The Genome of Cardinium cBtQ1 Provides Insights into Genome Reduction, Symbiont Motility, and Its Settlement in Bemisia tabaci

PubMed Central

Santos-Garcia, Diego; Rollat-Farnier, Pierre-Antoine; Beitia, Francisco; Zchori-Fein, Einat; Vavre, Fabrice; Mouton, Laurence; Moya, Andrés; Latorre, Amparo; Silva, Francisco J.

2014-01-01

Many insects harbor inherited bacterial endosymbionts. Although some of them are not strictly essential and are considered facultative, they can be a key to host survival under specific environmental conditions, such as parasitoid attacks, climate changes, or insecticide pressures. The whitefly Bemisia tabaci is at the top of the list of organisms inflicting agricultural damage and outbreaks, and changes in its distribution may be associated to global warming. In this work, we have sequenced and analyzed the genome of Cardinium cBtQ1, a facultative bacterial endosymbiont of B. tabaci and propose that it belongs to a new taxonomic family, which also includes Candidatus Amoebophilus asiaticus and Cardinium cEper1, endosymbionts of amoeba and wasps, respectively. Reconstruction of their last common ancestors’ gene contents revealed an initial massive gene loss from the free-living ancestor. This was followed in Cardinium by smaller losses, associated with settlement in arthropods. Some of these losses, affecting cofactor and amino acid biosynthetic encoding genes, took place in Cardinium cBtQ1 after its divergence from the Cardinium cEper1 lineage and were related to its settlement in the whitefly and its endosymbionts. Furthermore, the Cardinium cBtQ1 genome displays a large proportion of transposable elements, which have recently inactivated genes and produced chromosomal rearrangements. The genome also contains a chromosomal duplication and a multicopy plasmid, which harbors several genes putatively associated with gliding motility, as well as two other genes encoding proteins with potential insecticidal activity. As gene amplification is very rare in endosymbionts, an important function of these genes cannot be ruled out. PMID:24723729

Olfactory response of predatory Macrolophus caliginosus Wagner (Heteroptera: Miridae) to the odours host plant infested by Bemisia tabaci

NASA Astrophysics Data System (ADS)

Saad, Khalid A.; Roff, M. N. Mohamad; Salam, Mansour; Hanifah Mohd, Y.; Idris, A. B.

2014-09-01

Plant infested with herbivores, release volatile that can be used by natural enemies to locate their herbivorous prey. Laboratory studies were carried out to determine the olfactory responses of predator Macrolophus caliginosus Wagner (Heteroptera: Miridae), to chili plant infected with eggs, nymphs of Bemisia tabaci, using Y-tube olfactometer. The results shown that predator, M. caliginosus has ability to discriminate between non-infested and infested plant by B. tabaci. Moreover, the predator preferred plants with nymphs over plants with eggs. This suggested that M. caliginous uses whitefly-induced volatile as reliable indicators to distinguish between infested chili plants by nymphs, eggs and non-infested plants. These results enhance our understanding of the olfactory cues that guide foraging by M. caliginosus to plant with and without Bemisia tabaci.

Impact of pymetrozine on Bemisia tabaci (MED whitefly) and Amblyseius swirskii, 2017

USDA-ARS?s Scientific Manuscript database

Bemisia tabaci is a polyphagous pest known to feed upon over 900 plant taxa, and is an effective vector of more than 100 plant damaging viruses. Among different biotypes of this cryptic species complex, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED) whitefly are the two most destructive me...

Efficacy of Eretmocerus eremicus and flupyradifurone on Bemisia tabaci (MED whitefly), 2017

USDA-ARS?s Scientific Manuscript database

Bemisia tabaci is a polyphagous pest known to feed on over 900 plant taxa, and is an effective vector of more than 100 plant damaging viruses. Among different biotypes of this cryptic species complex, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED) whitefly are the two most destructive memb...

Efficacy of Eretmocerus eremicus and cyantraniliprole on Bemisia tabaci (MED whitefly), 2017

USDA-ARS?s Scientific Manuscript database

Bemisia tabaci (Gennadius) feeds on more than 900 host plants and vectors over 111 plant virus species and is considered to be a major invasive species worldwide. Among different biotypes of this cryptic species complex, MEAM1 and MED whitefly are the two most destructive members posing threats to s...

Effect of dinotefuran on Bemisia tabaci (MED whitefly) and Amblyseius swirskii, 2016

USDA-ARS?s Scientific Manuscript database

Bemisia tabaci is a polyphagous pest known to feed upon over 900 plant taxa, and is an effective vector of more than 100 plant damaging viruses. Among different biotypes of this cryptic species complex, MEAM1 and MED whitefly are the two most destructive members posing threats of several crops of ec...

Pyrosequencing the Bemisia tabaci Transcriptome Reveals a Highly Diverse Bacterial Community and a Robust System for Insecticide Resistance

PubMed Central

Wu, Qing-jun; Wang, Shao-li; Yang, Xin; Yang, Ni-na; Li, Ru-mei; Jiao, Xiao-guo; Pan, Hui-peng; Liu, Bai-ming; Su, Qi; Xu, Bao-yun; Hu, Song-nian; Zhou, Xu-guo; Zhang, You-jun

2012-01-01

Background Bemisia tabaci (Gennadius) is a phloem-feeding insect poised to become one of the major insect pests in open field and greenhouse production systems throughout the world. The high level of resistance to insecticides is a main factor that hinders continued use of insecticides for suppression of B. tabaci. Despite its prevalence, little is known about B. tabaci at the genome level. To fill this gap, an invasive B. tabaci B biotype was subjected to pyrosequencing-based transcriptome analysis to identify genes and gene networks putatively involved in various physiological and toxicological processes. Methodology and Principal Findings Using Roche 454 pyrosequencing, 857,205 reads containing approximately 340 megabases were obtained from the B. tabaci transcriptome. De novo assembly generated 178,669 unigenes including 30,980 from insects, 17,881 from bacteria, and 129,808 from the nohit. A total of 50,835 (28.45%) unigenes showed similarity to the non-redundant database in GenBank with a cut-off E-value of 10–5. Among them, 40,611 unigenes were assigned to one or more GO terms and 6,917 unigenes were assigned to 288 known pathways. De novo metatranscriptome analysis revealed highly diverse bacterial symbionts in B. tabaci, and demonstrated the host-symbiont cooperation in amino acid production. In-depth transcriptome analysis indentified putative molecular markers, and genes potentially involved in insecticide resistance and nutrient digestion. The utility of this transcriptome was validated by a thiamethoxam resistance study, in which annotated cytochrome P450 genes were significantly overexpressed in the resistant B. tabaci in comparison to its susceptible counterparts. Conclusions This transcriptome/metatranscriptome analysis sheds light on the molecular understanding of symbiosis and insecticide resistance in an agriculturally important phloem-feeding insect pest, and lays the foundation for future functional genomics research of the B. tabaci complex

Novel molecular approach to define pest species status and tritrophic interactions from historical Bemisia specimens.

PubMed

Tay, W T; Elfekih, S; Polaszek, A; Court, L N; Evans, G A; Gordon, K H J; De Barro, P J

2017-03-27

Museum specimens represent valuable genomic resources for understanding host-endosymbiont/parasitoid evolutionary relationships, resolving species complexes and nomenclatural problems. However, museum collections suffer DNA degradation, making them challenging for molecular-based studies. Here, the mitogenomes of a single 1912 Sri Lankan Bemisia emiliae cotype puparium, and of a 1942 Japanese Bemisia puparium are characterised using a Next-Generation Sequencing approach. Whiteflies are small sap-sucking insects including B. tabaci pest species complex. Bemisia emiliae's draft mitogenome showed a high degree of homology with published B. tabaci mitogenomes, and exhibited 98-100% partial mitochondrial DNA Cytochrome Oxidase I (mtCOI) gene identity with the B. tabaci species known as Asia II-7. The partial mtCOI gene of the Japanese specimen shared 99% sequence identity with the Bemisia 'JpL' genetic group. Metagenomic analysis identified bacterial sequences in both Bemisia specimens, while hymenopteran sequences were also identified in the Japanese Bemisia puparium, including complete mtCOI and rRNA genes, and various partial mtDNA genes. At 88-90% mtCOI sequence identity to Aphelinidae wasps, we concluded that the 1942 Bemisia nymph was parasitized by an Eretmocerus parasitoid wasp. Our approach enables the characterisation of genomes and associated metagenomic communities of museum specimens using 1.5 ng gDNA, and to infer historical tritrophic relationships in Bemisia whiteflies.

Plastic cup traps equipped with light-emitting diodes for monitoring adult Bemisia tabaci (Homoptera: Aleyrodidae).

