericin 3) were expressed specifically in the MSG and three fibroin genes (fibroin-H, fibroin-L, and fibroin/P25) were expressed specifically in the PSG. In addition, 32,297 Single-nucleotide polymorphisms (SNPs) and 361 insertion-deletions (INDELs) were detected. Comparison with the domesticated silkworm p50/Dazao identified 5,295 orthologous genes, among which 400 might have experienced or to be experiencing positive selection by Ka/Ks analysis. These data and analyses presented here provide insights into silkworm domestication and an invaluable resource for wild silkworm genomics research. PMID:25806526

  15. Evolutionary Pattern of the FAE1 Gene in Brassicaceae and Its Correlation with the Erucic Acid Trait

    PubMed Central

    Li, Mimi; Peng, Bin; Guo, Haisong; Yan, Qinqin; Hang, Yueyu

    2013-01-01

    The fatty acid elongase 1 (FAE1) gene catalyzes the initial condensation step in the elongation pathway of VLCFA (very long chain fatty acid) biosynthesis and is thus a key gene in erucic acid biosynthesis. Based on a worldwide collection of 62 accessions representing 14 tribes, 31 genera, 51 species, 4 subspecies and 7 varieties, we conducted a phylogenetic reconstruction and correlation analysis between genetic variations in the FAE1 gene and the erucic acid trait, attempting to gain insight into the evolutionary patterns and the correlations between genetic variations in FAE1 and trait variations. The five clear, deeply diverged clades detected in the phylogenetic reconstruction are largely congruent with a previous multiple gene-derived phylogeny. The Ka/Ks ratio (<1) and overall low level of nucleotide diversity in the FAE1 gene suggest that purifying selection is the major evolutionary force acting on this gene. Sequence variations in FAE1 show a strong correlation with the content of erucic acid in seeds, suggesting a causal link between the two. Furthermore, we detected 16 mutations that were fixed between the low and high phenotypes of the FAE1 gene, which constitute candidate active sites in this gene for altering the content of erucic acid in seeds. Our findings begin to shed light on the evolutionary pattern of this important gene and represent the first step in elucidating how the sequence variations impact the production of erucic acid in plants. PMID:24358289

  16. Sequence and gene expression evolution of paralogous genes in willows

    PubMed Central

    Harikrishnan, Srilakshmy L.; Pucholt, Pascal; Berlin, Sofia

    2015-01-01

    Whole genome duplications (WGD) have had strong impacts on species diversification by triggering evolutionary novelties, however, relatively little is known about the balance between gene loss and forces involved in the retention of duplicated genes originating from a WGD. We analyzed putative Salicoid duplicates in willows, originating from the Salicoid WGD, which took place more than 45 Mya. Contigs were constructed by de novo assembly of RNA-seq data derived from leaves and roots from two genotypes. Among the 48,508 contigs, 3,778 pairs were, based on fourfold synonymous third-codon transversion rates and syntenic positions, predicted to be Salicoid duplicates. Both copies were in most cases expressed in both tissues and 74% were significantly differentially expressed. Mean Ka/Ks was 0.23, suggesting that the Salicoid duplicates are evolving by purifying selection. Gene Ontology enrichment analyses showed that functions related to DNA- and nucleic acid binding were over-represented among the non-differentially expressed Salicoid duplicates, while functions related to biosynthesis and metabolism were over-represented among the differentially expressed Salicoid duplicates. We propose that the differentially expressed Salicoid duplicates are regulatory neo- and/or subfunctionalized, while the non-differentially expressed are dose sensitive, hence, functionally conserved. Multiple evolutionary processes, thus drive the retention of Salicoid duplicates in willows. PMID:26689951

  17. Species-Specific Expansion and Molecular Evolution of the 3-hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Plants

    PubMed Central

    Li, Wei; Liu, Wei; Wei, Hengling; He, Qiuling; Chen, Jinhong; Zhang, Baohong; Zhu, Shuijin

    2014-01-01

    The terpene compounds represent the largest and most diverse class of plant secondary metabolites which are important in plant growth and development. The 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR; EC 1.1.1.34) is one of the key enzymes contributed to terpene biosynthesis. To better understand the basic characteristics and evolutionary history of the HMGR gene family in plants, a genome-wide analysis of HMGR genes from 20 representative species was carried out. A total of 56 HMGR genes in the 14 land plant genomes were identified, but no genes were found in all 6 algal genomes. The gene structure and protein architecture of all plant HMGR genes were highly conserved. The phylogenetic analysis revealed that the plant HMGRs were derived from one ancestor gene and finally developed into four distinct groups, two in the monocot plants and two in dicot plants. Species-specific gene duplications, caused mainly by segmental duplication, led to the limited expansion of HMGR genes in Zea mays, Gossypium raimondii, Populus trichocarpa and Glycine max after the species diverged. The analysis of Ka/Ks ratios and expression profiles indicated that functional divergence after the gene duplications was restricted. The results suggested that the function and evolution of HMGR gene family were dramatically conserved throughout the plant kingdom. PMID:24722776

  18. Molecular evolution of myelin basic protein, an abundant structural myelin component.

    PubMed

    Nawaz, Schanila; Schweitzer, Jörn; Jahn, Olaf; Werner, Hauke B

    2013-08-01

    Rapid nerve conduction in jawed vertebrates is facilitated by the myelination of axons, which evolved in ancient cartilaginous fish. We aim to understand the coevolution of myelin and the major myelin proteins. We found that myelin basic protein (MBP) derived from living cartilaginous fish (sharks and rays) associated with the plasma membrane of glial cells similar to the phosphatidylinositol (4,5)-bisphosphate (PIP₂)-binding marker PH-PLCδ1, and that ionomycin-induced PIP₂-hydrolysis led to its cellular redistribution. We identified two paralogous mbp genes in multiple teleost species, consistent with a genome duplication at the root of the teleost clade. Zebrafish mbpb is organized in a complex transcription unit together with the unrelated gene-of-the-oligodendrocyte-lineage (golli) while mbpa does not encode GOLLI. Moreover, the embryonic expression of mbpa and mbpb differed, indicating functional specialization after duplication. However, both mbpa and mbpb-mRNAs were detected in mature oligodendrocytes and Schwann cells, MBPa and MBPb were mass spectrometrically identified in zebrafish myelin, both associated with the plasma membrane via PIP₂, and the ratio of nonsynonymous to synonymous nucleotide-substitution rates (Ka/Ks) was low. Together, this indicates selective pressure to conserve many aspects of the cellular expression and function of MBP across vertebrate species. We propose that the PIP₂-binding function of MBP is evolutionarily old and that its emergence in ancient gnathostomata provided glial cells with the competence to myelinate. PMID:24040667

  19. Adaptive introgression of anticoagulant rodent poison resistance by hybridization between Old World mice

    PubMed Central

    Song, Ying; Endepols, Stefan; Klemann, Nicole; Richter, Dania; Matuschka, Franz-Rainer; Shih, Ching-Hua; Nachman, Michael W.; Kohn, Michael H.

    2011-01-01

    Summary It is known that evolution by selection on new or standing single nucleotide polymorphisms (SNPs) in the vitamin K 2,3-epoxide reductase subcomponent 1 (vkorc1) of house mice (Mus musculus domesticus) can cause resistance to anticoagulant rodenticides such as warfarin [1–3]. Here we report an introgression in European M. m. domesticus spanning as much as ~20.3 megabases (Mb) and including vkorc1, the molecular target of anticoagulants [1–4], that stems from hybridization with the Algerian mouse (M. spretus). We show that in the laboratory the homozygous complete vkorc1 allele of M. spretus confers resistance when introgressed into M. m. domesticus. Consistent with selection on the introgression after the introduction of rodenticides in the 1950s we document historically adaptive population genetics of vkorc1 in M. m. domesticus. Furthermore, we detected adaptive protein evolution of vkorc1 in the M. spretus lineage (Ka/Ks=1.54–1.93) resulting in radical amino-acid substitutions that apparently have anticoagulant tolerance of M. spretus as pleiotropic effect. Thus, positive selection produced an adaptive, divergent and pleiotropic vkorc1 allele in the donor species, M. spretus, which crossed a species barrier where it is expressed as adaptive trait in the recipient species, M. m. domesticus. Resistant house mice originated from selection on new or standing vkorc1 polymorphisms and from selection on vkorc1 polymorphisms acquired by adaptive introgressive hybridization. PMID:21782438

  20. Mitogenomes from type specimens, a genotyping tool for morphologically simple species: ten genomes of agar-producing red algae

    PubMed Central

    Boo, Ga Hun; Hughey, Jeffery R.; Miller, Kathy Ann; Boo, Sung Min

    2016-01-01

    DNA sequences from type specimens provide independent, objective characters that enhance the value of type specimens and permit the correct application of species names to phylogenetic clades and specimens. We provide mitochondrial genomes (mitogenomes) from archival type specimens of ten species in agar-producing red algal genera Gelidium and Pterocladiella. The genomes contain 43–44 genes, ranging in size from 24,910 to 24,970 bp with highly conserved gene synteny. Low Ka/Ks ratios of apocytochrome b and cytochrome oxidase genes support their utility as markers. Phylogenies of mitogenomes and cox1+rbcL sequences clarified classification at the genus and species levels. Three species formerly in Gelidium and Pterocladia are transferred to Pterocladiella: P. media comb. nov., P. musciformis comb. nov., and P. luxurians comb. and stat. nov. Gelidium sinicola is merged with G. coulteri because they share identical cox1 and rbcL sequences. We describe a new species, Gelidium millariana sp. nov., previously identified as G. isabelae from Australia. We demonstrate that mitogenomes from type specimens provide a new tool for typifying species in the Gelidiales and that there is an urgent need for analyzing mitogenomes from type specimens of red algae and other morphologically simple organisms for insight into their nomenclature, taxonomy and evolution. PMID:27739454

  1. Molecular evolution of myelin basic protein, an abundant structural myelin component.

    PubMed

    Nawaz, Schanila; Schweitzer, Jörn; Jahn, Olaf; Werner, Hauke B

    2013-08-01

    Rapid nerve conduction in jawed vertebrates is facilitated by the myelination of axons, which evolved in ancient cartilaginous fish. We aim to understand the coevolution of myelin and the major myelin proteins. We found that myelin basic protein (MBP) derived from living cartilaginous fish (sharks and rays) associated with the plasma membrane of glial cells similar to the phosphatidylinositol (4,5)-bisphosphate (PIP₂)-binding marker PH-PLCδ1, and that ionomycin-induced PIP₂-hydrolysis led to its cellular redistribution. We identified two paralogous mbp genes in multiple teleost species, consistent with a genome duplication at the root of the teleost clade. Zebrafish mbpb is organized in a complex transcription unit together with the unrelated gene-of-the-oligodendrocyte-lineage (golli) while mbpa does not encode GOLLI. Moreover, the embryonic expression of mbpa and mbpb differed, indicating functional specialization after duplication. However, both mbpa and mbpb-mRNAs were detected in mature oligodendrocytes and Schwann cells, MBPa and MBPb were mass spectrometrically identified in zebrafish myelin, both associated with the plasma membrane via PIP₂, and the ratio of nonsynonymous to synonymous nucleotide-substitution rates (Ka/Ks) was low. Together, this indicates selective pressure to conserve many aspects of the cellular expression and function of MBP across vertebrate species. We propose that the PIP₂-binding function of MBP is evolutionarily old and that its emergence in ancient gnathostomata provided glial cells with the competence to myelinate.

  2. Population diversity and adaptive evolution in keratinization genes: impact of environment in shaping skin phenotypes.

    PubMed

    Gautam, Pramod; Chaurasia, Amit; Bhattacharya, Aniket; Grover, Ritika; Mukerji, Mitali; Natarajan, Vivek T

    2015-03-01

    Several studies have demonstrated the role of climatic factors in shaping skin phenotypes, particularly pigmentation. Keratinization is another well-designed feature of human skin, which is involved in modulating transepidermal water loss (TEWL). Although this physiological process is closely linked to climate, presently it is not clear whether genetic diversity is observed in keratinization and whether this process also responds to the environmental pressure. To address this, we adopted a multipronged approach, which involved analysis of 1) copy number variations in diverse Indian and HapMap populations from varied geographical regions; 2) genetic association with geoclimatic parameters in 61 populations of dbCLINE database in a set of 549 genes from four processes namely keratinization, pigmentation, epidermal differentiation, and housekeeping functions; 3) sequence divergence in 4,316 orthologous promoters and corresponding exonic regions of human and chimpanzee with macaque as outgroup, and 4) protein sequence divergence (Ka/Ks) across nine vertebrate classes, which differ in their extent of TEWL. Our analyses demonstrate that keratinization and epidermal differentiation genes are under accelerated evolution in the human lineage, relative to pigmentation and housekeeping genes. We show that this entire pathway may have been driven by environmental selection pressure through concordant functional polymorphisms across several genes involved in skin keratinization. Remarkably, this underappreciated function of skin may be a crucial determinant of adaptation to diverse environmental pressures across world populations.

  3. DED: Database of Evolutionary Distances.

    PubMed

    Veeramachaneni, Vamsi; Makalowski, Wojciech

    2005-01-01

    A large database of homologous sequence alignments with good estimates of evolutionary distances can be a valuable resource for molecular evolutionary studies and phylogenetic research in particular. We recently created a database containing 159,921 transcripts from human, mouse, rat, zebrafish and fugu species. Approximately 1,000 homology groups were identified with the help of Ensembl homology evidence. At the macro-level, the database allows us to answer queries of the form: 1. What is the average k-distance between 5' untranslated regions of human and mouse? 2. List the 10 groups with the highest K(a)/K(s) ratio between mouse and rat. 3. List all identical proteins between human and rat. Researchers interested in specific proteins can use a simple web interface to retrieve the homology groups of interest, examine all pairwise distances between members of the group and study the conservation of exon-intron gene structures using a graphical interface. The database is available at http://warta.bio.psu.edu/DED/.