PubMed

Chu, Chang-Chi; Jackson, Charles G; Alexander, Patrick J; Karut, Kamil; Henneberry, Thomas J

2003-06-01

Equipping the standard plastic cup trap, also known as the CC trap, with lime-green light-emitting diodes (LED-plastic cup trap) increased its efficacy for catching Bemisia tabaci by 100%. Few Eretmocerus eremicus Rose and Zolnerowich and Encarsia formosa Gahan were caught in LED-plastic cup traps. The LED-plastic cup traps are less expensive than yellow sticky card traps for monitoring adult whiteflies in greenhouse crop production systems and are more compatible with whitefly parasitoids releases for Bemisia nymph control.

Insecticidal Activity of Chromobacterium subtsugae on the Sweet Potato Whitefly, Bemisia tabaci, Biotype B

USDA-ARS?s Scientific Manuscript database

Chromobacterium subtsugae crude extracts contain compounds that are toxic to nymphal and adult Bemisia tabaci. When fed on artificial diet containing 10% of the supernatant of an aqueous cell-free extract of C subtsugae, the number of 2nd and 4th instar nymphs and of emerged adults was significantl...

Aerial electrostatic-charged spray for deposition and efficacy against sweetpotato whitefly (Bemisia tabaci) on cotton

USDA-ARS?s Scientific Manuscript database

Efficacy of aerial electrostatic-charged sprays was evaluated for spray deposit characteristics and season-long control of sweet potato whitefly (SWF), Bemisia tabaci biotype B (a.k.a. B. argentifolii), in an irrigated 24-ha cotton field. Treatments included electrostatic-charged sprays at full and ...

Identification and characterization of functional aquaporin water channel protein from alimentary tract of whitefly, Bemisia tabaci

USDA-ARS?s Scientific Manuscript database

Some hemipteran xylem and phloem feeding insects have evolved specialized alimentary structures or filter chambers that rapidly transport water for excretion or osmoregulation. In the whitefly, Bemisia tabaci, mass movement of water through opposing alimentary tract tissues within the filter chamber...

Investigating contact toxicity of Geranium and Artemisia essential oils on Bemisia tabaci Gen.

PubMed

Yarahmadi, Fatemeh; Rajabpour, Ali; Zandi Sohani, Nooshin; Ramezani, Leila

2013-01-01

Sweet potato whitefly, Bemisia tabaci Gen. (B. tabaci), is one of the most important pests of various greenhouse crops in Iran. Nowadays, chemical insecticides are broadly used for control of the pests that causes risk to consumer's health. For the first time, contact toxicity of Pelargonium roseum Andrews and Artemisia sieberi Besser essential oils on B. tabaci and its possible application against the whitefly was evaluated in 2012. Essential oil with concentrations of 2500, 1250, 125, and 12 ppm were used. Infested leaves of greenhouse cucumber were treated by mentioned concentrations. After 24 hours, mortality of B. tabaci was recorded and compared after correcting by Abbot's formula. RESULTS showed that all concentrations of the essential oil could significantly reduce population of B. tabaci compared with the control treatment. Phytotoxicity of the treated leaves were recorded after 24, 48, and 72 hours and compared with the control. Concentrations of 2500, 1250, and 125 ppm caused severe phytotoxicity on greenhouse cucumber leaves and therefore are not suitable for greenhouse application. Phytotoxicity of 12 ppm was relatively low. This data implicated suitable protective effects of the essential oils to the pest infestation. Therefore, essential oils distillated from Geranium and Artemisia could be applied to control B. tabaci in greenhouse cucumber at V/V 12 ppm.

Identification of glutathione S-transferases in Bemisia tabaci (Hemiptera: Aleyrodidae) and evidence that GSTd7 helps explain the difference in insecticide susceptibility between B. tabaci Middle East-Minor Asia 1 and Mediterranean.

PubMed

He, C; Xie, W; Yang, X; Wang, S-L; Wu, Q-J; Zhang, Y-J

2018-02-01

The Bemisia tabaci (Gennadius) (Hemiptera:Aleyrodidae) species complex includes invasive and destructive pests of field crops, and the sibling species MEAM1 and MED are its two most damaging members. Previous research indicated that the replacement of Middle East-Minor Asia 1 (MEAM1) by Mediterranean (MED) as the dominant B. tabaci species in China can be mainly attributed to MED's greater tolerance to insecticides. Glutathione S-transferases (GSTs) play important roles in the detoxification of hydrophobic toxic compounds. To increase our understanding of differences in insecticide resistance between B. tabaci MEAM1 and MED, we searched the genomic and transcriptomic databases and identified 23 putative GSTs in both B. tabaci MEAM1 and MED. Through measuring mRNA levels of 18 of the GSTs after B. tabaci MEAM1 and MED adults were exposed to the insecticide imidacloprid, we found that the expression levels were increased more in B. tabaci MED than in MEAM1 (in particular, the expression level of GST-d7 was increased by 4.39-fold relative to the control). Knockdown of GST-d7 in B. tabaci MED but not in B. tabaci MEAM1 resulted in a substantial increase in the mortality of imidacloprid-treated adults. These results indicate that differences in GST-d7 may help explain why insecticide tolerance is greater in B. tabaci MED than in B. tabaci MEAM1. © 2017 The Royal Entomological Society.

Indigenous American species of the Bemisia tabaci complex are still widespread in the Americas.

PubMed

Barbosa, Leonardo da F; Marubayashi, Julio M; De Marchi, Bruno R; Yuki, Valdir A; Pavan, Marcelo A; Moriones, Enrique; Navas-Castillo, Jesús; Krause-Sakate, Renate

2014-10-01

Bemisia tabaci is a complex of at least 36 putative cryptic species. Since the late 1980s, the Middle East-Asia Minor 1 species (MEAM1, formerly known as the B biotype), has emerged in many tropical and subtropical regions of the world and in some areas has displaced the indigenous populations of B. tabaci. Based on analysis of the mtCOI gene, two indigenous species native to America have been reported: New World (NW, formerly the A biotype) and New World 2 (NW2). NW is present at least in Argentina, Brazil, Martinique, Mexico, Texas and Venezuela, and NW2 in Argentina, Bolivia and Brazil. Wild plants (Euphorbia sp. and Ipomoea sp.), as well as important crops such as tomato, bean and cotton, are still hosts for native B. tabaci populations in the Americas. MEAM1 has not completely displaced the native B. tabaci from the Americas. © 2014 Society of Chemical Industry.

Compatibility of the insect pathogenic fungus Beauveria bassiana with neem against sweetpotato whitefly, Bemisia tabaci, on eggplant

USDA-ARS?s Scientific Manuscript database

A study on the compatibility of the entomopathogenic fungus Beauveria bassiana (Balsamo) Vuillemin (Ascomycota: Hypocreales) with neem was conducted against sweetpotato whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), on eggplant. Initially, three concentrations of B. bassiana (106, 1...

Effect of drench application of flupyradifurone on Bemisia tabaci(MED whitefly) and Amblyseius swirskii, 2017

USDA-ARS?s Scientific Manuscript database

Bemisia tabaci is a polyphagous pest known to feed on over 900 plant taxa, and is an effective vector of more than 100 plant damaging viruses. Among different biotypes of this cryptic species complex, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED)whitefly are the two most destructive membe...

Climate change and Bemisia tabaci (Hemiptera: Aleyrodidae): Impacts of temperature and carbon dioxide on life history

USDA-ARS?s Scientific Manuscript database

Climate change is relevant to life around the globe. A rise in ambient temperature and CO2 may have various impacts on arthropods such as altered life cycles, modified reproductive patterns, and changes in distribution. The sweetpotato whitefly, Bemisia tabaci (Gennadius), is a global agricultural...

Characterization of a Newly Discovered Symbiont of the Whitefly Bemisia tabaci (Hemiptera: Aleyrodidae)

PubMed Central

Bing, Xiao-Li; Yang, Jiao; Zchori-Fein, Einat; Wang, Xiao-Wei

2013-01-01

Bemisia tabaci (Hemiptera: Aleyrodidae) is a species complex containing >28 cryptic species, some of which are important crop pests worldwide. Like many other sap-sucking insects, whiteflies harbor an obligatory symbiont, “Candidatus Portiera aleyrodidarum,” and a number of secondary symbionts. So far, six genera of secondary symbionts have been identified in B. tabaci. In this study, we report and describe the finding of an additional bacterium in the indigenous B. tabaci cryptic species China 1 (formerly known as B. tabaci biotype ZHJ3). Phylogenetic analysis based on the 16S rRNA and gltA genes showed that the bacterium belongs to the Alphaproteobacteria subdivision of the Proteobacteria and has a close relationship with human pathogens of the genus Orientia. Consequently, we temporarily named it Orientia-like organism (OLO). OLO was found in six of eight wild populations of B. tabaci China 1, with the infection rate ranging from 46.2% to 76.8%. Fluorescence in situ hybridization (FISH) of B. tabaci China 1 in nymphs and adults revealed that OLOs are confined to the bacteriome and co-occur with “Ca. Portiera aleyrodidarum.” The vertical transmission of OLO was demonstrated by detection of OLO at the anterior pole end of the oocytes through FISH. Quantitative PCR analysis of population dynamics suggested a complex interaction between “Ca. Portiera aleyrodidarum” and OLO. Based on these results, we propose “Candidatus Hemipteriphilus asiaticus” for the classification of this symbiont from B. tabaci. PMID:23144129

Investigating contact toxicity of Geranium and Artemisia essential oils on Bemisia tabaci Gen.

PubMed Central

Yarahmadi, Fatemeh; Rajabpour, Ali; Zandi Sohani, Nooshin; Ramezani, Leila

2013-01-01

Objective: Sweet potato whitefly, Bemisia tabaci Gen. (B. tabaci), is one of the most important pests of various greenhouse crops in Iran. Nowadays, chemical insecticides are broadly used for control of the pests that causes risk to consumer's health. For the first time, contact toxicity of Pelargonium roseum Andrews and Artemisia sieberi Besser essential oils on B. tabaci and its possible application against the whitefly was evaluated in 2012. Materials and Methods: Essential oil with concentrations of 2500, 1250, 125, and 12 ppm were used. Infested leaves of greenhouse cucumber were treated by mentioned concentrations. After 24 hours, mortality of B. tabaci was recorded and compared after correcting by Abbot's formula. Results: Results showed that all concentrations of the essential oil could significantly reduce population of B. tabaci compared with the control treatment. Phytotoxicity of the treated leaves were recorded after 24, 48, and 72 hours and compared with the control. Concentrations of 2500, 1250, and 125 ppm caused severe phytotoxicity on greenhouse cucumber leaves and therefore are not suitable for greenhouse application. Phytotoxicity of 12 ppm was relatively low. Conclusions: This data implicated suitable protective effects of the essential oils to the pest infestation. Therefore, essential oils distillated from Geranium and Artemisia could be applied to control B. tabaci in greenhouse cucumber at V/V 12 ppm. PMID:25050264

Impact of drench application of cyantraniliprole on Bemisia tabaci (MED whitefly) and Amblyseius swirskii, 2016

USDA-ARS?s Scientific Manuscript database

Bemisia tabaci is a polyphagous pest known to feed on over 900 plant taxa, and is an effective vector of more than 100 plant damaging viruses. Among different biotypes of this cryptic species complex, MEAM1 and MED whitefly are the two most destructive members posing threats of several crops of econ...

Effect of Eretmocerus eremicus and soil application of cyantraniliprole on Bemisia tabaci (MED whitefly), 2016

USDA-ARS?s Scientific Manuscript database

Bemisia tabaci is a polyphagous pest known to feed on over 900 plant taxa, and is an effective vector of more than 100 plant damaging viruses. Among different biotypes of this cryptic species complex, MEAM1 and MED whitefly are the two most destructive members posing threats to several crops of econ...

Effect of soil application of cyantraniliprole on Bemisia tabaci (MED whitefly) and Amblyseius swirskii, 2016

USDA-ARS?s Scientific Manuscript database

Bemisia tabaci is a polyphagous pest known to feed upon over 900 plant taxa, and is an effective vector of more than 100 plant damaging viruses. Among different biotypes of this cryptic species complex, MEAM1 and MED whitefly are the two most destructive members posing threats of several crops of ec...

Effect of foliar application of pymetrozine on Bemisia tabaci (MED whitefly) and Amblyseius swirskii, 2016

USDA-ARS?s Scientific Manuscript database

Bemisia tabaci is a polyphagous pest known to feed upon over 900 plant taxa, and is an effective vector of more than 100 plant damaging viruses. Among different biotypes of this cryptic species complex, MEAM1 and MED whitefly are the two most destructive members posing threats of several crops of ec...

Efficacy of foliar application of flupyradifurone on Bemisia tabaci (MED whitefly) and Amblyseius swirskii, 2017

USDA-ARS?s Scientific Manuscript database

Bemisia tabaci is a polyphagous pest known to feed upon over 900 plant taxa, and is an effective vector of more than 100 plant damaging viruses. Among different biotypes of this cryptic species complex, MEAM1 and MED whitefly are the two most destructive members posing threats of several crops of ec...

Molecular and functional characterization of Bemisia tabaci aquaporins reveals the water channel diversity of hemipteran insects

USDA-ARS?s Scientific Manuscript database

The Middle East-Asia Minor 1 (MEAM1) whitefly, Bemisia tabaci (Gennadius) is an economically important pest of food, fiber, and ornamental crops. This pest has evolved a number of adaptations to overcome physiological challenges, including 1) the ability to regulate osmotic stress between gut lumen ...

Selection of Lecanicillium Strain with High Virulence against Developmental Stages of Bemisia tabaci

PubMed Central

Park, Heeyong

2010-01-01

Selection of fungal strains with high virulence against the developmental stages of Bemisia tabaci was performed using internal transcribed spacer regions. The growth rate of hyphae was measured and bioassay of each developmental stage of B. tabaci was conducted for seven days. All of the fungal strains tested were identified as Lecanicillium spp., with strain 4078 showing the fastest mycelium growth rate (colony diameter, 16.3 ± 0.9 mm) among the strains. Compared to strain 4075, which showed the slowest growth rate, the growth rate of strain 4078 was increased almost 2-fold after seven days. Strains 4078 and Btab01 were most virulent against the egg and larva stages, respectively. The virulence of fungal strains against the adult stage was high, except for strains 41185 and 3387. Based on the growth rate of mycelium and level of virulence, strains 4078 and Btab01 were selected as the best fungal strains for application to B. tabaci, regardless of developmental stage. PMID:23956657

Spatiotemporal Dynamics of Whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) in Commercial Watermelon Crops.

PubMed

Lima, Carlos H O; Sarmento, Renato A; Galdino, Tarcísio V S; Pereira, Poliana S; Silva, Joedna; Souza, Danival J; Dos Santos, Gil R; Costa, Thiago L; Picanço, Marcelo C

2018-04-16

Spatiotemporal dynamics studies of crop pests enable the determination of the colonization pattern and dispersion of these insects in the landscape. Geostatistics is an efficient tool for these studies: to determine the spatial distribution pattern of the pest in the crops and to make maps that represent this situation. Analysis of these maps across the development of plants can be used as a tool in precision agriculture programs. Watermelon, Citrullus lanatus (Thunb.) Matsum. and Nakai (Cucurbitales: Cucurbitaceae), is the second most consumed fruit in the world, and the whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is one of the most important pests of this crop. Thus, the objective of this work was to determine the spatiotemporal distribution of B. tabaci in commercial watermelon crops using geostatistics. For 2 yr, we monitored adult whitefly densities in eight watermelon crops in a tropical climate region. The location of the samples and other crops in the landscape was georeferenced. Experimental data were submitted to geostatistical analysis. The colonization of B. tabaci had two patterns. In the first, the colonization started at the outermost parts of the crop. In the second, the insects occupied the whole area of the crop since the beginning of cultivation. The maximum distance between sites of watermelon crops in which spatial dependence of B. tabaci densities was observed was 19.69 m. The adult B. tabaci densities in the eight watermelon fields were positively correlated with rainfall and relative humidity, whereas wind speed negatively affected whiteflies population.

Infection of the whitefly Bemisia tabaci with Rickettsia spp. alters its interactions with Tomato yellow leaf curl virus

USDA-ARS?s Scientific Manuscript database

Numerous animal and plant viruses are transmitted by arthropod vectors in a persistent, circulative manner. Tomato yellow leaf curl virus (TYLCV) is transmitted by the sweet potato whitefly Bemisia tabaci. Here we report that infection with Rickettsia spp., a facultative endosymbiont of whiteflies...

Mitigating trans-boundary movement of Bemisia tabaci (Hemiptera: Aleyrodidae) on Mentha sp. by pre-shipping treaments of biopesticides

USDA-ARS?s Scientific Manuscript database

Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a major pest of several important crops including vegetables, cereals, fruits, and ornamentals grown worldwide. One important mode of its dispersal is through the trans-boundary movement of infested plant materials. In order to prevent the sprea...

Biotype Characterization, Developmental Profiling, Insecticide Response and Binding Property of Bemisia tabaci Chemosensory Proteins: Role of CSP in Insect Defense

PubMed Central

Liu, Guoxia; Ma, Hongmei; Xie, Hongyan; Xuan, Ning; Guo, Xia; Fan, Zhongxue; Rajashekar, Balaji; Arnaud, Philippe; Offmann, Bernard; Picimbon, Jean-François

2016-01-01

Chemosensory proteins (CSPs) are believed to play a key role in the chemosensory process in insects. Sequencing genomic DNA and RNA encoding CSP1, CSP2 and CSP3 in the sweet potato whitefly Bemisia tabaci showed strong variation between B and Q biotypes. Analyzing CSP-RNA levels showed not only biotype, but also age and developmental stage-specific expression. Interestingly, applying neonicotinoid thiamethoxam insecticide using twenty-five different dose/time treatments in B and Q young adults showed that Bemisia CSP1, CSP2 and CSP3 were also differentially regulated over insecticide exposure. In our study one of the adult-specific gene (CSP1) was shown to be significantly up-regulated by the insecticide in Q, the most highly resistant form of B. tabaci. Correlatively, competitive binding assays using tryptophan fluorescence spectroscopy and molecular docking demonstrated that CSP1 protein preferentially bound to linoleic acid, while CSP2 and CSP3 proteins rather associated to another completely different type of chemical, i.e. α-pentyl-cinnamaldehyde (jasminaldehyde). This might indicate that some CSPs in whiteflies are crucial to facilitate the transport of fatty acids thus regulating some metabolic pathways of the insect immune response, while some others are tuned to much more volatile chemicals known not only for their pleasant odor scent, but also for their potent toxic insecticide activity. PMID:27167733

Compatibility of the entomopathogenic fungus Lecanicillium muscarium and insecticides for eradication of sweetpotato whitefly, Bemisia tabaci.