  4. Shotgun assembly of the mitochondrial genome from Fenneropenaeus penicillatus with phylogenetic consideration.

    PubMed

    Zhang, Dianchang; Gong, Fahui; Liu, Tiantian; Guo, Huayang; Zhang, Nan; Zhu, Kecheng; Jiang, Shigui

    2015-12-01

    The complete mitochondrial genome is of great importance for better understanding of the genome-level characteristics and phylogenetic relationships among related species. In this study, Fenneropenaeus penicillatus mitochondrial genome sequence was determined by next-generation sequencing. The complete genome DNA was 16,040 bp in length and consisted of a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). The gene arrangement is identical to the pancrustacean pattern. The overall base composition of its mitochondrial genome is estimated to be 34.1% for A, 34.1% for T, 12.5% for G and 19.3% for C with a high A+T content (68.2%). The analysis of the average Ka/Ks in the 13 mitochondrial protein-coding genes of penaeid shrimps indicated a strong purifying selection within this group. The phylogenetic analysis based on mitochondrial sequences and 13 concatenated protein-coding genes showed strong statistic support for the following relationship among the five genera ((Penaeus s.s+Fenneropenaeus)+(Litopenaeus+Farfantepenaeus))+Marsupenaeus. The sequence data of F. penicillatus can provide useful information for the studies on molecular systematics, population structure, stock evaluation and conservation genetics.

  5. The Use of 3D Graphic Modelling in Geoarchaeological Investigations (Bykowszczyzna Archaeological Site near Kock, E Poland)

    NASA Astrophysics Data System (ADS)

    Łojek, Jacek

    2012-01-01

    The objective of this paper was to use the ArcView 3.2 application for spatial modelling of the exploration forms (pits) in the Bykowszczyzna 8 archaeological site. The 3D digital documentation at a specific scale makes possible easy archiving, presentation, and simple spatial analyses of the examined objects. The ArcView 3.2 programme and its extensions (Spatial Analyst and 3D Analyst), commonly used as analytical tools in geomorphology, were inventively used for inventory-making in the archaeological site. Traditional field sketches were only a base, which enables entering data into the programme, and don't documentation material in itself as it used to be. The method of data visual ization proposed by the author gives new possibilities for using the GIS platform software. W artykule zaprezentowano projekt wykorzystania aplikacji ArcView 3.2 w modelowaniu obrazu form eksploracyjnych na stanowisku archeologicznym Bykowszczyzna 8. Stanowisko zostało objęte programem ratowniczych badań archeologicznych w związku z budową obwodnicy miasta Kocka na trasie krajowej nr 19 relacji Siemiatycze-Lublin-Nisko. Zasadniczy etap prac archeologicznych na stanowisku Bykowszczyzna 8 obejmował pozyskanie oraz inwentaryzację materiału zabytkowego wypełniającego formy. W wyniku wybrania tego materiału, w obszarze stanowiska pozostają charakterystyczne jamy gospodarcze, które stanowią negatywowy obraz wypełnienia formy. Kształt jam jest dokumentowany w postaci szkiców oraz fotografii. Dokumentacja ta stanowi punkt wyjścia procesu digitalizacji (materiał źródłowy). Treścią artykułu jest sporządzenie cyfrowej dokumentacji zawierającej plany stanowiska w kilku poziomach szczegółowości (dla pasa, pola oraz pojedynczych form) oraz wygenerowanie modeli w standardzie 3D. Dokumentacja taka umożliwia łatwą archiwizację oraz czytelną prezentację wybranych obiektów. Możliwe jest również wykonanie analiz przestrzennych. Funkcje programu ArcView 3.2. oraz

  6. MYB Transcription Factors in Chinese Pear (Pyrus bretschneideri Rehd.): Genome-Wide Identification, Classification, and Expression Profiling during Fruit Development.

    PubMed

    Cao, Yunpeng; Han, Yahui; Li, Dahui; Lin, Yi; Cai, Yongping

    2016-01-01

    The MYB family is one of the largest families of transcription factors in plants. Although, some MYBs were reported to play roles in secondary metabolism, no comprehensive study of the MYB family in Chinese pear (Pyrus bretschneideri Rehd.) has been reported. In the present study, we performed genome-wide analysis of MYB genes in Chinese pear, designated as PbMYBs, including analyses of their phylogenic relationships, structures, chromosomal locations, promoter regions, GO annotations, and collinearity. A total of 129 PbMYB genes were identified in the pear genome and were divided into 31 subgroups based on phylogenetic analysis. These PbMYBs were unevenly distributed among 16 chromosomes (total of 17 chromosomes). The occurrence of gene duplication events indicated that whole-genome duplication and segmental duplication likely played key roles in expansion of the PbMYB gene family. Ka/Ks analysis suggested that the duplicated PbMYBs mainly experienced purifying selection with restrictive functional divergence after the duplication events. Interspecies microsynteny analysis revealed maximum orthology between pear and peach, followed by plum and strawberry. Subsequently, the expression patterns of 20 PbMYB genes that may be involved in lignin biosynthesis according to their phylogenetic relationships were examined throughout fruit development. Among the 20 genes examined, PbMYB25 and PbMYB52 exhibited expression patterns consistent with the typical variations in the lignin content previously reported. Moreover, sub-cellular localization analysis revealed that two proteins PbMYB25 and PbMYB52 were localized to the nucleus. All together, PbMYB25 and PbMYB52 were inferred to be candidate genes involved in the regulation of lignin biosynthesis during the development of pear fruit. This study provides useful information for further functional analysis of the MYB gene family in pear. PMID:27200050

  7. New insights on the evolution of Leafy cotyledon1 (LEC1) type genes in vascular plants.

    PubMed

    Cagliari, Alexandro; Turchetto-Zolet, Andreia Carina; Korbes, Ana Paula; Maraschin, Felipe Dos Santos; Margis, Rogerio; Margis-Pinheiro, Marcia

    2014-01-01

    NF-Y is a conserved oligomeric transcription factor found in all eukaryotes. In plants, this regulator evolved with a broad diversification of the genes coding for its three subunits (NF-YA, NF-YB and NF-YC). The NF-YB members can be divided into Leafy Cotyledon1 (LEC1) and non-LEC1 types. Here we presented a comparative genomic study using phylogenetic analyses to validate an evolutionary model for the origin of LEC-type genes in plants and their emergence from non-LEC1-type genes. We identified LEC1-type members in all vascular plant genomes, but not in amoebozoa, algae, fungi, metazoa and non-vascular plant representatives, which present exclusively non-LEC1-type genes as constituents of their NF-YB subunits. The non-synonymous to synonymous nucleotide substitution rates (Ka/Ks) between LEC1 and non-LEC1-type genes indicate the presence of positive selection acting on LEC1-type members to the fixation of LEC1-specific amino acid residues. The phylogenetic analyses demonstrated that plant LEC1-type genes are evolutionary divergent from the non-LEC1-type genes of plants, fungi, amoebozoa, algae and animals. Our results point to a scenario in which LEC1-type genes have originated in vascular plants after gene expansion in plants. We suggest that processes of neofunctionalization and/or subfunctionalization were responsible for the emergence of a versatile role for LEC1-type genes in vascular plants, especially in seed plants. LEC1-type genes besides being phylogenetic divergent also present different expression profile when compared with non-LEC1-type genes. Altogether, our data provide new insights about the LEC1 and non-LEC1 evolutionary relationship during the vascular plant evolution.

  8. Five Drosophila genomes reveal nonneutral evolution and the signature of host specialization in the chemoreceptor superfamily.

    PubMed

    McBride, Carolyn S; Arguello, J Roman; O'Meara, Brian C

    2007-11-01

    The insect chemoreceptor superfamily comprises the olfactory receptor (Or) and gustatory receptor (Gr) multigene families. These families give insects the ability to smell and taste chemicals in the environment and are thus rich resources for linking molecular evolutionary and ecological processes. Although dramatic differences in family size among distant species and high divergence among paralogs have led to the belief that the two families evolve rapidly, a lack of evolutionary data over short time scales has frustrated efforts to identify the major forces shaping this evolution. Here, we investigate patterns of gene loss/gain, divergence, and polymorphism in the entire repertoire of approximately 130 chemoreceptor genes from five closely related species of Drosophila that share a common ancestor within the past 12 million years. We demonstrate that the overall evolution of the Or and Gr families is nonneutral. We also show that selection regimes differ both between the two families as wholes and within each family among groups of genes with varying functions, patterns of expression, and phylogenetic histories. Finally, we find that the independent evolution of host specialization in Drosophila sechellia and D. erecta is associated with a fivefold acceleration of gene loss and increased rates of amino acid evolution at receptors that remain intact. Gene loss appears to primarily affect Grs that respond to bitter compounds while elevated Ka/Ks is most pronounced in the subset of Ors that are expressed in larvae. Our results provide strong evidence that the observed phenomena result from the invasion of a novel ecological niche and present a unique synthesis of molecular evolutionary analyses with ecological data.

  9. Identification and characterization of insect-specific proteins by genome data analysis

    PubMed Central

    Zhang, Guojie; Wang, Hongsheng; Shi, Junjie; Wang, Xiaoling; Zheng, Hongkun; Wong, Gane Ka-Shu; Clark, Terry; Wang, Wen; Wang, Jun; Kang, Le

    2007-01-01

    Background Insects constitute the vast majority of known species with their importance including biodiversity, agricultural, and human health concerns. It is likely that the successful adaptation of the Insecta clade depends on specific components in its proteome that give rise to specialized features. However, proteome determination is an intensive undertaking. Here we present results from a computational method that uses genome analysis to characterize insect and eukaryote proteomes as an approximation complementary to experimental approaches. Results Homologs in common to Drosophila melanogaster, Anopheles gambiae, Bombyx mori, Tribolium castaneum, and Apis mellifera were compared to the complete genomes of three non-insect eukaryotes (opisthokonts) Homo sapiens, Caenorhabditis elegans and Saccharomyces cerevisiae. This operation yielded 154 groups of orthologous proteins in Drosophila to be insect-specific homologs; 466 groups were determined to be common to eukaryotes (represented by three opisthokonts). ESTs from the hemimetabolous insect Locust migratoria were also considered in order to approximate their corresponding genes in the insect-specific homologs. Stress and stimulus response proteins were found to constitute a higher fraction in the insect-specific homologs than in the homologs common to eukaryotes. Conclusion The significant representation of stress response and stimulus response proteins in proteins determined to be insect-specific, along with specific cuticle and pheromone/odorant binding proteins, suggest that communication and adaptation to environments may distinguish insect evolution relative to other eukaryotes. The tendency for low Ka/Ks ratios in the insect-specific protein set suggests purifying selection pressure. The generally larger number of paralogs in the insect-specific proteins may indicate adaptation to environment changes. Instances in our insect-specific protein set have been arrived at through experiments reported in the

  10. Transcriptome sequencing of a highly salt tolerant mangrove species Sonneratia alba using Illumina platform.

    PubMed

    Chen, Sufang; Zhou, Renchao; Huang, Yelin; Zhang, Meng; Yang, Guili; Zhong, Cairong; Shi, Suhua

    2011-06-01

    Mangroves are critical and threatened marine resources, yet few transcriptomic and genomic data are available in public databases. The transcriptome of a highly salt tolerant mangrove species, Sonneratia alba, was sequenced using the Illumina Genome Analyzer in this study. Over 15 million 75-bp paired-end reads were assembled into 30,628 unique sequences with an average length of 581 bp. Of them, 2358 SSRs were detected, with di-nucleotide repeats (59.2%) and tri-nucleotide repeats (37.7%) being the most common. Analysis of codon usage bias based on 20,945 coding sequences indicated that genes of S. alba were less biased than those of some microorganisms and Drosophila and that codon usage variation in S. alba was due primarily to compositional mutation bias, while translational selection has a relatively weak effect. Genome-wide gene ontology (GO) assignments showed that S. alba shared a similar GO slim classification with Arabidopsis thaliana. High percentages of sequences assigned to GO slim category 'mitochondrion' and four KEGG pathways, such as carbohydrates and secondary metabolites metabolism, may contribute to salt adaptation of S. alba. In addition, 1266 unique sequences matched to 273 known salt responsive genes (gene families) in other species were screened as candidates for salt tolerance of S. alba, and some of these genes showed fairly high coverage depth. At last, we identified four genes with signals of strong diversifying selection (K(a)/K(s)>1) by comparing the transcriptome sequences of S. alba with 249 known ESTs from its congener S. caseolaris. This study demonstrated a successful application of the Illumina platform to de novo assembly of the transcriptome of a non-model organism. Abundant SSR markers, salt responsive genes and four genes with signature of natural selection obtained from S. alba provide abundant sequence sources for future genetic diversity, salt adaptation and speciation studies. PMID:21620334

  11. Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean

    PubMed Central

    Singh, Vikash K.; Jain, Mukesh

    2015-01-01

    Auxin plays a central role in many aspects of plant growth and development. Auxin/Indole-3-Acetic Acid (Aux/IAA) genes cooperate with several other components in the perception and signaling of plant hormone auxin. An investigation of chickpea and soybean genomes revealed 22 and 63 putative Aux/IAA genes, respectively. These genes were classified into six subfamilies on the basis of phylogenetic analysis. Among 63 soybean Aux/IAA genes, 57 (90.5%) were found to be duplicated via whole genome duplication (WGD)/segmental events. Transposed duplication played a significant role in tandem arrangements between the members of different subfamilies. Analysis of Ka/Ks ratio of duplicated Aux/IAA genes revealed purifying selection pressure with restricted functional divergence. Promoter sequence analysis revealed several cis-regulatory elements related to auxin, abscisic acid, desiccation, salt, seed, and endosperm, indicating their role in development and stress responses. Expression analysis of chickpea and soybean Aux/IAA genes in various tissues and stages of development demonstrated tissue/stage specific differential expression. In soybean, at least 16 paralog pairs, duplicated via WGD/segmental events, showed almost indistinguishable expression pattern, but eight pairs exhibited significantly diverse expression patterns. Under abiotic stress conditions, such as desiccation, salinity and/or cold, many Aux/IAA genes of chickpea and soybean revealed differential expression. qRT-PCR analysis confirmed the differential expression patterns of selected Aux/IAA genes in chickpea. The analyses presented here provide insights on putative roles of chickpea and soybean Aux/IAA genes and will facilitate elucidation of their precise functions during development and abiotic stress responses. PMID:26579165

  12. Genome-Wide Identification, Classification, and Expression Analysis of Autophagy-Associated Gene Homologues in Rice (Oryza sativa L.)