PubMed

Cuthbertson, Andrew G S; Walters, Keith F A; Deppe, Carola

2005-08-01

The compatibility of the entomopathogenic fungus Lecanicillium muscarium and chemical insecticides used to control the second instar stages of the sweetpotato whitefly, Bemisia tabaci, was investigated. The effect on spore germination of direct exposure for 24 h to the insecticides imidacloprid, buprofezin, teflubenzuron and nicotine was determined. Only exposure to buprofezin was followed by acceptable spore germination. However, all chemicals significantly reduced spore germination when compared to a water control. Infectivity of L. muscarium in the presence of dry residues of buprofezin, teflubenzuron and nicotine (imidacloprid is a systemic pesticide) on foliage were also investigated. No significant detrimental effects on the level of control of B. tabaci was recorded when compared with fungi applied to residue free foliage on either tomato or verbena plants. Fungi in combination with imidacloprid gave higher B. tabaci mortality on verbena foliage compared to either teflubenzuron or nicotine and fungi combinations. Use of these chemical insecticides with L. muscarium in integrated control programmes for B. tabaci is discussed.

Comparative transcriptome analysis reveals networks of genes activated in the whitefly, Bemisia tabaci when fed on tomato plants infected with Tomato yellow leaf curl virus

USDA-ARS?s Scientific Manuscript database

The whitefly Bemisia tabaci can transmit hundreds of viruses to numerous agricultural crops in the world. Five genera of viruses, including Begomovirus and Crinivirus, are transmitted by B. tabaci. There is little knowledge about the genes involved in virus acquisition and transmission by whiteflies...

Repellent Effects of Different Celery Varieties in Bemisia tabaci (Hemiptera: Aleyrodidae) Biotype Q.

PubMed

Tu, Hongtao; Qin, Yuchuan

2017-06-01

Y-tube olfactometer and net cages experiments were used to investigate the repellent effects of different celery varieties in biotype Q of sweetpotato whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), on cucumber, Cucumis sativus L. (Cucurbitaceae). Y-tube olfactometer tests showed that whiteflies have strong repellent behavior to different celery varieties. Intercropping different celery varieties with cucumbers had significant repellent effects and oviposition deterrent effects in whiteflies. Results obtained demonstrated that the Western Europe celery varieties, Juventus and Ventura, and the Chinese celery variety, Jinnan, had good repellent efficacy against the whitefly. D-Limonene, β-myrcene, and (E)-β-ocimene might be the main active components in celery that affected the selection behavior of B. tabaci. In Western Europe celery varieties, D-limonene was the main volatile component for the repellent effects in B. tabaci; however, the two Chinese celery varieties that showed repellent effects had relatively higher volatilization quantities of β-myrcene than of D-limonene. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Cryptic Species Identification and Composition of Bemisia tabaci (Hemiptera: Aleyrodidae) Complex in Henan Province, China

PubMed Central

Hu, Jian; Wang, Lun-Ji; Dong, Jun-Feng; Song, Yue-Qin; Sun, Hui-Zhong

2017-01-01

Abstract Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex, causing significant crop losses in China during the last decade. Although knowledge of cryptic species composition and dynamics within B. tabaci complex is critical for developing sustainable pest management strategies, limited information is available on this pest in the Henan province of China. A systematic survey of the cryptic species composition and distribution of B. tabaci complex in different locations of Henan province was conducted in 2012. The results of RAPD-PCR and the gene for the mitochondrial cytochrome oxidase subunit-1 (mtCOI) based phylogenetic relationships established using Bayesian method indicated there were four known cryptic species MEAM1, MED, Asia II 3, Asia II 9 and a new cryptic species named China 6 in Henan province. In the survey, the invasive cryptic species MED and MEAM1 were found to be predominant with wide spread distribution across the surveyed regions. On the contrary, the indigenous B. tabaci cryptic species including Asia II 3, Asia II 9 and China 6 remained with low prevalence in some surveyed regions. Cryptic species MEAM1 and MED have not completely displaced the native B. tabaci in Henan province. This current study for the first time unifies our knowledge of the diversity and distribution of B. tabaci across Henan province of China. PMID:28973577

Lack of resistance development in Bemisia tabaci to Isaria fumosorosea after multiple generations of selection

NASA Astrophysics Data System (ADS)

Gao, Tianni; Wang, Zhaolei; Huang, Yü; Keyhani, Nemat O.; Huang, Zhen

2017-02-01

The emergence of insecticide resistant insect pests is of significant concern worldwide. The whitefly, Bemisia tabaci, is an important agricultural pest and has shown incredible resilience developing resistance to a number of chemical pesticides. Entomopathogenic fungi such as Isaria fumosorosea offer an attractive alternative to chemical pesticides for insect control, and this fungus has been shown to be an effective pathogen of B. tabaci. Little is known concerning the potential for the development of resistance to I. fumosorosea by B. tabaci. Five generations of successive survivors of B. tabaci infected by I. fumosorosea were assayed with I. fumosorosea. No significant differences in susceptibility to I. fumosorosea, number of ovarioles, or ovipostioning were seen between any of the generations tested. Effects of I. fumosorosea and cell-free ethyl acetate fractions derived from the fungus on the B. tabaci fat body, ovary, and vitellogenin were also investigated. These data revealed significant deformation and degradation of ovary tissues and associated vitellogenin by the fungal mycelium as well as by cell-free ethyl acetate fungal extracts. These data indicate the lack of the emergence of resistance to I. fumosorosea under the conditions tested and demonstrate invasion of the insect reproductive tissues during fungal infection.

Cross-resistance relationships between neonicotinoids and pymetrozine in Bemisia tabaci (Hemiptera: Aleyrodidae).

PubMed

Gorman, Kevin; Slater, Russell; Blande, James D; Clarke, Alison; Wren, Jodie; McCaffery, Alan; Denholm, Ian

2010-11-01

Although cross-resistance between compounds in the same insecticide group is a frequently observed phenomenon, cross-resistance between groups that differ in structural and functional characteristics can be extremely unpredictable. In the case of controlling the whitefly, Bemisia tabaci Gennadius, neonicotinoids and the pyridine azomethine antifeedant pymetrozine represent independent lines of discovery that should be suited for alternation to avoid prolonged selection for the same resistance mechanism. Reports of an association between responses to neonicotinoids and pymetrozine were investigated by resistance profiling of seven B. tabaci strains and complementary reciprocal selection experiments. All strains demonstrated a consistent correlation between responses to three neonicotinoid compounds: thiamethoxam, imidacloprid and acetamiprid. Responses to neonicotinoids for six field strains clearly correlated with responses to pymetrozine. Reciprocal selection experiments confirmed an unexpected case of intergroup cross-resistance. A seventh strain exhibited a so far unique phenotype of strong resistance to pymetrozine but full susceptibility to neonicotinoids. Selection experiments confirmed that in this strain the mechanism of pymetrozine resistance is specific and has no implications for neonicotinoids. Cross-resistance between neonicotinoids and pymetrozine in B. tabaci probably reflects the overexpression of a cytochrome-P450-dependent monooxygenase capable of metabolising both types of compound in spite of their apparent structural dissimilarity. Given the predominance of this mechanism in B. tabaci, both can contribute to resistance management but should be placed within the same treatment 'window'. Copyright © 2010 Society of Chemical Industry.

Transcriptomic and Proteomic Responses of Sweetpotato Whitefly, Bemisia tabaci, to Thiamethoxam

PubMed Central

Yang, Nina; Xie, Wen; Yang, Xin; Wang, Shaoli; Wu, Qingjun; Li, Rumei; Pan, Huipeng; Liu, Baiming; Shi, Xiaobin; Fang, Yong; Xu, Baoyun; Zhou, Xuguo; Zhang, Youjun

2013-01-01

Background The sweetpotato whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), is one of the most widely distributed agricultural pests. Although it has developed resistance to many registered insecticides including the neonicotinoid insecticide thiamethoxam, the mechanisms that regulate the resistance are poorly understood. To understand the molecular basis of thiamethoxam resistance, “omics” analyses were carried out to examine differences between resistant and susceptible B. tabaci at both transcriptional and translational levels. Results A total of 1,338 mRNAs and 52 proteins were differentially expressed between resistant and susceptible B. tabaci. Among them, 11 transcripts had concurrent transcription and translation profiles. KEGG analysis mapped 318 and 35 differentially expressed genes and proteins, respectively, to 160 and 59 pathways (p<0.05). Thiamethoxam treatment activated metabolic pathways (e.g., drug metabolism), in which 118 transcripts were putatively linked to insecticide resistance, including up-regulated glutathione-S-transferase, UDP glucuronosyltransferase, glucosyl/glucuronosyl transferase, and cytochrome P450. Gene Ontology analysis placed these genes and proteins into protein complex, metabolic process, cellular process, signaling, and response to stimulus categories. Quantitative real-time PCR analysis validated “omics” response, and suggested a highly overexpressed P450, CYP6CX1, as a candidate molecular basis for the mechanistic study of thiamethoxam resistance in whiteflies. Finally, enzymatic activity assays showed elevated detoxification activities in the resistant B. tabaci. Conclusions This study demonstrates the applicability of high-throughput omics tools for identifying molecular candidates related to thiamethoxam resistance in an agricultural important insect pest. In addition, transcriptomic and proteomic analyses provide a solid foundation for future functional investigations into the complex molecular mechanisms

Cryptic Species Identification and Composition of Bemisia tabaci (Hemiptera: Aleyrodidae) Complex in Henan Province, China.

PubMed

Jiu, Min; Hu, Jian; Wang, Lun-Ji; Dong, Jun-Feng; Song, Yue-Qin; Sun, Hui-Zhong

2017-05-01

Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex, causing significant crop losses in China during the last decade. Although knowledge of cryptic species composition and dynamics within B. tabaci complex is critical for developing sustainable pest management strategies, limited information is available on this pest in the Henan province of China. A systematic survey of the cryptic species composition and distribution of B. tabaci complex in different locations of Henan province was conducted in 2012. The results of RAPD-PCR and the gene for the mitochondrial cytochrome oxidase subunit-1 (mtCOI) based phylogenetic relationships established using Bayesian method indicated there were four known cryptic species MEAM1, MED, Asia II 3, Asia II 9 and a new cryptic species named China 6 in Henan province. In the survey, the invasive cryptic species MED and MEAM1 were found to be predominant with wide spread distribution across the surveyed regions. On the contrary, the indigenous B. tabaci cryptic species including Asia II 3, Asia II 9 and China 6 remained with low prevalence in some surveyed regions. Cryptic species MEAM1 and MED have not completely displaced the native B. tabaci in Henan province. This current study for the first time unifies our knowledge of the diversity and distribution of B. tabaci across Henan province of China. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America.

Effects of cucumber mosaic virus-infected chilli plants on non-vector Bemisia tabaci (Hemiptera: Aleyrodidae).

PubMed

Saad, Khalid A; Mohamad Roff, M N; Hallett, Rebecca H; ABd-Ghani, Idris B

2017-06-08

Plant virus infections are known to alter host plant attractiveness and suitability for insect herbivores. This study was conducted to determine how cucumber mosaic virus (CMV)-infected chilli plants affect the fitness and settling preferences of nonvector whitefly, Bemisia tabaci adults under dual-choice conditions with volatile organic compounds analyzed using solid phase microextraction coupled with gas chromatography-mass spectrometry (GC-MS). Results showed that the presence of CMV in chilli plants substantially affects the settling preferences of the B. tabaci, which preferred to settle on noninfected plants. Duration of the egg stage and the longevity and fecundity of adult B. tabaci on CMV-infected chilli plants were not markedly different from those on noninfected chilli plants. In contrast, the developmental time from egg to adult was significantly reduced in CMV-infected chilli plants compared to the noninfected plants. The results also showed that CMV-infected chilli plants released significantly more linalool and phenylacetaldehyde than noninfected plants. Overall, it was suggested that the behavioral response of B. tabaci might be modified by CMV-infected plants, which alter the release of specific headspace volatiles. Based on these results, the modification of plant volatile profiles may help in enhancing the effectiveness of biological control and the protection of crop plants against B. tabaci. © 2017 Institute of Zoology, Chinese Academy of Sciences.

Transcriptome analysis reveals a comprehensive insect resistance response mechanism in cotton to infestation by the phloem feeding insect Bemisia tabaci (whitefly)

USDA-ARS?s Scientific Manuscript database

The whitefly (Bemisia tabaci) causes tremendous damage to cotton production worldwide. However, very limited information is available about how plants perceive and defend themselves from this destructive pest. In this study, the transcriptomics differences between two cotton cultivars that exhibit e...

Response of Bemisia tabaci Genn. (Hemiptera: Aleyrodidae) biotype B to genotypes of pepper Capsicum annuum (Solanales: Solanaceae).

PubMed

Ballina-Gomez, H; Ruiz-Sanchez, E; Chan-Cupul, W; Latournerie-Moreno, L; Hernández-Alvarado, L; Islas-Flores, I; Zuñiga-Aguilar, J J

2013-04-01

Bemisia tabaci Genn. biotype B is a widely distributed plant pest that represents one of the major constraints for horticultural crop production. The purpose of the present work was to evaluate the oviposition preference, survivorship, and development of B. tabaci biotype B on semi-cultivated genotypes of Capsicum annuum from southeast Mexico. In free-choice experiments to evaluate the oviposition preference, lower number of eggs laid by B. tabaci biotype B was observed in the genotypes Maax and Xcat´ik relative to that in the commercial genotype Parado. Egg hatchability was significantly lower in Pico Paloma, Bolita, Blanco, Chawa, Payaso, and Xcat´ik than in the rest of the genotypes, including the commercial genotype Jalapeño. Likewise, survivorship of nymphs was significantly lower in Pico Paloma, Bolita, and Blanco than in the remaining genotypes. Nymph developmental time and the period of development from egg to adult were the shortest in Amaxito. Therefore, sources of resistance to B. tabaci biotype B by antibiosis (accumulation of plant defense compounds) might be found in the semi-cultivated genotypes Pico Paloma, Bolita, and Blanco.

Protecting Unrooted Cuttings From Bemisia tabaci (Hemiptera Aleyrodidae) During Propagation

PubMed Central

Krauter, Peter C.; Arthurs, Steven

2017-01-01

Abstract In North America, the sweetpotato whitefly, Bemisia tabaci Genn., is an important pest of greenhouse poinsettia. Growers have limited options to control this pest during propagation of cuttings, which are rooted under mist for several weeks. Early establishment of this pest increases the difficulty of managing the whitefly and retaining high aesthetic standard during the remaining crop production phase. We evaluated two neonicotinoids with translaminar activity, thiamethoxam (Flagship 25WG), and acetamiprid (TriStar 70 WSP), for control of B. tabaci pre-infested on unrooted cuttings propagated under mist. In an experimental greenhouse, both materials significantly reduced whitefly populations, providing an average reduction of 87.8% and 61.5% total recovered whitefly stages respectively, compared with controls. In another test, dipping cuttings in thiamethoxam (immersion treatment) did not improve control significantly, when compared with foliar sprays applied at label rate. In a commercial greenhouse operation, immersion treatments of thiamethoxam on pre-infested poinsettia cuttings maintained whiteflies at ≤ 0.02/plant, compared with up to 0.33/plant in untreated cuttings. Our data suggest that treating unrooted cuttings before or at the start of propagation can be part of an overall strategy for growers to manage whiteflies in poinsettia production. PMID:28973486

Implication of the Bacterial Endosymbiont Rickettsia spp. in Interactions of the Whitefly Bemisia tabaci with Tomato yellow leaf curl virus

PubMed Central

Kliot, Adi; Cilia, Michelle; Czosnek, Henryk

2014-01-01

ABSTRACT Numerous animal and plant viruses are transmitted by arthropod vectors in a persistent, circulative manner. Tomato yellow leaf curl virus (TYLCV) is transmitted by the sweet potato whitefly Bemisia tabaci. We report here that infection with Rickettsia spp., a facultative endosymbiont of whiteflies, altered TYLCV-B. tabaci interactions. A B. tabaci strain infected with Rickettsia acquired more TYLCV from infected plants, retained the virus longer, and exhibited nearly double the transmission efficiency compared to an uninfected B. tabaci strain with the same genetic background. Temporal and spatial antagonistic relationships were discovered between Rickettsia and TYLCV within the whitefly. In different time course experiments, the levels of virus and Rickettsia within the insect were inversely correlated. Fluorescence in situ hybridization analysis of Rickettsia-infected midguts provided evidence for niche exclusion between Rickettsia and TYLCV. In particular, high levels of the bacterium in the midgut resulted in higher virus concentrations in the filter chamber, a favored site for virus translocation along the transmission pathway, whereas low levels of Rickettsia in the midgut resulted in an even distribution of the virus. Taken together, these results indicate that Rickettsia, by infecting the midgut, increases TYLCV transmission efficacy, adding further insights into the complex association between persistent plant viruses, their insect vectors, and microorganism tenants that reside within these insects. IMPORTANCE Interest in bacterial endosymbionts in arthropods and many aspects of their host biology in agricultural and human health systems has been increasing. A recent and relevant studied example is the influence of Wolbachia on dengue virus transmission by mosquitoes. In parallel with our recently studied whitefly-Rickettsia-TYLCV system, other studies have shown that dengue virus levels in the mosquito vector are inversely correlated with