    PubMed Central

    Xia, Kuaifei; Liu, Tao; Ouyang, Jie; Wang, Ren; Fan, Tian; Zhang, Mingyong

    2011-01-01

    Autophagy is an intracellular degradation process for recycling macromolecules and organelles. It plays important roles in plant development and in response to nutritional demand, stress, and senescence. Organisms from yeast to plants contain many autophagy-associated genes (ATG). In this study, we found that a total of 33 ATG homologues exist in the rice [Oryza sativa L. (Os)] genome, which were classified into 13 ATG subfamilies. Six of them are alternatively spliced genes. Evolutional analysis showed that expansion of 10 OsATG homologues occurred via segmental duplication events and that the occurrence of these OsATG homologues within each subfamily was asynchronous. The Ka/Ks ratios suggested purifying selection for four duplicated OsATG homologues and positive selection for two. Calculating the dates of the duplication events indicated that all duplication events might have occurred after the origin of the grasses, from 21.43 to 66.77 million years ago. Semi-quantitative RT–PCR analysis and mining the digital expression database of rice showed that all 33 OsATG homologues could be detected in at least one cell type of the various tissues under normal or stress growth conditions, but their expression was tightly regulated. The 10 duplicated genes showed expression divergence. The expression of most OsATG homologues was regulated by at least one treatment, including hormones, abiotic and biotic stresses, and nutrient limitation. The identification of OsATG homologues showing constitutive expression or responses to environmental stimuli provides new insights for in-depth characterization of selected genes of importance in rice. PMID:21795261

  13. Overlapping genetic codes for overlapping frameshifted genes in Testudines, and Lepidochelys olivacea as special case.

    PubMed

    Seligmann, Hervé

    2012-12-01

    Mitochondrial genes code for additional proteins after +2 frameshifts by reassigning stops to code for amino acids, which defines overlapping genetic codes for overlapping genes. Turtles recode stops UAR → Trp and AGR → Lys (AGR → Gly in the marine Olive Ridley turtle, Lepidochelys olivacea). In Lepidochelys the +2 frameshifted mitochondrial Cytb gene lacks stops, open reading frames from other genes code for unknown proteins, and for regular mitochondrial proteins after frameshifts according to the overlapping genetic code. Lepidochelys' inversion between proteins coded by regular and overlapping genetic codes substantiates the existence of overlap coding. ND4 differs among Lepidochelys mitochondrial genomes: it is regular in DQ486893; in NC_011516, the open reading frame codes for another protein, the regular ND4 protein is coded by the frameshifted sequence reassigning stops as in other turtles. These systematic patterns are incompatible with Genbank/sequencing errors and DNA decay. Random mixing of synonymous codons, conserving main frame coding properties, shows optimization of natural sequences for overlap coding; Ka/Ks analyses show high positive (directional) selection on overlapping genes. Tests based on circular genetic codes confirm programmed frameshifts in ND3 and ND4l genes, and predicted frameshift sites for overlap coding in Lepidochelys. Chelonian mitochondria adapt for overlapping gene expression: cloverleaf formation by antisense tRNAs with predicted anticodons matching stops coevolves with overlap coding; antisense tRNAs with predicted expanded anticodons (frameshift suppressor tRNAs) associate with frameshift-coding in ND3 and ND4l, a potential regulation of frameshifted overlap coding. Anaeroby perhaps switched between regular and overlap coding genes in Lepidochelys.

  14. Dimerization and Transactivation Domains as Candidates for Functional Modulation and Diversity of Sox9

    PubMed Central

    Geraldo, Marcos Tadeu; Valente, Guilherme Targino; Nakajima, Rafael Takahiro; Martins, Cesar

    2016-01-01

    Sox9 plays an important role in a large variety of developmental pathways in vertebrates. It is composed of three domains: high-mobility group box (HMG box), dimerization (DIM) and transactivation (TAD). One of the main processes for regulation and variability of the pathways involving Sox9 is the self-gene expression regulation of Sox9. However, the subsequent roles of the Sox9 domains can also generate regulatory modulations. Studies have shown that TADs can bind to different types of proteins and its function seems to be influenced by DIM. Therefore, we hypothesized that both domains are directly associated and can be responsible for the functional variability of Sox9. We applied a method based on a broad phylogenetic context, using sequences of the HMG box domain, to ensure the homology of all the Sox9 copies used herein. The data obtained included 4,921 sequences relative to 657 metazoan species. Based on coevolutionary and selective pressure analyses of the Sox9 sequences, we observed coevolutions involving DIM and TADs. These data, along with the experimental data from literature, indicate a functional relationship between these domains. Moreover, DIM and TADs may be responsible for the functional plasticity of Sox9 because they are more tolerant for molecular changes (higher Ka/Ks ratio than the HMG box domain). This tolerance could allow a differential regulation of target genes or promote novel targets during transcriptional activation. In conclusion, we suggest that DIM and TADs functional association may regulate differentially the target genes or even promote novel targets during transcription activation mediated by Sox9 paralogs, contributing to the subfunctionalization of Sox9a and Sox9b in teleosts. PMID:27196604

  15. Fast protein evolution and germ line expression of a Drosophila parental gene and its young retroposed paralog.

    PubMed

    Betrán, Esther; Bai, Yongsheng; Motiwale, Mansi

    2006-11-01

    This is the first detailed study of the evolution, phylogenetic distribution, and transcription of one young retroposed gene, CG13732, and its parental gene CG15645, whose functions are unknown. CG13732 is a recognizable retroposed copy of CG15645 retaining the signals of this process. We name the parental gene Cervantes and the retrogene Quijote. To determine when this duplication occurred and the phylogenetic distribution of Quijote, we employed polymerase chain reaction, Southern blotting, and the available information on sequenced Drosophila genomes. Interestingly, these analyses revealed that Quijote is present only in 4 species of Drosophila (Drosophila melanogaster, Drosophila simulans, Drosophila sechellia, and Drosophila mauritiana) and that retroposed copies of Cervantes have also originated in the lineages leading to Drosophila yakuba and Drosophila erecta independently in the 3 instances. We name the new retrogene in the D. yakuba lineage Rocinante and the new retrogene in the D. erecta lineage Sancho. In this work, we present data on Quijote and its parental gene Cervantes. Polymorphism analysis of the derived gene and divergence data for both parental and derived genes were used to determine that both genes likely produce functional proteins and that they are changing at a fast rate (KA/KS approximately 0.38). The negative value of H of Fay and Wu in the non-African sample reveals an excess of derived variants at high frequency. This could be explained either by positive selection in the region or by demographic effects. The comparative expression pattern shows that both genes express in the same adult tissues (male and female germ line) in D. melanogaster. Quijote is also expressed in male and female in D. simulans, D. sechellia, and D. mauritiana. We argue that the fast rate of evolution of these genes could be related to their putative germ line function and are further studying the independent recruitment of Cervantes-derived retrogenes in

  16. Elevated levels of adaption in Helicobacter pylori genomes from Japan; a link to higher incidences of gastric cancer?

    PubMed Central

    Soto-Girón, Maria Juliana; Ospina, Oscar E.; Massey, Steven Edward

    2015-01-01

    Helicobacter pylori is a bacterium that lives in the human stomach and is a major risk factor for gastric cancer and ulcers. H.pylori is host dependent and has been carried with human populations around the world after their departure from Africa. We wished to investigate how H.pylori has coevolved with its host during that time, focusing on strains from Japanese and European populations, given that gastric cancer incidence is high in Japanese populations, while low in European. A positive selection analysis of eight H.pylori genomes was conducted, using maximum likelihood based pairwise comparisons in order to maximize the number of strain-specific genes included in the study. Using the genic Ka/Ks ratio, comparisons of four Japanese H.pylori genomes suggests 25–34 genes under positive selection, while four European H.pylori genomes suggests 16–21 genes; few of the genes identified were in common between lineages. Of the identified genes which were annotated, 38% possessed homologs associated with pathogenicity and / or host adaptation, consistent with their involvement in a coevolutionary ‘arms race’ with the host. Given the efficacy of identifying host interaction factors de novo, in the absence of functionally annotated homologs our evolutionary approach may have value in identifying novel genes which H.pylori employs to interact with the human gut environment. In addition, the larger number of genes inferred as being under positive selection in Japanese strains compared to European implies a stronger overall adaptive pressure, potentially resulting from an elevated immune response which may be linked to increased inflammation, an initial stage in the development of gastric cancer. PMID:25788149

  17. The mitochondrial genomes of two nemerteans, Cephalothrix sp. (Nemertea: Palaeonemertea) and Paranemertes cf. peregrina (Nemertea: Hoplonemertea).

    PubMed

    Chen, Hai-Xia; Sundberg, Per; Wu, Hai-Yi; Sun, Shi-Chun

    2011-10-01

    The mitochondrial genome sequences were determined for two species of nemerteans, Cephalothrix sp. (15,800 bp sequenced, near-complete) and Paranemertes cf. peregrina (14,558 bp, complete). As seen in most metazoans, the genomes encode 13 protein, 2 ribosomal RNA and 22 transfer RNA genes. The nucleotide composition is strongly biased toward A and T, as is typical for metazoan mtDNAs. There is also a significant strand skew in the distribution of these nucleotides, with the coding strand being richer in T than A and in G than C. All genes are transcribed in the same direction except for trnP and trnT, which is consistent with that reported for Cephalothrix hongkongiensis and Lineus viridis. Gene arrangement of Cephalothrix sp. is identical to that of C. hongkongiensis, while in P. cf. peregrina it is similar to L. viridis, but differs significantly from the three Cephalothrix species in the position of four protein-coding genes and seven tRNAs. Some protein-coding genes have 3' end stem-loop structures, which may allow mRNA processing without flanking tRNAs. The major non-coding regions observed in the two genomes with potential to form stem-loop structures may be involved in the initiation of replication or transcription. The average Ka/Ks values, varying from 0.12 to 0.89, are markedly different among the 13 mitochondrial protein-coding genes, suggesting that there may exist different selective pressure among mitochondrial genes of nemerteans.

  18. Transcriptome Characterization and Functional Marker Development in Sorghum Sudanense

    PubMed Central

    Zhan, Qiuwen; Liu, Yanlong; Yang, Xiaocui

    2016-01-01

    Sudangrass, Sorghum sudanense, is an important forage in warm regions. But little is known about its genome. In this study, the transcriptomes of sudangrass S722 and sorghum Tx623B were sequenced by Illumina sequencing. More than 4Gb bases were sequenced for each library. For Tx623B and S722, 88.79% and 83.88% reads, respectively were matched to the Sorghum bicolor genome. A total of 2,397 differentially expressed genes (DEGs) were detected by RNA-Seq between the two libraries, including 849 up-regulated genes and 1,548 down-regulated genes. These DEGs could be divided into three groups by annotation analysis. A total of 44,495 single nucleotide polymorphisms (SNPs) were discovered by aligning S722 reads to the sorghum reference genome. Of these SNPs, 61.37% were transition, and this value did not differ much between different chromosomes. In addition, 16,928 insertion and deletion (indel) loci were identified between the two genomes. A total of 5,344 indel markers were designed, 15 of which were selected to construct the genetic map derived from the cross of Tx623A and Sa. It was indicated that the indel markers were useful and versatile between sorghum and sudangrass. Comparison of synonymous base substitutions (Ks) and non-synonymous base substitutions (Ka) between the two libraries showed that 95% orthologous pairs exhibited Ka/Ks<1.0, indicating that these genes were influenced by purifying selection. The results from this study provide important information for molecular genetic research and a rich resource for marker development in sudangrass and other Sorghum species. PMID:27152648

  19. Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implications.