Odor, Not Performance, Dictates Bemisia tabaci's Selection between Healthy and Virus Infected Plants

PubMed Central

Chen, Gong; Su, Qi; Shi, Xiaobin; Liu, Xin; Peng, Zhengke; Zheng, Huixin; Xie, Wen; Xu, Baoyun; Wang, Shaoli; Wu, Qingjun; Zhou, Xuguo; Zhang, Youjun

2017-01-01

Although, insect herbivores are generally thought to select hosts that favor the fitness of their progeny, this “mother-knows-best” hypothesis may be challenged by the presence of a plant virus. Our previous study showed that the whitefly, Bemisia tabaci, the obligate vector for transmitting Tomato yellow leaf curl virus (TYLCV), preferred to settle and oviposit on TYLCV-infected rather than healthy host plant, Datura stramonium. The performances of B. tabaci larvae and adults were indeed improved on virus-infected D. stramonium, which is consistent with “mother-knows-best” hypothesis. In this study, B. tabaci Q displayed the same preference to settle and oviposit on Tomato spotted wilt virus (TSWV)-infected host plants, D. stramonium and Capsicum annuum, respectively. As a non-vector of TSWV, however, insect performance was impaired since adult body size, longevity, survival, and fecundity were reduced in TSWV infected D. stramonium. This appears to be an odor-mediated behavior, as plant volatile profiles are modified by viral infection. Infected plants have reduced quantities of o-xylene and α-pinene, and increased levels of phenol and 2-ethyl-1-hexanol in their headspace. Subsequent behavior experiments showed that o-xylene and α-pinene are repellant, while phenol and 2-ethyl-1-hexanol are attractive. This indicates that the preference of B. tabaci for virus-infected plants is modulated by the dynamic changes in the volatile profiles rather than the subsequent performances on virus-infected plants. PMID:28360861

Transcriptome analysis of Bemisia tabaci during tomato yellow leaf curl virus acquisition and ribonucleic acid interference to manage whitefly-transmitted viruses

USDA-ARS?s Scientific Manuscript database

Over 300 viruses are transmitted by the whitefly, Bemisia tabaci, with 90% of them belonging to the genus, Begomovirus. Begomoviruses are obligately transmitted by whiteflies to a wide range of agriculture crops, resulting in billions of dollars lost annually, while jeopardizing food security worldw...

Establishment of papaya banker plant system for Parasitoid, Encarsia sophia (Hymenoptera: Aphilidae) against Bemisia tabaci (Hemiptera: Aleyrodidae) in greenhouse tomato production

USDA-ARS?s Scientific Manuscript database

The silverleaf whitefly, Bemisia tabaci biotype B (Gennadius) (Hemiptera:Aleyrodidae), is a key pest of tomato (Solanum lycopersicum L.) and other vegetable crops worldwide. To combat this pest, a non-crop banker plant system was evaluated that employs a parasitoid, Encarsia sophia (Girault & Dodd) ...

Acylsucrose-Producing Tomato Plants Forces Bemisia tabaci to Shift Its Preferred Settling and Feeding Site

PubMed Central

Rodríguez-López, Maria Jose; Garzo, Elisa; Bonani, Jean Patrick; Fernández-Muñoz, Rafael; Moriones, Enrique; Fereres, Alberto

2012-01-01

Background The whitefly Bemisia tabaci (Genn.) causes dramatic damage to plants by transmitting yield-limiting virus diseases. Previous studies proved that the tomato breeding line ABL 14-8 was resistant to B. tabaci, the vector of tomato yellow leaf curl disease (TYLCD). This resistance is based on the presence of type IV glandular trichomes and acylsucrose production. These trichomes deter settling and probing of B. tabaci in ABL 14-8, which reduces primary and secondary spread of TYLCD. Methodology/Principal Findings Whitefly settlement preference was evaluated on the adaxial and abaxial leaf surfaces of nearly-isogenic tomato lines with and without B. tabaci-resistance traits, ‘ABL 14-8 and Moneymaker’ respectively, under non-choice and free-choice conditions. In addition, the Electrical Penetration Graph technique was used to study probing and feeding activities of B. tabaci on the adaxial and abaxial leaf surfaces of the same genotypes. B. tabaci preferred to settle on the abaxial than on the adaxial surface of ‘Moneymaker’ leaves, whereas no such preference was observed on ABL 14-8 tomato plants at the ten-leaf growth stage. Furthermore, B. tabaci preferred to feed on the abaxial than on the adaxial leaf surface of ‘Moneymarker’ susceptible tomato plants as shown by a higher number of sustained phloem feeding ingestion events and a shorter time to reach the phloem. However, B. tabaci standard probing and feeding behavior patterns were altered in ABL 14-8 plants and whiteflies were unable to feed from the phloem and spent more time in non-probing activities when exposed to the abaxial leaf surface. Conclusions/Significance The distorted behavior of B. tabaci on ABL 14-8 protects tomato plants from the transmission of phloem-restricted viruses such as Tomato yellow leaf curl virus (TYLCV), and forces whiteflies to feed on the adaxial side of leaves where they feed less efficiently and become more vulnerable to natural enemies. PMID:22427950

Aphid-induced Defences in Chilli Affect Preferences of the Whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae).

PubMed

Saad, Khalid A; Mohamad Roff, M N; Hallett, Rebecca H; Idris, A B

2015-09-03

The sweetpotato whitefly (WF), Bemisia tabaci, is a major pest that damages a wide range of vegetable crops in Malaysia. WF infestation is influenced by a variety of factors, including previous infestation of the host plant by other insect pests. This study investigated the effects of previous infestation of host chilli plants by the green peach aphid (Myzus persicae) on the olfactory behavioural response of B. tabaci, using free-choice bioassay with a Y-tube olfactometer. We analysed volatile organic compounds (VOCs) emitted by non-infested and M. persicae-infested chilli plants using solid-phase microextraction and gas chromatography-mass spectrometry. Our results showed that female WFs preferred non-infested to pre-infested plants. Collection and analysis of volatile compounds emitted by infested plants confirmed that there were significant increases in the production of monoterpenes (cymene; 1,8-cineole), sesquiterpenes (β-cadinene, α-copaene), and methyl salicylate (MeSA) compared to non-infested plants. Our results suggest that host plant infestation by aphids may induce production of secondary metabolites that deter B. tabaci from settling on its host plants. These results provide important information for understanding WF host selection and dispersal among crops, and also for manipulating WF behaviour to improve IPM in chilli.

Unravelling the Genetic Diversity among Cassava Bemisia tabaci Whiteflies Using NextRAD Sequencing.

PubMed

Wosula, Everlyne N; Chen, Wenbo; Fei, Zhangjun; Legg, James P

2017-11-01

Bemisia tabaci threatens production of cassava in Africa through vectoring viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). B. tabaci sampled from cassava in eight countries in Africa were genotyped using NextRAD sequencing, and their phylogeny and population genetics were investigated using the resultant single nucleotide polymorphism (SNP) markers. SNP marker data and short sequences of mitochondrial DNA cytochrome oxidase I (mtCOI) obtained from the same insect were compared. Eight genetically distinct groups were identified based on mtCOI, whereas phylogenetic analysis using SNPs identified six major groups, which were further confirmed by PCA and multidimensional analyses. STRUCTURE analysis identified four ancestral B. tabaci populations that have contributed alleles to the six SNP-based groups. Significant gene flows were detected between several of the six SNP-based groups. Evidence of gene flow was strongest for SNP-based groups occurring in central Africa. Comparison of the mtCOI and SNP identities of sampled insects provided a strong indication that hybrid populations are emerging in parts of Africa recently affected by the severe CMD pandemic. This study reveals that mtCOI is not an effective marker at distinguishing cassava-colonizing B. tabaci haplogroups, and that more robust SNP-based multilocus markers should be developed. Significant gene flows between populations could lead to the emergence of haplogroups that might alter the dynamics of cassava virus spread and disease severity in Africa. Continuous monitoring of genetic compositions of whitefly populations should be an essential component in efforts to combat cassava viruses in Africa. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

RNA interference-mediated knockdown of the hydroxyacid-oxoacid transhydrogenase gene decreases thiamethoxam resistance in adults of the whitefly Bemisia tabaci

PubMed Central

Yang, Xin; Xie, Wen; Li, Ru-mei; Zhou, Xiao-mao; Wang, Shao-li; Wu, Qing-jun; Yang, Ni-na; Xia, Ji-xing; Yang, Ze-zong; Guo, Li-tao; Liu, Ya-ting; Zhang, You-jun

2017-01-01

Bemisia tabaci has developed a high level of resistance to thiamethoxam, a second generation neonicotinoid insecticide that has been widely used to control this pest. In this study, we investigated whether hydroxyacid-oxoacid transhydrogenase (HOT) is involved in resistance to the neonicotinoid insecticide thiamethoxam in the whitefly. We cloned the full-length gene that encodes HOT in B. tabaci. Its cDNA contains a 1428-bp open reading frame encoding 475 amino acid residues. Then we evaluated the mRNA expression level of HOT in different developmental stages, and found HOT expression was significantly greater in thiamethoxam resistance adults than in thiamethoxam susceptible adults. Subsequently, seven field populations of B. tabaci adults were sampled, the expression of mRNA level of HOT significant positive correlated with thiamethoxam resistance level. At last, we used a modified gene silencing system to knock-down HOT expression in B. tabaci adults. The results showed that the HOT mRNA levels decreased by 57% and thiamethoxam resistance decreased significantly after 2 days of feeding on a diet containing HOT dsRNA. The results indicated that down-regulation of HOT expression decreases thiamethoxam resistance in B. tabaci adults. PMID:28117358

Standardized molecular diagnostic tool for the identification of cryptic species within the Bemisia tabaci complex.