    PubMed

    Kim, Young-Kyu; Park, Chong-wook; Kim, Ki-Joong

    2009-03-31

    The chloroplast DNA sequences of Megaleranthis saniculifolia, an endemic and monotypic endangered plant species, were completed in this study (GenBank FJ597983). The genome is 159,924 bp in length. It harbors a pair of IR regions consisting of 26,608 bp each. The lengths of the LSC and SSC regions are 88,326 bp and 18,382 bp, respectively. The structural organizations, gene and intron contents, gene orders, AT contents, codon usages, and transcription units of the Megaleranthis chloroplast genome are similar to those of typical land plant cp DNAs. However, the detailed features of Megaleranthis chloroplast genomes are substantially different from that of Ranunculus, which belongs to the same family, the Ranunculaceae. First, the Megaleranthis cp DNA was 4,797 bp longer than that of Ranunculus due to an expanded IR region into the SSC region and duplicated sequence elements in several spacer regions of the Megaleranthis cp genome. Second, the chloroplast genomes of Megaleranthis and Ranunculus evidence 5.6% sequence divergence in the coding regions, 8.9% sequence divergence in the intron regions, and 18.7% sequence divergence in the intergenic spacer regions, respectively. In both the coding and noncoding regions, average nucleotide substitution rates differed markedly, depending on the genome position. Our data strongly implicate the positional effects of the evolutionary modes of chloroplast genes. The genes evidencing higher levels of base substitutions also have higher incidences of indel mutations and low Ka/Ks ratios. A total of 54 simple sequence repeat loci were identified from the Megaleranthis cp genome. The existence of rich cp SSR loci in the Megaleranthis cp genome provides a rare opportunity to study the population genetic structures of this endangered species. Our phylogenetic trees based on the two independent markers, the nuclear ITS and chloroplast matK sequences, strongly support the inclusion of the Megaleranthis to the Trollius. Therefore, our

  20. Selective Loss of Cysteine Residues and Disulphide Bonds in a Potato Proteinase Inhibitor II Family

    PubMed Central

    Li, Xiu-Qing; Zhang, Tieling; Donnelly, Danielle

    2011-01-01

    Disulphide bonds between cysteine residues in proteins play a key role in protein folding, stability, and function. Loss of a disulphide bond is often associated with functional differentiation of the protein. The evolution of disulphide bonds is still actively debated; analysis of naturally occurring variants can promote understanding of the protein evolutionary process. One of the disulphide bond-containing protein families is the potato proteinase inhibitor II (PI-II, or Pin2, for short) superfamily, which is found in most solanaceous plants and participates in plant development, stress response, and defence. Each PI-II domain contains eight cysteine residues (8C), and two similar PI-II domains form a functional protein that has eight disulphide bonds and two non-identical reaction centres. It is still unclear which patterns and processes affect cysteine residue loss in PI-II. Through cDNA sequencing and data mining, we found six natural variants missing cysteine residues involved in one or two disulphide bonds at the first reaction centre. We named these variants Pi7C and Pi6C for the proteins missing one or two pairs of cysteine residues, respectively. This PI-II-7C/6C family was found exclusively in potato. The missing cysteine residues were in bonding pairs but distant from one another at the nucleotide/protein sequence level. The non-synonymous/synonymous substitution (Ka/Ks) ratio analysis suggested a positive evolutionary gene selection for Pi6C and various Pi7C. The selective deletion of the first reaction centre cysteine residues that are structure-level-paired but sequence-level-distant in PI-II illustrates the flexibility of PI-II domains and suggests the functionality of their transient gene versions during evolution. PMID:21494600

  1. Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

    PubMed

    Zhao, Yongzhong; Epstein, Richard J

    2008-08-01

    Tumor suppressor genes are classified by their somatic behavior either as caretakers (CTs) that maintain DNA integrity or as gatekeepers (GKs) that regulate cell survival, but the germ line role of these disease-related gene subgroups may differ. To test this hypothesis, we have used genomic data mining to compare the features of human CTs (n = 38), GKs (n = 36), DNA repair genes (n = 165), apoptosis genes (n = 622), and their orthologs. This analysis reveals that repair genes are numerically less common than apoptosis genes in the genomes of multicellular organisms (P < 0.01), whereas CT orthologs are commoner than GK orthologs in unicellular organisms (P < 0.05). Gene targeting data show that CTs are less essential than GKs for survival of multicellular organisms (P < 0.0005) and that CT knockouts often permit offspring viability at the cost of male sterility. Patterns of human familial oncogenic mutations confirm that isolated CT loss is commoner than is isolated GK loss (P < 0.00001). In sexually reproducing species, CTs appear subject to less efficient purifying selection (i.e., higher Ka/Ks) than GKs (P = 0.000003); the faster evolution of CTs seems likely to be mediated by gene methylation and reduced transcription-coupled repair, based on differences in dinucleotide patterns (P = 0.001). These data suggest that germ line CT/repair gene function is relatively dispensable for survival, and imply that milder (e.g., epimutational) male prezygotic repair defects could enhance sperm variation-and hence environmental adaptation and speciation-while sparing fertility. We submit that CTs and repair genes are general targets for epigenetically initiated adaptive evolution, and propose a model in which human cancers arise in part as an evolutionarily programmed side effect of age- and damage-inducible genetic instability affecting both somatic and germ line lineages. PMID:18535014

  2. RNA-Seq using two populations reveals genes and alleles controlling wood traits and growth in Eucalyptus nitens.

    PubMed

    Thavamanikumar, Saravanan; Southerton, Simon; Thumma, Bala

    2014-01-01

    Eucalyptus nitens is a perennial forest tree species grown mainly for kraft pulp production in many parts of the world. Kraft pulp yield (KPY) is a key determinant of plantation profitability and increasing the KPY of trees grown in plantations is a major breeding objective. To speed up the breeding process, molecular markers that can predict KPY are desirable. To achieve this goal, we carried out RNA-Seq studies on trees at extremes of KPY in two different trials to identify genes and alleles whose expression correlated with KPY. KPY is positively correlated with growth measured as diameter at breast height (DBH) in both trials. In total, six RNA bulks from two treatments were sequenced on an Illumina HiSeq platform. At 5% false discovery rate level, 3953 transcripts showed differential expression in the same direction in both trials; 2551 (65%) were down-regulated and 1402 (35%) were up-regulated in low KPY samples. The genes up-regulated in low KPY trees were largely involved in biotic and abiotic stress response reflecting the low growth among low KPY trees. Genes down-regulated in low KPY trees mainly belonged to gene categories involved in wood formation and growth. Differential allelic expression was observed in 2103 SNPs (in 1068 genes) and of these 640 SNPs (30%) occurred in 313 unique genes that were also differentially expressed. These SNPs may represent the cis-acting regulatory variants that influence total gene expression. In addition we also identified 196 genes which had Ka/Ks ratios greater than 1.5, suggesting that these genes are under positive selection. Candidate genes and alleles identified in this study will provide a valuable resource for future association studies aimed at identifying molecular markers for KPY and growth.

  3. Allelic diversity of S-RNase at the self-incompatibility locus in natural flowering cherry populations (Prunus lannesiana var. speciosa).

    PubMed

    Kato, S; Mukai, Y

    2004-03-01

    In the Rosaceae family, which includes Prunus, gametophytic self-incompatibility (GSI) is controlled by a single multiallelic locus (S-locus), and the S-locus product expressed in the pistils is a glycoprotein with ribonuclease activity (S-RNase). Two populations of flowering cherry (Prunus lannesiana var. speciosa), located on Hachijo Island in Japan's Izu Islands, were sampled, and S-allele diversity was surveyed based on the sequence polymorphism of S-RNase. A total of seven S-alleles were cloned and sequenced. The S-RNases of flowering cherry showed high homology to those of Prunus cultivars (P. avium and P. dulcis). In the phylogenetic tree, the S-RNases of flowering cherry and other Prunus cultivars formed a distinct group, but they did not form species-specific subgroups. The nucleotide substitution pattern in S-RNases of flowering cherry showed no excess of nonsynonymous substitutions relative to synonymous substitutions. However, the S-RNases of flowering cherry had a higher Ka/Ks ratio than those of other Prunus cultivars, and a subtle heterogeneity in the nucleotide substitution rates was observed among the Prunus species. The S-genotype of each individual was determined by Southern blotting of restriction enzyme-digested genomic DNA, using cDNA for S-RNase as a probe. A total of 22 S-alleles were identified. All individuals examined were heterozygous, as expected under GSI. The allele frequencies were, contrary to the expectation under GSI, significantly unequal. The two populations studied showed a high degree of overlap, with 18 shared alleles. However, the allele frequencies differed considerably between the two populations.

  4. Head Transcriptomes of Two Closely Related Species of Fruit Flies of the Anastrepha fraterculus Group Reveals Divergent Genes in Species with Extensive Gene Flow

    PubMed Central

    Rezende, Victor Borges; Congrains, Carlos; Lima, André Luís A.; Campanini, Emeline Boni; Nakamura, Aline Minali; de Oliveira, Janaína Lima; Chahad-Ehlers, Samira; Junior, Iderval Sobrinho; Alves de Brito, Reinaldo

    2016-01-01

    Several fruit flies species of the Anastrepha fraterculus group are of great economic importance for the damage they cause to a variety of fleshy fruits. Some species in this group have diverged recently, with evidence of introgression, showing similar morphological attributes that render their identification difficult, reinforcing the relevance of identifying new molecular markers that may differentiate species. We investigated genes expressed in head tissues from two closely related species: A. obliqua and A. fraterculus, aiming to identify fixed single nucleotide polymorphisms (SNPs) and highly differentiated transcripts, which, considering that these species still experience some level of gene flow, could indicate potential candidate genes involved in their differentiation process. We generated multiple libraries from head tissues of these two species, at different reproductive stages, for both sexes. Our analyses indicate that the de novo transcriptome assemblies are fairly complete. We also produced a hybrid assembly to map each species’ reads, and identified 67,470 SNPs in A. fraterculus, 39,252 in A. obliqua, and 6386 that were common to both species. We identified 164 highly differentiated unigenes that had a mean interspecific index (D¯) of at least 0.94. We selected unigenes that had Ka/Ks higher than 0.5, or had at least three or more highly differentiated SNPs as potential candidate genes for species differentiation. Among these candidates, we identified proteases, regulators of redox homeostasis, and an odorant-binding protein (Obp99c), among other genes. The head transcriptomes described here enabled the identification of thousands of genes hitherto unavailable for these species, and generated a set of candidate genes that are potentially important to genetically identify species and understand the speciation process in the presence of gene flow of A. obliqua and A. fraterculus. PMID:27558666

  5. Dimerization and Transactivation Domains as Candidates for Functional Modulation and Diversity of Sox9.

    PubMed

    Geraldo, Marcos Tadeu; Valente, Guilherme Targino; Nakajima, Rafael Takahiro; Martins, Cesar

    2016-01-01

    Sox9 plays an important role in a large variety of developmental pathways in vertebrates. It is composed of three domains: high-mobility group box (HMG box), dimerization (DIM) and transactivation (TAD). One of the main processes for regulation and variability of the pathways involving Sox9 is the self-gene expression regulation of Sox9. However, the subsequent roles of the Sox9 domains can also generate regulatory modulations. Studies have shown that TADs can bind to different types of proteins and its function seems to be influenced by DIM. Therefore, we hypothesized that both domains are directly associated and can be responsible for the functional variability of Sox9. We applied a method based on a broad phylogenetic context, using sequences of the HMG box domain, to ensure the homology of all the Sox9 copies used herein. The data obtained included 4,921 sequences relative to 657 metazoan species. Based on coevolutionary and selective pressure analyses of the Sox9 sequences, we observed coevolutions involving DIM and TADs. These data, along with the experimental data from literature, indicate a functional relationship between these domains. Moreover, DIM and TADs may be responsible for the functional plasticity of Sox9 because they are more tolerant for molecular changes (higher Ka/Ks ratio than the HMG box domain). This tolerance could allow a differential regulation of target genes or promote novel targets during transcriptional activation. In conclusion, we suggest that DIM and TADs functional association may regulate differentially the target genes or even promote novel targets during transcription activation mediated by Sox9 paralogs, contributing to the subfunctionalization of Sox9a and Sox9b in teleosts. PMID:27196604

  6. Molecular characterization and phylogenetic analysis of three odorant binding protein gene transcripts in Dendrolimus species (Lepidoptera: Lasiocampidae).

    PubMed

    Zhang, Su-Fang; Zhang, Zhen; Kong, Xiang-Bo; Wang, Hong-Bin

    2014-10-01

    Pine caterpillar moths, Dendrolimus spp. (Lepidoptera: Lasiocampidae), are serious economic pest of pines. Previously, phylogenetic analyses of Dendrolimus using different methods yielded inconsistent results. The chemosensory systems of insects may play fundamental roles in promoting speciation. Odorant-binding proteins (OBPs) participate in the first step of odor detection. Studying the evolution of OBPs in closely related species may help us to identify their role in speciation. We identified three OBPs - one pheromone-binding protein and two general odorant-binding proteins - from male antennae of four Dendrolimus species, D. superans (Butler), D. punctatus (Walker), D. kikuchii Matsumura, and D. houi Lajonquiere, the olfactory recognition systems of which had not been previously investigated. We analyzed their molecular characteristics and compared their sequences to those of OBPs in D. tabulaeformis Tsai et Liu. Ka/Ks ratio analyses among the five Dendrolimus species indicate that PBP1 genes experienced more evolutionary pressure than the GOBPs. Phylogenetic relationships of PBP1 and GOBP1 both indicated that D. houi was the basal species, then branched D. kikuchii, while D. tabulaeformis, D. punctatus, and D. superans evolved more recently. These relationships are consistent with the changes in sex pheromone components of these five species. Dendrolimus tabulaeformis and D. punctatus are closely related sister species. However, the distances among GOBP2 sequences in the five Dendrolimus were very short, and the relationships of D. houi and D. kikuchii could not be resolved. Integrating our results with those of previous studies, we hypothesized that D. kikuchii, D. punctatus and D. superans evolved from the basal ancestor because of sex pheromone mutations and environmental pressure.

  7. MYB Transcription Factors in Chinese Pear (Pyrus bretschneideri Rehd.): Genome-Wide Identification, Classification, and Expression Profiling during Fruit Development.

    PubMed

    Cao, Yunpeng; Han, Yahui; Li, Dahui; Lin, Yi; Cai, Yongping

    2016-01-01

    The MYB family is one of the largest families of transcription factors in plants. Although, some MYBs were reported to play roles in secondary metabolism, no comprehensive study of the MYB family in Chinese pear (Pyrus bretschneideri Rehd.) has been reported. In the present study, we performed genome-wide analysis of MYB genes in Chinese pear, designated as PbMYBs, including analyses of their phylogenic relationships, structures, chromosomal locations, promoter regions, GO annotations, and collinearity. A total of 129 PbMYB genes were identified in the pear genome and were divided into 31 subgroups based on phylogenetic analysis. These PbMYBs were unevenly distributed among 16 chromosomes (total of 17 chromosomes). The occurrence of gene duplication events indicated that whole-genome duplication and segmental duplication likely played key roles in expansion of the PbMYB gene family. Ka/Ks analysis suggested that the duplicated PbMYBs mainly experienced purifying selection with restrictive functional divergence after the duplication events. Interspecies microsynteny analysis revealed maximum orthology between pear and peach, followed by plum and strawberry. Subsequently, the expression patterns of 20 PbMYB genes that may be involved in lignin biosynthesis according to their phylogenetic relationships were examined throughout fruit development. Among the 20 genes examined, PbMYB25 and PbMYB52 exhibited expression patterns consistent with the typical variations in the lignin content previously reported. Moreover, sub-cellular localization analysis revealed that two proteins PbMYB25 and PbMYB52 were localized to the nucleus. All together, PbMYB25 and PbMYB52 were inferred to be candidate genes involved in the regulation of lignin biosynthesis during the development of pear fruit. This study provides useful information for further functional analysis of the MYB gene family in pear.

  8. EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp ( Litopenaeus vannamei)

    NASA Astrophysics Data System (ADS)

    Liu, Chengzhang; Wang, Xia; Xiang, Jianhai; Li, Fuhua

    2012-09-01

    Pacific white shrimp has become a major aquaculture and fishery species worldwide. Although a large scale EST resource has been publicly available since 2008, the data have not yet been widely used for SNP discovery or transcriptome-wide assessment of selective pressure. In this study, a set of 155 411 expressed sequence tags (ESTs) from the NCBI database were computationally analyzed and 17 225 single nucleotide polymorphisms (SNPs) were predicted, including 9 546 transitions, 5 124 transversions and 2 481 indels. Among the 7 298 SNP substitutions located in functionally annotated contigs, 58.4% (4 262) are non-synonymous SNPs capable of introducing amino acid mutations. Two hundred and fifty nonsynonymous SNPs in genes associated with economic traits have been identified as candidates for markers in selective breeding. Diversity estimates among the synonymous nucleotides were on average 3.49 times greater than those in non-synonymous, suggesting negative selection. Distribution of non-synonymous to synonymous substitutions (Ka/Ks) ratio ranges from 0 to 4.01, (average 0.42, median 0.26), suggesting that the majority of the affected genes are under purifying selection. Enrichment analysis identified multiple gene ontology categories under positive or negative selection. Categories involved in innate immune response and male gamete generation are rich in positively selected genes, which is similar to reports in Drosophila and primates. This work is the first transcriptome-wide assessment of selective pressure in a Penaeid shrimp species. The functionally annotated SNPs provide a valuable resource of potential molecular markers for selective breeding.

  9. Analysis of S-RNase alleles of almond (Prunus dulcis): characterization of new sequences, resolution of synonyms and evidence of intragenic recombination.

    PubMed

    Ortega, Encarnación; Bosković, Radovan I; Sargent, Daniel J; Tobutt, Kenneth R

    2006-11-01

    Cross-compatibility relationships in almond are controlled by a gametophytically expressed incompatibility system partly mediated by stylar RNases, of which 29 have been reported. To resolve possible synonyms and to provide data for phylogenetic analysis, 21 almond S-RNase alleles were cloned and sequenced from SP (signal peptide region) or C1 (first conserved region) to C5, except for the S29 allele, which could be cloned only from SP to C1. Nineteen sequences (S4, S6, S11-S22, S25-S29)) were potentially new whereas S10 and S24 had previously been published but with different labels. The sequences for S16 and S17 were identical to that for S1, published previously; likewise, S15 was identical to S5. In addition, S4 and S20 were identical, as were S13 and S19. A revised version of the standard table of almond incompatibility genotypes is presented. Several alleles had AT or GA tandem repeats in their introns. Sequences of the 23 distinct newly cloned or already published alleles were aligned. Sliding windows analysis of Ka/Ks identified regions where positive selection may operate; in contrast to the Maloideae, most of the region from the beginning of C3 to the beginning of RC4 appeared not to be under positive selection. Phylogenetic analysis indicated four pairs of alleles had "bootstrap" support > 80%: S5/S10, S4/S8, S11/S24, and S3/S6. Various motifs up to 19 residues long occurred in at least two alleles, and their distributions were consistent with intragenic recombination, as were separate phylogenetic analyses of the 5' and 3' sections. Sequence comparison of phylogenetically related alleles indicated the significance of the region between RC4 and C5 in defining specificity.

  10. RNA-Seq Using Two Populations Reveals Genes and Alleles Controlling Wood Traits and Growth in Eucalyptus nitens

    PubMed Central

    Thavamanikumar, Saravanan; Southerton, Simon; Thumma, Bala

    2014-01-01

    Eucalyptus nitens is a perennial forest tree species grown mainly for kraft pulp production in many parts of the world. Kraft pulp yield (KPY) is a key determinant of plantation profitability and increasing the KPY of trees grown in plantations is a major breeding objective. To speed up the breeding process, molecular markers that can predict KPY are desirable. To achieve this goal, we carried out RNA-Seq studies on trees at extremes of KPY in two different trials to identify genes and alleles whose expression correlated with KPY. KPY is positively correlated with growth measured as diameter at breast height (DBH) in both trials. In total, six RNA bulks from two treatments were sequenced on an Illumina HiSeq platform. At 5% false discovery rate level, 3953 transcripts showed differential expression in the same direction in both trials; 2551 (65%) were down-regulated and 1402 (35%) were up-regulated in low KPY samples. The genes up-regulated in low KPY trees were largely involved in biotic and abiotic stress response reflecting the low growth among low KPY trees. Genes down-regulated in low KPY trees mainly belonged to gene categories involved in wood formation and growth. Differential allelic expression was observed in 2103 SNPs (in 1068 genes) and of these 640 SNPs (30%) occurred in 313 unique genes that were also differentially expressed. These SNPs may represent the cis-acting regulatory variants that influence total gene expression. In addition we also identified 196 genes which had Ka/Ks ratios greater than 1.5, suggesting that these genes are under positive selection. Candidate genes and alleles identified in this study will provide a valuable resource for future association studies aimed at identifying molecular markers for KPY and growth. PMID:24967893

  11. Five Drosophila genomes reveal nonneutral evolution and the signature of host specialization in the chemoreceptor superfamily.

    PubMed

    McBride, Carolyn S; Arguello, J Roman; O'Meara, Brian C

    2007-11-01

    The insect chemoreceptor superfamily comprises the olfactory receptor (Or) and gustatory receptor (Gr) multigene families. These families give insects the ability to smell and taste chemicals in the environment and are thus rich resources for linking molecular evolutionary and ecological processes. Although dramatic differences in family size among distant species and high divergence among paralogs have led to the belief that the two families evolve rapidly, a lack of evolutionary data over short time scales has frustrated efforts to identify the major forces shaping this evolution. Here, we investigate patterns of gene loss/gain, divergence, and polymorphism in the entire repertoire of approximately 130 chemoreceptor genes from five closely related species of Drosophila that share a common ancestor within the past 12 million years. We demonstrate that the overall evolution of the Or and Gr families is nonneutral. We also show that selection regimes differ both between the two families as wholes and within each family among groups of genes with varying functions, patterns of expression, and phylogenetic histories. Finally, we find that the independent evolution of host specialization in Drosophila sechellia and D. erecta is associated with a fivefold acceleration of gene loss and increased rates of amino acid evolution at receptors that remain intact. Gene loss appears to primarily affect Grs that respond to bitter compounds while elevated Ka/Ks is most pronounced in the subset of Ors that are expressed in larvae. Our results provide strong evidence that the observed phenomena result from the invasion of a novel ecological niche and present a unique synthesis of molecular evolutionary analyses with ecological data. PMID:18039874

  12. MYB Transcription Factors in Chinese Pear (Pyrus bretschneideri Rehd.): Genome-Wide Identification, Classification, and Expression Profiling during Fruit Development

    PubMed Central

    Cao, Yunpeng; Han, Yahui; Li, Dahui; Lin, Yi; Cai, Yongping

    2016-01-01

    The MYB family is one of the largest families of transcription factors in plants. Although, some MYBs were reported to play roles in secondary metabolism, no comprehensive study of the MYB family in Chinese pear (Pyrus bretschneideri Rehd.) has been reported. In the present study, we performed genome-wide analysis of MYB genes in Chinese pear, designated as PbMYBs, including analyses of their phylogenic relationships, structures, chromosomal locations, promoter regions, GO annotations, and collinearity. A total of 129 PbMYB genes were identified in the pear genome and were divided into 31 subgroups based on phylogenetic analysis. These PbMYBs were unevenly distributed among 16 chromosomes (total of 17 chromosomes). The occurrence of gene duplication events indicated that whole-genome duplication and segmental duplication likely played key roles in expansion of the PbMYB gene family. Ka/Ks analysis suggested that the duplicated PbMYBs mainly experienced purifying selection with restrictive functional divergence after the duplication events. Interspecies microsynteny analysis revealed maximum orthology between pear and peach, followed by plum and strawberry. Subsequently, the expression patterns of 20 PbMYB genes that may be involved in lignin biosynthesis according to their phylogenetic relationships were examined throughout fruit development. Among the 20 genes examined, PbMYB25 and PbMYB52 exhibited expression patterns consistent with the typical variations in the lignin content previously reported. Moreover, sub-cellular localization analysis revealed that two proteins PbMYB25 and PbMYB52 were localized to the nucleus. All together, PbMYB25 and PbMYB52 were inferred to be candidate genes involved in the regulation of lignin biosynthesis during the development of pear fruit. This study provides useful information for further functional analysis of the MYB gene family in pear. PMID:27200050

  13. A novel dromedary camel enterovirus in the family Picornaviridae from dromedaries in the Middle East.

    PubMed

    Woo, Patrick C Y; Lau, Susanna K P; Li, Tong; Jose, Shanty; Yip, Cyril C Y; Huang, Yi; Wong, Emily Y M; Fan, Rachel Y Y; Cai, Jian-Piao; Wernery, Ulrich; Yuen, Kwok-Yung

    2015-07-01

    The recent emergence of Middle East respiratory syndrome coronavirus from the Middle East and the discovery of the virus from dromedary camels have boosted interest in the search for novel viruses in dromedaries. Whilst picornaviruses are known to infect various animals, their existence in dromedaries was unknown. We describe the discovery of a novel picornavirus, dromedary camel enterovirus (DcEV), from dromedaries in Dubai. Among 215 dromedaries, DcEV was detected in faecal samples of four (1.9 %) dromedaries [one (0.5 %) adult dromedary and three (25 %) dromedary calves] by reverse transcription PCR. Analysis of two DcEV genomes showed that DcEV was clustered with other species of the genus Enterovirus and was most closely related to and possessed highest amino acid identities to the species Enterovirus E and Enterovirus F found in cattle. The G+C content of DcEV was 45 mol%, which differed from that of Enterovirus E and Enterovirus F (49-50 mol%) by 4-5 %. Similar to other members of the genus Enterovirus, the 5' UTR of DcEV possessed a putative type I internal ribosome entry site. The low ratios of the number of nonsynonymous substitutions per non-synonymous site to the number of synonymous substitutions per synonymous site (Ka/Ks) of various coding regions suggested that dromedaries are the natural reservoir in which DcEV has been stably evolving. These results suggest that DcEV is a novel species of the genus Enterovirus in the family Picornaviridae. Western blot analysis using recombinant DcEV VP1 polypeptide showed a high seroprevalence of 52 % among serum samples from 172 dromedaries for IgG, concurring with its much higher infection rates in dromedary calves than in adults. Further studies are important to understand the pathogenicity, epidemiology and genetic evolution of DcEV in this unique group of animals.