PubMed

Elfekih, Samia; Tay, Wee Tek; Gordon, Karl; Court, Leon N; De Barro, Paul J

2018-01-01

The whitefly Bemisia tabaci complex harbours over 40 cryptic species that have been placed in 11 phylogenetically distinct clades based on the molecular characterization of partial mitochondrial DNA COI (mtCOI) gene region. Four cryptic species are currently within the invasive clade, i.e. MED, MEAM1, MEAM2 and IO. Correct identification of these species is a critical step towards implementing reliable measures for plant biosecurity and border protection; however, no standardized B. tabaci-specific primers are currently available which has caused inconsistencies in the species identification processes. We report three sets of polymerase chain reaction (PCR) primers developed to amplify the mtCOI region which can be used for genotyping MED, MEAM1 and IO species, and tested these primers on 91 MED, 35 MEAM1 and five IO individuals. PCR and sequencing of amplicons identified a total of 21, six and one haplotypes in MED, MEAM1 and IO respectively, of which six haplotypes were new to the B. tabaci database. These primer pairs enabled standardization and robust molecular species identification via mtCOI screening of the targeted invasive cryptic species and will improve quarantine decisions. Use of this diagnostic tool could be extended to other species within the complex. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Non-invasive delivery of dsGST is lethal to the sweet potato whitefly, Bemisia tabaci (G.) (Hemiptera: Aleyrodidae).

PubMed

Asokan, R; Rebijith, K B; Roopa, H K; Kumar, N K Krishna

2015-02-01

The sweet potato whitefly, Bemisia tabaci (G.) biotype B (Hemiptera: Aleyrodidae), is one of the most economically important pest, by being a dreaded vector of Geminiviruses, and also causes direct damage to the crops by sucking phloem sap. Glutathione S-transferase (GST) is a large family of multifunctional enzymes that play pivotal roles in the detoxification of secondary allelochemical produced by the host plants and in insecticide resistance, thus regulates insect growth and development. The objective of this study is to show the potential of RNA interference (RNAi) in the management of B. tabaci. RNAi is a sequence-specific gene silencing mechanism induced by double-stranded RNA (dsRNA) which holds tremendous potential in pest management. In this regard, we sequenced the GST from B. tabaci and synthesized approximately 500-bp dsRNA from the above and delivered through diet to B. tabaci. Real-time quantitative PCR (RT-qPCR) showed that continuous application of dsGST at 1.0, 0.5, and 0.25 μg/μl reduced mRNA expression levels for BtGST by 77.43, 64.86, and 52.95 % which resulted in mortality by 77, 59, and 40 %, respectively, after 72 h of application. Disruption of BtGST expression will enable the development of novel strategies in pest management and functional analysis of vital genes in B. tabaci.

Characterization of Antixenosis in Soybean Genotypes to Bemisia tabaci (Hemiptera: Aleyrodidae) Biotype B.

PubMed

Baldin, E L L; Cruz, P L; Morando, R; Silva, I F; Bentivenha, J P F; Tozin, L R S; Rodrigues, T M

2017-08-01

Bemisia tabaci biotype B (Gennadius) is one of the most important soybean pest worldwide. Herein, 15 soybean genotypes were evaluated, to characterize the occurrence of antixenosis to B. tabaci biotype B. Initially, a multiple-choice test with all genotypes was carried out, evaluating the settling and oviposition preference at 3 d after infestation, and the colonization by nymphs after 48 d of infestation. Subsequently, a no-choice test, using 14 genotypes, was conducted with infested plants individually, and the number of eggs was counted after 72 h. Then, 10 genotypes were selected (indicative of resistance and susceptibility), which were evaluated for whitefly settling 24, 48, and 72 h after infestation and for oviposition 72 h after infestation. The trichomes of the leaflets were characterized for density, size, and inclination to establish possible correlations with the settling and oviposition in the genotypes. In the first multiple-choice test, involving 15 genotypes, 'IAC-17,' 'IAC-19,' and UX-2569-159 expressed antixenosis against B. tabaci. 'Jackson,' 'P98Y11,' and PI-229358 exhibited the same behavior in the no-choice test. In the multiple-choice test, 'Jackson,' 'P98Y11,' and 'TMG1176 RR' were the least attractive and least used for oviposition. The antixenosis shown by 'Jackson,' 'P98Y11,' and PI-229358 may be related to the characteristics of the trichomes (lower density and inclined). Based on the experiments carried out, 'IAC-17,' 'IAC-19,' 'Jackson,' 'P98Y11,' PI-229358, TMG1176 RR, and UX-2569-159 are considered promising for resistance to B. tabaci biotype B and may be exploited in soybean breeding programs for resistance to insects. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Sensitivity of Bemisia Tabaci (Hemiptera: Aleyrodidae) to Several New Insecticides in China: Effects of Insecticide Type and Whitefly Species, Strain, and Stage

PubMed Central

Xie, Wen; Liu, Yang; Wang, Shaoli; Wu, Qingjun; Pan, Huipeng; Yang, Xin; Guo, Litao; Zhang, Youjun

2014-01-01

Abstract Whitefly biotypes B and Q are the two most damaging members of the Bemisia tabaci (Hemiptera: Aleyrodidae) species complex. Control of B. tabaci (and especially of Q) has been impaired by resistance to commonly used insecticides. To find new insecticides for B. tabaci management in China, we investigated the sensitivity of eggs, larvae, and adults of laboratory strains of B and Q (named Lab-B and Lab-Q) and field strains of Q to several insecticides. For eggs, larvae, and adults of B. tabaci and for six insecticides (cyantraniliprole, chlorantraniliprole, pyriproxyfen, buprofezin, acetamiprid, and thiamethoxam), LC 50 values were higher for Lab-Q than for Lab-B; avermectin LC 50 values, however, were low for adults of both Lab-Q and Lab-B. Based on the laboratory results, insecticides were selected to test against eggs, larvae, and adults of four field strains of B. tabaci Q. Although the field strains differed in their sensitivity to the insecticides, the eggs and larvae of all strains were highly sensitive to cyantraniliprole, and the adults of all strains were highly sensitive to avermectin. The eggs, larvae, and adults of B. tabaci Q were generally more resistant than those of B. tabaci B to the tested insecticides. B. tabaci Q eggs and larvae were sensitive to cyantraniliprole and pyriproxyfen, whereas B. tabaci Q adults were sensitive to avermectin. Field trials should be conducted with cyantraniliprole, pyriproxyfen, and avermectin for control of B. tabaci Q and B in China. PMID:25434040

Global Population Structure of a Worldwide Pest and Virus Vector: Genetic Diversity and Population History of the Bemisia tabaci Sibling Species Group

PubMed Central

2016-01-01

The whitefly Bemisia tabaci sibling species (sibsp.) group comprises morphologically indiscernible lineages of well-known exemplars referred to as biotypes. It is distributed throughout tropical and subtropical latitudes and includes the contemporary invasive haplotypes, termed B and Q. Several well-studied B. tabaci biotypes exhibit ecological and biological diversity, however, most members are poorly studied or completely uncharacterized. Genetic studies have revealed substantial diversity within the group based on a fragment of the mitochondrial cytochrome oxidase I (mtCOI) sequence (haplotypes), with other tested markers being less useful for deep phylogenetic comparisons. The view of global relationships within the B. tabaci sibsp. group is largely derived from this single marker, making assessment of gene flow and genetic structure difficult at the population level. Here, the population structure was explored for B. tabaci in a global context using nuclear data from variable microsatellite markers. Worldwide collections were examined representing most of the available diversity, including known monophagous, polyphagous, invasive, and indigenous haplotypes. Well-characterized biotypes and other related geographic lineages discovered represented highly differentiated genetic clusters with little or no evidence of gene flow. The invasive B and Q biotypes exhibited moderate to high levels of genetic diversity, suggesting that they stemmed from large founding populations that have maintained ancestral variation, despite homogenizing effects, possibly due to human-mediated among-population gene flow. Results of the microsatellite analyses are in general agreement with published mtCOI phylogenies; however, notable conflicts exist between the nuclear and mitochondrial relationships, highlighting the need for a multifaceted approach to delineate the evolutionary history of the group. This study supports the hypothesis that the extant B. tabaci sibsp. group contains