  14. Free Surface of the Liquid-Gas Phase Separation as a Measuring Membrane of a Device for Measuring Small Hydrostatic Pressure Difference Values / Powierzchnia Swobodna Rozdziału Faz Ciecz-Gaz Jako Membrana Pomiarowa Urządzenia Do Pomiaru Małych Wartości Różnicy Ciśnienia Hydrostatycznego

    NASA Astrophysics Data System (ADS)

    Filipek, Wiktor; Broda, Krzysztof; Branny, Marian

    2015-03-01

    wykorzystaniem napisanego w języku Delphi autorskiego programu do obróbki numerycznej zdjęć. Występujące trudności ilustruje rysunek 2 przedstawiający przesunięcie linii odniesienia w trzech kolejno po sobie wykonanych zdjęciach. Następnie omówiono sposób przygotowania stanowiska do pomiarów oraz sposób ich przeprowadzania czego ilustracją są rysunki 3 i 4. Przedstawiono występujące problemy oraz zastosowane sposoby ich rozwiązania. Zarejestrowany przykładowy obraz po przejściu promienia lasera przez badaną strukturę dla wybranych wartości różnicy ciśnień hydrostatycznych uzyskany za pomocą kulek ceramicznych przedstawiono na rysunku 5. Rysunek 6 wyjaśnia metodę obróbki numerycznej zdjęć w oparciu o autorski program i zależności (1),(2),(3). Na rysunkach 7 i 9 zestawiono otrzymane krzywe zmienności intensywności barw uzyskane w trakcie opracowania numerycznego. Zwrócono także uwagę na rozkład zmian intensywności barw dla różnicy między powierzchniami swobodnymi cieczy w cylindrach (Rys. 8-11) dla wybranych serii pomiarowych. W dalszej części artykułu dokonano analizy otrzymanych obrazów zwracając uwagę na włączenie metody transformacji Fouriera lub "Falkowej" (Ziółko, 2000) do numerycznej analizy posiadanych danych (Rys. 12-14). Na rysunku 12 pokazano wybrane trzy zależności opisujące zmienność natężania barwy w funkcji położenia ramki (1), dla których dokonano transformacji Fouriera według zależności (3). Analizy dokonano metodą arytmetyczna Perry'ego (Ziółko, 2000) w okienku o szerokości n = 2300 przyjmując jako położenie startowe wartość x = 1600. Rysunek 13 przedstawia wartości współczynnika Ak a rys.14 przedstawia wartości kąta przesunięcia jk dla pierwszych 58 harmonicznych. Prace nad udoskonaleniem metody trwają. W dalszej części artykułu autorzy podsumowują osiągnięte wyniki zwracając uwagę na uzyskaną precyzję pomiarów oraz korzystne zastosowanie powierzchni swobodnej

  15. IPNV with high and low virulence: host immune responses and viral mutations during infection

    PubMed Central

    2011-01-01

    Background Infectious pancreatic necrosis virus (IPNV) is an aquatic member of the Birnaviridae family that causes widespread disease in salmonids. IPNV is represented by multiple strains with markedly different virulence. Comparison of isolates reveals hyper variable regions (HVR), which are presumably associated with pathogenicity. However little is known about the rates and modes of sequence divergence and molecular mechanisms that determine virulence. Also how the host response may influence IPNV virulence is poorly described. Methods In this study we compared two field isolates of IPNV (NFH-Ar and NFH-El). The sequence changes, replication and mortality were assessed following experimental challenge of Atlantic salmon. Gene expression analyses with qPCR and microarray were applied to examine the immune responses in head kidney. Results Significant differences in mortality were observed between the two isolates, and viral load in the pancreas at 13 days post infection (d p.i.) was more than 4 orders of magnitude greater for NFH-Ar in comparison with NFH-El. Sequence comparison of five viral genes from the IPNV isolates revealed different mutation rates and Ka/Ks ratios. A strong tendency towards non-synonymous mutations was found in the HRV of VP2 and in VP3. All mutations in VP5 produced precocious stop codons. Prior to the challenge, NFH-Ar and NFH-El possessed high and low virulence motifs in VP2, respectively. Nucleotide substitutions were noticed already during passage of viruses in CHSE-214 cells and their accumulation continued in the challenged fish. The sequence changes were notably directed towards low virulence. Co-ordinated activation of anti-viral genes with diverse functions (IFN-a1 and c, sensors - Rig-I, MDA-5, TLR8 and 9, signal transducers - Srk2, MyD88, effectors - Mx, galectin 9, galectin binding protein, antigen presentation - b2-microglobulin) was observed at 13 d p.i. (NFH-Ar) and 29 d p.i. (both isolates). Conclusions Mortality and

  16. Phosphoglucose isomerases of hagfish, zebrafish, gray mullet, toad, and snake, with reference to the evolution of the genes in vertebrates.

    PubMed

    Kao, Hsiao-wei; Lee, Sin-Che

    2002-04-01

    Phosphoglucose isomerase (PGI) is a protein with multiple functions. To infer its structure changes and evolution in vertebrates, we cloned cDNAs encoding PGI genes from hagfish (Paramyxine yangi), gray mullet (Mugil cephalus), zebrafish (Danio rerio), toad (Bufo melanosticus), and snake (Boiga kraepelini). Only one PGI gene was cloned in each of hagfish, toad, and snake, but two PGI genes were found in zebrafish and gray mullet, respectively. The PGI of hagfish encodes 554 amino acids, in contrast to the PGIs of bonyfishes, toad, and snake which encode 553 amino acids and the PGIs of mammals which encode 558 amino acids. Among 558 aligned amino acid sites, there are 314 sites (56.27%) totally conserved. To see if diversifying selection acts on PGI amino acids of vertebrates, we calculated the pairwise ratio of nonsynonymous versus synonymous substitution per site (Ka/Ks) and the ratio of radical amino acid changes versus conservative amino acid changes per sites (dR/dC) between PGI sequences. The average pairwise ratio between nonsynonymous substitutions per nucleotide (Ka) and synonymous substitutions per nucleotide (Ks) among vertebrate PGI sequences equals 0.047 +/- 0.019. The average pairwise ratio between radical amino acid changes and conservative amino acid changes (dR/dC) among the vertebrate PGIs equal 0.938 +/- 0.158 for charge changes, 0.558 +/- 0.085 for polarity changes, and 0.465 +/- 0.0714 when both polarity and volume are considered. There is no amino acid within the vertebrate PGIs under diversifying selection as analyzed by the method of Yang et al. (2000b). The results suggest that the present vertebrate PGIs are at evolutionary stasis and are being subjected to intense purifying selection. The purifying selection is to maintain polarity and volume of the protein but not the charge groups of amino acids. Phylogenetic analysis reveals that vertebrate PGIs can be classified into three major groups: the mammalian, amphibian-reptilian, and

  17. The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); comparative evolutionary analyses with other three asterids.

    PubMed

    Yi, Dong-Keun; Lee, Hae-Lim; Sun, Byung-Yun; Chung, Mi Yoon; Kim, Ki-Joong

    2012-05-01

    This study reports the complete chloroplast (cp) DNA sequence of Eleutherococcus senticosus (GenBank: JN 637765), an endangered endemic species. The genome is 156,768 bp in length, and contains a pair of inverted repeat (IR) regions of 25,930 bp each, a large single copy (LSC) region of 86,755 bp and a small single copy (SSC) region of 18,153 bp. The structural organization, gene and intron contents, gene order, AT content, codon usage, and transcription units of the E. senticosus chloroplast genome are similar to that of typical land plant cp DNA. We aligned and analyzed the sequences of 86 coding genes, 19 introns and 113 intergenic spacers (IGS) in three different taxonomic hierarchies; Eleutherococcus vs. Panax, Eleutherococcus vs. Daucus, and Eleutherococcus vs. Nicotiana. The distribution of indels, the number of polymorphic sites and nucleotide diversity indicate that positional constraint is more important than functional constraint for the evolution of cp genome sequences in Asterids. For example, the intron sequences in the LSC region exhibited base substitution rates 5-11-times higher than that of the IR regions, while the intron sequences in the SSC region evolved 7-14-times faster than those in the IR region. Furthermore, the Ka/Ks ratio of the gene coding sequences supports a stronger evolutionary constraint in the IR region than in the LSC or SSC regions. Therefore, our data suggest that selective sweeps by base collection mechanisms more frequently eliminate polymorphisms in the IR region than in other regions. Chloroplast genome regions that have high levels of base substitutions also show higher incidences of indels. Thirty-five simple sequence repeat (SSR) loci were identified in the Eleutherococcus chloroplast genome. Of these, 27 are homopolymers, while six are di-polymers and two are tri-polymers. In addition to the SSR loci, we also identified 18 medium size repeat units ranging from 22 to 79 bp, 11 of which are distributed in the IGS or

  18. The Complete Chloroplast DNA Sequence of Eleutherococcus senticosus (Araliaceae); Comparative Evolutionary Analyses with Other Three Asterids

    PubMed Central

    Yi, Dong-Keun; Lee, Hae-Lim; Sun, Byung-Yun; Chung, Mi Yoon; Kim, Ki-Joong

    2012-01-01

    This study reports the complete chloroplast (cp) DNA sequence of Eleutherococcus senticosus (GenBank: JN 637765), an endangered endemic species. The genome is 156,768 bp in length, and contains a pair of inverted repeat (IR) regions of 25,930 bp each, a large single copy (LSC) region of 86,755 bp and a small single copy (SSC) region of 18,153 bp. The structural organization, gene and intron contents, gene order, AT content, codon usage, and transcription units of the E. senticosus chloroplast genome are similar to that of typical land plant cp DNA. We aligned and analyzed the sequences of 86 coding genes, 19 introns and 113 intergenic spacers (IGS) in three different taxonomic hierarchies; Eleutherococcus vs. Panax, Eleutherococcus vs. Daucus, and Eleutherococcus vs. Nicotiana. The distribution of indels, the number of polymorphic sites and nucleotide diversity indicate that positional constraint is more important than functional constraint for the evolution of cp genome sequences in Asterids. For example, the intron sequences in the LSC region exhibited base substitution rates 5-11-times higher than that of the IR regions, while the intron sequences in the SSC region evolved 7-14-times faster than those in the IR region. Furthermore, the Ka/Ks ratio of the gene coding sequences supports a stronger evolutionary constraint in the IR region than in the LSC or SSC regions. Therefore, our data suggest that selective sweeps by base collection mechanisms more frequently eliminate polymorphisms in the IR region than in other regions. Chloroplast genome regions that have high levels of base substitutions also show higher incidences of indels. Thirty-five simple sequence repeat (SSR) loci were identified in the Eleutherococcus chloroplast genome. Of these, 27 are homopolymers, while six are di-polymers and two are tri-polymers. In addition to the SSR loci, we also identified 18 medium size repeat units ranging from 22 to 79 bp, 11 of which are distributed in the IGS or

  19. Molecular Genetic Analysis and Evolution of Segment 7 in Rice Black-Streaked Dwarf Virus in China.

    PubMed

    Zhou, Yu; Weng, Jianfeng; Chen, Yanping; Wu, Jirong; Meng, Qingchang; Han, Xiaohua; Hao, Zhuanfang; Li, Mingshun; Yong, Hongjun; Zhang, Degui; Zhang, Shihuang; Li, Xinhai

    2015-01-01

    Rice black-streaked dwarf virus (RBSDV) causes maize rough dwarf disease or rice black-streaked dwarf disease and can lead to severe yield losses in maize and rice. To analyse RBSDV evolution, codon usage bias and genetic structure were investigated in 111 maize and rice RBSDV isolates from eight geographic locations in 2013 and 2014. The linear dsRNA S7 is A+U rich, with overall codon usage biased toward codons ending with A (A3s, S7-1: 32.64%, S7-2: 29.95%) or U (U3s, S7-1: 44.18%, S7-2: 46.06%). Effective number of codons (Nc) values of 45.63 in S7-1 (the first open reading frame of S7) and 39.96 in S7-2 (the second open reading frame of S7) indicate low degrees of RBSDV-S7 codon usage bias, likely driven by mutational bias regardless of year, host, or geographical origin. Twelve optimal codons were detected in S7. The nucleotide diversity (π) of S7 sequences in 2013 isolates (0.0307) was significantly higher than in 2014 isolates (0.0244, P = 0.0226). The nucleotide diversity (π) of S7 sequences in isolates from Jinan (0.0391) was higher than that from the other seven locations (P < 0.01). Only one S7 recombinant was detected in Baoding. RBSDV isolates could be phylogenetically classified into two groups according to S7 sequences, and further classified into two subgroups. S7-1 and S7-2 were under negative and purifying selection, with respective Ka/Ks ratios of 0.0179 and 0.0537. These RBSDV populations were expanding (P < 0.01) as indicated by negative values for Tajima's D, Fu and Li's D, and Fu and Li's F. Genetic differentiation was detected in six RBSDV subpopulations (P < 0.05). Absolute Fst (0.0790) and Nm (65.12) between 2013 and 2014, absolute Fst (0.1720) and Nm (38.49) between maize and rice, and absolute Fst values of 0.0085-0.3069 and Nm values of 0.56-29.61 among these eight geographic locations revealed frequent gene flow between subpopulations. Gene flow between 2013 and 2014 was the most frequent. PMID:26121638

  20. Molecular Genetic Analysis and Evolution of Segment 7 in Rice Black-Streaked Dwarf Virus in China.

    PubMed

    Zhou, Yu; Weng, Jianfeng; Chen, Yanping; Wu, Jirong; Meng, Qingchang; Han, Xiaohua; Hao, Zhuanfang; Li, Mingshun; Yong, Hongjun; Zhang, Degui; Zhang, Shihuang; Li, Xinhai

    2015-01-01

    Rice black-streaked dwarf virus (RBSDV) causes maize rough dwarf disease or rice black-streaked dwarf disease and can lead to severe yield losses in maize and rice. To analyse RBSDV evolution, codon usage bias and genetic structure were investigated in 111 maize and rice RBSDV isolates from eight geographic locations in 2013 and 2014. The linear dsRNA S7 is A+U rich, with overall codon usage biased toward codons ending with A (A3s, S7-1: 32.64%, S7-2: 29.95%) or U (U3s, S7-1: 44.18%, S7-2: 46.06%). Effective number of codons (Nc) values of 45.63 in S7-1 (the first open reading frame of S7) and 39.96 in S7-2 (the second open reading frame of S7) indicate low degrees of RBSDV-S7 codon usage bias, likely driven by mutational bias regardless of year, host, or geographical origin. Twelve optimal codons were detected in S7. The nucleotide diversity (π) of S7 sequences in 2013 isolates (0.0307) was significantly higher than in 2014 isolates (0.0244, P = 0.0226). The nucleotide diversity (π) of S7 sequences in isolates from Jinan (0.0391) was higher than that from the other seven locations (P < 0.01). Only one S7 recombinant was detected in Baoding. RBSDV isolates could be phylogenetically classified into two groups according to S7 sequences, and further classified into two subgroups. S7-1 and S7-2 were under negative and purifying selection, with respective Ka/Ks ratios of 0.0179 and 0.0537. These RBSDV populations were expanding (P < 0.01) as indicated by negative values for Tajima's D, Fu and Li's D, and Fu and Li's F. Genetic differentiation was detected in six RBSDV subpopulations (P < 0.05). Absolute Fst (0.0790) and Nm (65.12) between 2013 and 2014, absolute Fst (0.1720) and Nm (38.49) between maize and rice, and absolute Fst values of 0.0085-0.3069 and Nm values of 0.56-29.61 among these eight geographic locations revealed frequent gene flow between subpopulations. Gene flow between 2013 and 2014 was the most frequent.

  1. Genome-Wide Analysis of the Fasciclin-Like Arabinogalactan Protein Gene Family Reveals Differential Expression Patterns, Localization, and Salt Stress Response in Populus

    PubMed Central

    Zang, Lina; Zheng, Tangchun; Chu, Yanguang; Ding, Changjun; Zhang, Weixi; Huang, Qinjun; Su, Xiaohua

    2015-01-01

    Fasciclin-like arabinogalactan proteins (FLAs) are a subclass of arabinogalactan proteins (AGPs) involved in plant growth, development and response to abiotic stress. Although many studies have been performed to identify molecular functions of individual family members, little information is available on genome-wide identification and characterization of FLAs in the genus Populus. Based on genome-wide analysis, we have identified 35 Populus FLAs which were distributed on 16 chromosomes and phylogenetically clustered into four major groups. Gene structure and motif composition were relatively conserved in each group. All the members contained N-terminal signal peptide, 23 of which included predicted glycosylphosphatidylinositol (GPI) modification sites and were anchored to plasma membranes. Subcellular localization analysis showed that PtrFLA2/20/26 were localized in cell membrane and cytoplasm of protoplasts from Populus stem-differentiating xylem. The Ka/Ks ratios showed that purifying selection has played a leading role in the long-term evolutionary period which greatly maintained the function of this family. The expression profiles showed that 32 PtrFLAs were differentially expressed in four tissues at four seasons based on publicly available microarray data. 18 FLAs were further verified with qRT-PCR in different tissues, which indicated that PtrFLA1/2/3/7/11/12/20/21/22/24/26/30 were significantly expressed in male and female flowers, suggesting close correlations with the reproductive development. In addition, PtrFLA1/9/10/11/17/21/23/24/26/28 were highly expressed in the stems and differentiating xylem, which may be involved in stem development. To determine salt response of FLAs, qRT-PCR was performed to analyze the expression of 18 genes under salinity stress across two time points. Results demonstrated that all the 18 FLAs were expressed in root tissues; especially, PtrFLA2/12/20/21/24/30 were significantly induced at different time points. In summary

  2. Discovery of a Novel Bottlenose Dolphin Coronavirus Reveals a Distinct Species of Marine Mammal Coronavirus in Gammacoronavirus

    PubMed Central

    Woo, Patrick C. Y.; Lau, Susanna K. P.; Lam, Carol S. F.; Tsang, Alan K. L.; Hui, Suk-Wai; Fan, Rachel Y. Y.; Martelli, Paolo

    2014-01-01

    While gammacoronaviruses mainly comprise infectious bronchitis virus (IBV) and its closely related bird coronaviruses (CoVs), the only mammalian gammacoronavirus was discovered from a white beluga whale (beluga whale CoV [BWCoV] SW1) in 2008. In this study, we discovered a novel gammacoronavirus from fecal samples from three Indo-Pacific bottlenose dolphins (Tursiops aduncus), which we named bottlenose dolphin CoV (BdCoV) HKU22. All the three BdCoV HKU22-positive samples were collected on the same date, suggesting a cluster of infection, with viral loads of 1 × 103 to 1 × 105 copies per ml. Clearance of virus was associated with a specific antibody response against the nucleocapsid of BdCoV HKU22. Complete genome sequencing and comparative genome analysis showed that BdCoV HKU22 and BWCoV SW1 have similar genome characteristics and structures. Their genome size is about 32,000 nucleotides, the largest among all CoVs, as a result of multiple unique open reading frames (NS5a, NS5b, NS5c, NS6, NS7, NS8, NS9, and NS10) between their membrane (M) and nucleocapsid (N) protein genes. Although comparative genome analysis showed that BdCoV HKU22 and BWCoV SW1 should belong to the same species, a major difference was observed in the proteins encoded by their spike (S) genes, which showed only 74.3 to 74.7% amino acid identities. The high ratios of the number of synonymous substitutions per synonymous site (Ks) to the number of nonsynonymous substitutions per nonsynonymous site (Ka) in multiple regions of the genome, especially the S gene (Ka/Ks ratio, 2.5), indicated that BdCoV HKU22 may be evolving rapidly, supporting a recent transmission event to the bottlenose dolphins. We propose a distinct species, Cetacean coronavirus, in Gammacoronavirus, to include BdCoV HKU22 and BWCoV SW1, whereas IBV and its closely related bird CoVs represent another species, Avian coronavirus, in Gammacoronavirus. PMID:24227844

  3. Vertebrate Paralogous MEF2 Genes: Origin, Conservation, and Evolution

    PubMed Central

    Wu, Wenwu; de Folter, Stefan; Shen, Xia; Zhang, Wenqian; Tao, Shiheng

    2011-01-01

    Background The myocyte enhancer factor 2 (MEF2) gene family is broadly expressed during the development and maintenance of muscle cells. Although a great deal has been elucidated concerning MEF2 transcription factors' regulation of specific gene expression in diverse programs and adaptive responses, little is known about the origin and evolution of the four members of the MEF2 gene family in vertebrates. Methodology/Principal Findings By phylogenetic analyses, we investigated the origin, conservation, and evolution of the four MEF2 genes. First, among the four MEF2 paralogous branches, MEF2B is clearly distant from the other three branches in vertebrates, mainly because it lacks the HJURP_C (Holliday junction recognition protein C-terminal) region. Second, three duplication events might have occurred to produce the four MEF2 paralogous genes and the latest duplication event occurred near the origin of vertebrates producing MEF2A and MEF2C. Third, the ratio (Ka/Ks) of non-synonymous to synonymous nucleotide substitution rates showed that MEF2B evolves faster than the other three MEF2 proteins despite purifying selection on all of the four MEF2 branches. Moreover, a pair model of M0 versus M3 showed that variable selection exists among MEF2 proteins, and branch-site analysis presented that sites 53 and 64 along the MEF2B branch are under positive selection. Finally, and interestingly, substitution rates showed that type II MADS genes (i.e., MEF2-like genes) evolve as slowly as type I MADS genes (i.e., SRF-like genes) in animals, which is inconsistent with the fact that type II MADS genes evolve much slower than type I MADS genes in plants. Conclusion Our findings shed light on the relationship of MEF2A, B, C, and D with functional conservation and evolution in vertebrates. This study provides a rationale for future experimental design to investigate distinct but overlapping regulatory roles of the four MEF2 genes in various tissues. PMID:21394201

  4. Selection maintaining protein stability at equilibrium.

    PubMed

    Miyazawa, Sanzo

    2016-02-21

    The common understanding of protein evolution has been that neutral mutations are fixed by random drift, and a proportion of neutral mutations depending on the strength of structural and functional constraints primarily determines evolutionary rate. Recently it was indicated that fitness costs due to misfolded proteins are a determinant of evolutionary rate and selection originating in protein stability is a driving force of protein evolution. Here we examine protein evolution under the selection maintaining protein stability. Protein fitness is a generic form of fitness costs due to misfolded proteins; s=κexp(ΔG/kT)(1-exp(ΔΔG/kT)), where s and ΔΔG are selective advantage and stability change of a mutant protein, ΔG is the folding free energy of the wildtype protein, and κ is a parameter representing protein abundance and indispensability. The distribution of ΔΔG is approximated to be a bi-Gaussian distribution, which represents structurally slightly- or highly-constrained sites. Also, the mean of the distribution is negatively proportional to ΔG. The evolution of this gene has an equilibrium point (ΔGe) of protein stability, the range of which is consistent with observed values in the ProTherm database. The probability distribution of Ka/Ks, the ratio of nonsynonymous to synonymous substitution rate per site, over fixed mutants in the vicinity of the equilibrium shows that nearly neutral selection is predominant only in low-abundant, non-essential proteins of ΔGe>-2.5 kcal/mol. In the other proteins, positive selection on stabilizing mutations is significant to maintain protein stability at equilibrium as well as random drift on slightly negative mutations, although the average 〈Ka/Ks〉 is less than 1. Slow evolutionary rates can be caused by both high protein abundance/indispensability and large effective population size, which produces positive shifts of ΔΔG through decreasing ΔGe, and strong structural constraints, which directly make

  5. Insights into the Indian Peanut Genotypes for ahFAD2 Gene Polymorphism Regulating Its Oleic and Linoleic Acid Fluxes

    PubMed Central

    Nawade, Bhagwat; Bosamia, Tejas C.; Thankappan, Radhakrishnan; Rathnakumar, Arulthambi L.; Kumar, Abhay; Dobaria, Jentilal R.; Kundu, Rahul; Mishra, Gyan P.

    2016-01-01

    In peanut (Arachis hypogaea L.), the customization of fatty acid profile is an evolving area to fulfill the nutritional needs in the modern market. A total of 174 peanut genotypes, including 167 Indian cultivars, 6 advanced breeding lines and “SunOleic95R”—a double mutant line, were investigated using AS-PCRs, CAPS and gene sequencing for the ahFAD2 allele polymorphism, along with its fatty acid compositions. Of these, 80 genotypes were found having substitution (448G>A) mutation only in ahFAD2A gene, while none recorded 1-bp insertion (441_442insA) mutation in ahFAD2B gene. Moreover, 22 wild peanut accessions found lacking both the mutations. Among botanical types, the ahFAD2A mutation was more frequent in ssp. hypogaea (89%) than in ssp. fastigiata (17%). This single allele mutation, found affecting not only oleic to linoleic acid fluxes, but also the composition of other fatty acids in the genotypes studied. Repeated use of a few selected genotypes in the Indian varietal development programs were also eminently reflected in its ahFAD2 allele polymorphism. Absence of known mutations in the wild-relatives indicated the possible origin of these mutations, after the allotetraploidization of cultivated peanut. The SNP analysis of both ahFAD2A and ahFAD2B genes, revealed haplotype diversity of 1.05% and 0.95%, while Ka/Ks ratio of 0.36 and 0.39, respectively, indicating strong purifying selection pressure on these genes. Cluster analysis, using ahFAD2 gene SNPs, showed presence of both mutant and non-mutant genotypes in the same cluster, which might be due the presence of ahFAD2 gene families. This investigation provided insights into the large number of Indian peanut genotypes, covering various aspects related to O/L flux regulation and ahFAD2 gene polymorphism. PMID:27610115

  6. An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora

    PubMed Central

    2011-01-01

    Background Coffee is one of the world's most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries. Coffea arabica and C. canephora are responsible for 70 and 30% of commercial production, respectively. C. arabica is an allotetraploid from a recent hybridization of the diploid species, C. canephora and C. eugenioides. C. arabica has lower genetic diversity and results in a higher quality beverage than C. canephora. Research initiatives have been launched to produce genomic and transcriptomic data about Coffea spp. as a strategy to improve breeding efficiency. Results Assembling the expressed sequence tags (ESTs) of C. arabica and C. canephora produced by the Brazilian Coffee Genome Project and the Nestlé-Cornell Consortium revealed 32,007 clusters of C. arabica and 16,665 clusters of C. canephora. We detected different GC3 profiles between these species that are related to their genome structure and mating system. BLAST analysis revealed similarities between coffee and grape (Vitis vinifera) genes. Using KA/KS analysis, we identified coffee genes under purifying and positive selection. Protein domain and gene ontology analyses suggested differences between Coffea spp. data, mainly in relation to complex sugar synthases and nucleotide binding proteins. OrthoMCL was used to identify specific and prevalent coffee protein families when compared to five other plant species. Among the interesting families annotated are new cystatins, glycine-rich proteins and RALF-like peptides. Hierarchical clustering was used to independently group C. arabica and C. canephora expression clusters according to expression data extracted from EST libraries, resulting in the identification of differentially expressed genes. Based on these results, we emphasize gene annotation and discuss plant defenses, abiotic stress and cup quality-related functional categories. Conclusion We present the first comprehensive genome-wide transcript

  7. Identification of novel conserved peptide uORF homology groups in Arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes

    PubMed Central

    Hayden, Celine A; Jorgensen, Richard A

    2007-01-01

    Background Upstream open reading frames (uORFs) can mediate translational control over the largest, or major ORF (mORF) in response to starvation, polyamine concentrations, and sucrose concentrations. One plant uORF with conserved peptide sequences has been shown to exert this control in an amino acid sequence-dependent manner but generally it is not clear what kinds of genes are regulated, or how extensively this mechanism is invoked in a given genome. Results By comparing full-length cDNA sequences from Arabidopsis and rice we identified 26 distinct homology groups of conserved peptide uORFs, only three of which have been reported previously. Pairwise Ka/Ks analysis showed that purifying selection had acted on nearly all conserved peptide uORFs and their associated mORFs. Functions of predicted mORF proteins could be inferred for 16 homology groups and many of these proteins appear to have a regulatory function, including 6 transcription factors, 5 signal transduction factors, 3 developmental signal molecules, a homolog of translation initiation factor eIF5, and a RING finger protein. Transcription factors are clearly overrepresented in this data set when compared to the frequency calculated for the entire genome (p = 1.2 × 10-7). Duplicate gene pairs arising from a whole genome duplication (ohnologs) with a conserved uORF are much more likely to have been retained in Arabidopsis (Arabidopsis thaliana) than are ohnologs of other genes (39% vs 14% of ancestral genes, p = 5 × 10-3). Two uORF groups were found in animals, indicating an ancient origin of these putative regulatory elements. Conclusion Conservation of uORF amino acid sequence, association with homologous mORFs over long evolutionary time periods, preferential retention after whole genome duplications, and preferential association with mORFs coding for transcription factors suggest that the conserved peptide uORFs identified in this study are strong candidates for translational controllers of

  8. Discovery of a novel bottlenose dolphin coronavirus reveals a distinct species of marine mammal coronavirus in Gammacoronavirus.

    PubMed

    Woo, Patrick C Y; Lau, Susanna K P; Lam, Carol S F; Tsang, Alan K L; Hui, Suk-Wai; Fan, Rachel Y Y; Martelli, Paolo; Yuen, Kwok-Yung

    2014-01-01

    While gammacoronaviruses mainly comprise infectious bronchitis virus (IBV) and its closely related bird coronaviruses (CoVs), the only mammalian gammacoronavirus was discovered from a white beluga whale (beluga whale CoV [BWCoV] SW1) in 2008. In this study, we discovered a novel gammacoronavirus from fecal samples from three Indo-Pacific bottlenose dolphins (Tursiops aduncus), which we named bottlenose dolphin CoV (BdCoV) HKU22. All the three BdCoV HKU22-positive samples were collected on the same date, suggesting a cluster of infection, with viral loads of 1 × 10(3) to 1 × 10(5) copies per ml. Clearance of virus was associated with a specific antibody response against the nucleocapsid of BdCoV HKU22. Complete genome sequencing and comparative genome analysis showed that BdCoV HKU22 and BWCoV SW1 have similar genome characteristics and structures. Their genome size is about 32,000 nucleotides, the largest among all CoVs, as a result of multiple unique open reading frames (NS5a, NS5b, NS5c, NS6, NS7, NS8, NS9, and NS10) between their membrane (M) and nucleocapsid (N) protein genes. Although comparative genome analysis showed that BdCoV HKU22 and BWCoV SW1 should belong to the same species, a major difference was observed in the proteins encoded by their spike (S) genes, which showed only 74.3 to 74.7% amino acid identities. The high ratios of the number of synonymous substitutions per synonymous site (Ks) to the number of nonsynonymous substitutions per nonsynonymous site (Ka) in multiple regions of the genome, especially the S gene (Ka/Ks ratio, 2.5), indicated that BdCoV HKU22 may be evolving rapidly, supporting a recent transmission event to the bottlenose dolphins. We propose a distinct species, Cetacean coronavirus, in Gammacoronavirus, to include BdCoV HKU22 and BWCoV SW1, whereas IBV and its closely related bird CoVs represent another species, Avian coronavirus, in Gammacoronavirus. PMID:24227844

  9. Insights into the Indian Peanut Genotypes for ahFAD2 Gene Polymorphism Regulating Its Oleic and Linoleic Acid Fluxes.

    PubMed

    Nawade, Bhagwat; Bosamia, Tejas C; Thankappan, Radhakrishnan; Rathnakumar, Arulthambi L; Kumar, Abhay; Dobaria, Jentilal R; Kundu, Rahul; Mishra, Gyan P

    2016-01-01

    In peanut (Arachis hypogaea L.), the customization of fatty acid profile is an evolving area to fulfill the nutritional needs in the modern market. A total of 174 peanut genotypes, including 167 Indian cultivars, 6 advanced breeding lines and "SunOleic95R"-a double mutant line, were investigated using AS-PCRs, CAPS and gene sequencing for the ahFAD2 allele polymorphism, along with its fatty acid compositions. Of these, 80 genotypes were found having substitution (448G>A) mutation only in ahFAD2A gene, while none recorded 1-bp insertion (441_442insA) mutation in ahFAD2B gene. Moreover, 22 wild peanut accessions found lacking both the mutations. Among botanical types, the ahFAD2A mutation was more frequent in ssp. hypogaea (89%) than in ssp. fastigiata (17%). This single allele mutation, found affecting not only oleic to linoleic acid fluxes, but also the composition of other fatty acids in the genotypes studied. Repeated use of a few selected genotypes in the Indian varietal development programs were also eminently reflected in its ahFAD2 allele polymorphism. Absence of known mutations in the wild-relatives indicated the possible origin of these mutations, after the allotetraploidization of cultivated peanut. The SNP analysis of both ahFAD2A and ahFAD2B genes, revealed haplotype diversity of 1.05% and 0.95%, while Ka/Ks ratio of 0.36 and 0.39, respectively, indicating strong purifying selection pressure on these genes. Cluster analysis, using ahFAD2 gene SNPs, showed presence of both mutant and non-mutant genotypes in the same cluster, which might be due the presence of ahFAD2 gene families. This investigation provided insights into the large number of Indian peanut genotypes, covering various aspects related to O/L flux regulation and ahFAD2 gene polymorphism. PMID:27610115

  10. Insights into the Indian Peanut Genotypes for ahFAD2 Gene Polymorphism Regulating Its Oleic and Linoleic Acid Fluxes

    PubMed Central

    Nawade, Bhagwat; Bosamia, Tejas C.; Thankappan, Radhakrishnan; Rathnakumar, Arulthambi L.; Kumar, Abhay; Dobaria, Jentilal R.; Kundu, Rahul; Mishra, Gyan P.

    2016-01-01

    In peanut (Arachis hypogaea L.), the customization of fatty acid profile is an evolving area to fulfill the nutritional needs in the modern market. A total of 174 peanut genotypes, including 167 Indian cultivars, 6 advanced breeding lines and “SunOleic95R”—a double mutant line, were investigated using AS-PCRs, CAPS and gene sequencing for the ahFAD2 allele polymorphism, along with its fatty acid compositions. Of these, 80 genotypes were found having substitution (448G>A) mutation only in ahFAD2A gene, while none recorded 1-bp insertion (441_442insA) mutation in ahFAD2B gene. Moreover, 22 wild peanut accessions found lacking both the mutations. Among botanical types, the ahFAD2A mutation was more frequent in ssp. hypogaea (89%) than in ssp. fastigiata (17%). This single allele mutation, found affecting not only oleic to linoleic acid fluxes, but also the composition of other fatty acids in the genotypes studied. Repeated use of a few selected genotypes in the Indian varietal development programs were also eminently reflected in its ahFAD2 allele polymorphism. Absence of known mutations in the wild-relatives indicated the possible origin of these mutations, after the allotetraploidization of cultivated peanut. The SNP analysis of both ahFAD2A and ahFAD2B genes, revealed haplotype diversity of 1.05% and 0.95%, while Ka/Ks ratio of 0.36 and 0.39, respectively, indicating strong purifying selection pressure on these genes. Cluster analysis, using ahFAD2 gene SNPs, showed presence of both mutant and non-mutant genotypes in the same cluster, which might be due the presence of ahFAD2 gene families. This investigation provided insights into the large number of Indian peanut genotypes, covering various aspects related to O/L flux regulation and ahFAD2 gene polymorphism.

  11. Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through Recombination

    PubMed Central

    Lau, Susanna K. P.; Feng, Yun; Chen, Honglin; Luk, Hayes K. H.; Yang, Wei-Hong; Li, Kenneth S. M.; Zhang, Yu-Zhen; Huang, Yi; Song, Zhi-Zhong; Chow, Wang-Ngai; Fan, Rachel Y. Y.; Ahmed, Syed Shakeel; Yeung, Hazel C.; Lam, Carol S. F.; Cai, Jian-Piao; Wong, Samson S. Y.; Chan, Jasper F. W.; Yuen, Kwok-Yung

    2015-01-01

    ABSTRACT Despite the identification of horseshoe bats as the reservoir of severe acute respiratory syndrome (SARS)-related coronaviruses (SARSr-CoVs), the origin of SARS-CoV ORF8, which contains the 29-nucleotide signature deletion among human strains, remains obscure. Although two SARS-related Rhinolophus sinicus bat CoVs (SARSr-Rs-BatCoVs) previously detected in Chinese horseshoe bats (Rhinolophus sinicus) in Yunnan, RsSHC014 and Rs3367, possessed 95% genome identities to human and civet SARSr-CoVs, their ORF8 protein exhibited only 32.2 to 33% amino acid identities to that of human/civet SARSr-CoVs. To elucidate the origin of SARS-CoV ORF8, we sampled 348 bats of various species in Yunnan, among which diverse alphacoronaviruses and betacoronaviruses, including potentially novel CoVs, were identified, with some showing potential interspecies transmission. The genomes of two betacoronaviruses, SARSr-Rf-BatCoV YNLF_31C and YNLF_34C, from greater horseshoe bats (Rhinolophus ferrumequinum), possessed 93% nucleotide identities to human/civet SARSr-CoV genomes. Although these two betacoronaviruses displayed lower similarities than SARSr-Rs-BatCoV RsSHC014 and Rs3367 in S protein to civet SARSr-CoVs, their ORF8 proteins demonstrated exceptionally high (80.4 to 81.3%) amino acid identities to that of human/civet SARSr-CoVs, compared to SARSr-BatCoVs from other horseshoe bats (23.2 to 37.3%). Potential recombination events were identified around ORF8 between SARSr-Rf-BatCoVs and SARSr-Rs-BatCoVs, leading to the generation of civet SARSr-CoVs. The expression of ORF8 subgenomic mRNA suggested that the ORF8 protein may be functional in SARSr-Rf-BatCoVs. The high Ka/Ks ratio among human SARS-CoVs compared to that among SARSr-BatCoVs supported that ORF8 is under strong positive selection during animal-to-human transmission. Molecular clock analysis using ORF1ab showed that SARSr-Rf-BatCoV YNLF_31C and YNLF_34C diverged from civet/human SARSr-CoVs in approximately 1990. SARS

  12. The Application of Modern Techniques and Measurement Devices for Identification of Copper Ore Types and Their Properties / Wykorzystanie nowoczesnych technik i urządzeń pomiarowych do identyfikacji typów rud miedzi i ich właściwości

    NASA Astrophysics Data System (ADS)

    Krawczykowska, Aldona; Trybalski, Kazimierz; Krawczykowski, Damian

    2013-06-01

    minerałów miedzionośnych oraz rodzajem ich skupień i wpryśnięć. Niezwykle istotne jest właściwe rozpoznanie rudy pod względem petrograficzno-mineralogicznym. Znajomość właściwości przerabianej rudy pozwala na pełniejsze jej wykorzystanie poprzez właściwe prowadzenie i sterowanie procesami, dobór ich parametrów takich m.in. jak: czas mielenia, parametry klasyfikacji, rodzaj odczynników flotacyjnych, czas flotacji. W artykule przedstawiono wyniki przeprowadzonych analiz mikroskopowych, analizy obrazów zdjęć skaningowych oraz procedury wykorzystania otrzymanych informacji do identyfikacji typów rud (zastosowanie sieci neuronowych do rozpoznawania składów litologicznych). W badaniach wykorzystano rudę miedzi, pochodzącą z jednego z zakładów górniczych KGHM Polska Miedź S.A. Pobrane próbki rudy reprezentowały każdy z trzech typów litologicznych występujących w krajowych złożach: węglanową, łupkową oraz piaskowcową. Przeprowadzono ilościową analizę mineralogiczno-petrograficzną przy pomocy mikroskopu optycznego w świetle odbitym, a wyniki przedstawiono w tabelach 1 i 2. Wyniki te określają ilościowo stopień uwolnienia i zrosty dla jednego rodzaju minerału. Pokazano także przykładowe zdjęcia mikroskopowe zgładów poszczególnych typów litologicznych rud oraz próbek proszkowych tych typów (rys. 1 i 2). W kolejnym etapie badań wykorzystano skaningowy mikroskop elektronowy. Zdjęcia morfologii próbek uzyskane z mikroskopu elektronowego (obrazy SEM) były przedmiotem komputerowej analizy obrazu, umożliwiającej mikrostrukturalną klasyfikację ilościową typów rud. Analizowano wszystkie próbki poszczególnych typów litologicznych rudy miedzi: węglanowej, łupkowej i piaskowcowej oraz mieszanki tych typów w trzech klasach ziarnowych: 0÷45 μm, 45÷71 μm i 71÷100 μm. Celem przekształceń wykorzystanych w procedurze komputerowej analizy obrazu jest otrzymanie poprawnie posegmentowanego obrazu binarnego, kt