Members of Bemisia tabaci (Hemiptera: Aleyrodidae) Cryptic Species and the Status of Two Invasive Alien Species in the Yunnan Province (China)

PubMed Central

Hu, Jian; Jiang, Zhi-Lin; Nardi, Francesco; Liu, Yuan-Yuan; Luo, Xiao-Rong; Li, Hong-Xiang; Zhang, Zhong-Kai

2014-01-01

Abstract Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex that includes some of the most significant pests of agriculture and horticulture worldwide. To understand the diversity and distribution of B. tabaci cryptic species in Yunnan, a famous biodiversity hotspot in China, a large-scale sampling was conducted from year 2010 to 2013 in 10 prefectures. Mitochondrial cytochrome oxidase I gene sequences were used to identify different cryptic species. Phylogenetic analyses were performed using Bayesian methods to assess the position of a new B. tabaci cryptic species in the context of the B. tabaci diversity in Asia. The survey indicates at least eight B. tabaci cryptic species are present in Yunnan, two invasive (MEAM1 and MED) and six indigenous (China 2, China3, China 4, Asia I, Asia II 1, and Asia II 6), MEAM1, MED, and Asia I being the three predominant cryptic species in Yunnan. Compared with MEAM1, MED has a wider distribution. Based on molecular data, a new cryptic species, here named China 4, was identified that appears to be related to China 1, China 2, and China 3. Future efforts should focus on the interactions between predominant B. tabaci cryptic species and begomoviruses and on the development of effective control strategies. PMID:25502045

Comparative transcriptome analysis in Bemisia tabaci in response to tomato yellow leaf curl virus and development of ribonucleic acid interference to manage whitefly-transmitted viruses

USDA-ARS?s Scientific Manuscript database

The whitefly, Bemisia tabaci transmits over 300 plant viruses, with the majority of them belonging to the Begomovirus genus. Begomoviruses are obligately transmitted to a wide range of agriculture crops, resulting in the loss of billions of dollars annually, while jeopardizing food security worldwid...

Two cytochrome P450 genes are involved in imidacloprid resistance in field populations of the whitefly, Bemisia tabaci, in China.

PubMed

Yang, Xin; Xie, Wen; Wang, Shao-li; Wu, Qing-jun; Pan, Hui-peng; Li, Ru-mei; Yang, Ni-na; Liu, Bai-ming; Xu, Bao-yun; Zhou, Xiaomao; Zhang, You-jun

2013-11-01

The sweet potato whitefly, Bemisia tabaci (Gennadius) (Hemiptera:Aleyrodidae), is an invasive and damaging pest of field crops worldwide. The neonicotinoid insecticide imidacloprid has been widely used to control this pest. We assessed the species composition (B vs. Q), imidacloprid resistance, and association between imidacloprid resistance and the expression of five P450 genes for 14-17 B. tabaci populations in 12 provinces in China. Fifteen of 17 populations contained only B. tabaci Q, and two populations contained both B and Q. Seven of 17 populations exhibited moderate to high resistance to imidacloprid, and eight populations exhibited low resistance to imidacloprid, compared with the most susceptible field WHHB population. In a study of 14 of the populations, resistance level was correlated with the expression of the P450 genes CYP6CM1 and CYP4C64 but not with the expression of CYP6CX1, CYP6CX4, or CYP6DZ7. This study indicates that B. tabaci Q has a wider distribution in China than previously reported. Resistance to imidacloprid in field populations of B. tabaci is associated with the increased expression of two cytochrome P450 genes (CYP6CM1 and CYP4C64). Crown Copyright © 2013. Published by Elsevier Inc. All rights reserved.

Toxicological and biochemical basis of synergism between the entomopathogenic fungus Lecanicillium muscarium and the insecticide matrine against Bemisia tabaci (Gennadius)

NASA Astrophysics Data System (ADS)

Ali, Shaukat; Zhang, Can; Wang, Zeqing; Wang, Xing-Min; Wu, Jian-Hui; Cuthbertson, Andrew G. S.; Shao, Zhenfang; Qiu, Bao-Li

2017-04-01

The sweetpotato whitefly Bemisia tabaci (Gennadius) was challenged with different combinations of matrine (insecticide) and Lecanicillium muscarium (entomopathogenic fungus). Our results revealed a synergistic relationship between matrine and L. muscarium on mortality and enzyme activities of B. tabaci. To illustrate the biochemical mechanisms involved in detoxification and immune responses of B. tabaci against both control agents, activities of different detoxifying and antioxidant enzymes were quantified. After combined application of matrine and L. muscarium, activities of carboxylestrease (CarE), glutathione-s-transferase (GSTs) and chitinase (CHI) decreased during the initial infection period. Acetylcholinestrase (AChE) activities increased during the entire experimental period, whereas those of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) decreased during the later infection period. The increased mortality and suppression of enzymatic response of B. tabaci following matrine and L. muscarium application suggests a strong synergistic effect between both agents. The strong synergistic effect is possibly related to the disturbance of acetylcholine balance and changes in AchE activities of the whitefly as both matrine and L. muscarium target insect acetylcholine (Ach) receptors which in turn effects AchE production. Therefore, our results have revealed the complex biochemical processes involved in the synergistic action of matrine and L. muscarium against B. tabaci.

Transgenic Cotton-Fed Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) Affects the Parasitoid Encarsia desantisi Viggiani (Hymenoptera: Aphelinidae) Development.

PubMed

Pessoa, R; Rossi, G D; Busoli, A C

2016-02-01

Cotton cultivars expressing Cry proteins are widely used to control lepidopteran pests. The effects of transgenic plants containing insecticidal Cry proteins on non-target species must be comprehended for a better and rational use of this technology for pest management. We investigated the influence of the Bt cotton cultivars NuOPAL and FM 975 on biological parameters of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), a non-target pest of Bt cotton cultivars and on its parasitoid Encarsia desantisi Viggiani (Hymenoptera: Aphelinidae). The experiments were conducted in a climatized room, and the non-transgenic near isolines were used for rearing whiteflies as control hosts. The effects of the Bt cotton cultivars on the period of embryonic and larval development and the percentage of adult emergence of B. tabaci were assessed. The period required for embryonic, larval, and pupal development and the percentage of emergence and longevity of E. desantisi females were determined using Bt cotton-fed and non-Bt cotton-fed B. tabaci as hosts. Both Bt cotton cultivars resulted in a decrease of approximately 20% of adult emergence of B. tabaci. Differently, an increase of approximately 10% of adult emergence of E. desantisi was observed for parasitoids that used hosts fed with both Bt cotton cultivars. However, female parasitoid longevity decreased when their hosts were fed on Bt cotton cultivars. Our data suggest that the use of Bt cotton cultivars in association with the biological control agent E. desantisi could be functional for the management of B. tabaci in Bt cotton crops.

Transcriptome profiling of the whitefly Bemisia tabaci reveals stage-specific gene expression signatures for thiamethoxam resistance

PubMed Central

Yang, N; Xie, W; Jones, CM; Bass, C; Jiao, X; Yang, X; Liu, B; Li, R; Zhang, Y

2013-01-01

Bemisia tabaci has developed high levels of resistance to many insecticides including the neonicotinoids and there is strong evidence that for some compounds resistance is stage-specific. To investigate the molecular basis of B. tabaci resistance to the neonicotinoid thiamethoxam we used a custom whitefly microarray to compare gene expression in the egg, nymph and adult stages of a thiamethoxam-resistant strain (TH-R) with a susceptible strain (TH-S). Gene ontology and bioinformatic analyses revealed that in all life stages many of the differentially expressed transcripts encoded enzymes involved in metabolic processes and/or metabolism of xenobiotics. Several of these are candidate resistance genes and include the cytochrome P450 CYP6CM1, which has been shown to confer resistance to several neonicotinoids previously, a P450 belonging to the Cytochrome P450s 4 family and a glutathione S-transferase (GST) belonging to the sigma class. Finally several ATP-binding cassette transporters of the ABCG subfamily were highly over-expressed in the adult stage of the TH-R strain and may play a role in resistance by active efflux. Here, we evaluated both common and stage-specific gene expression signatures and identified several candidate resistance genes that may underlie B. tabaci resistance to thiamethoxam. PMID:23889345

Asymmetric consequences of host plant occupation on the competition between the whiteflies Bemisia tabaci cryptic species MEAM1 and Trialeurodes vaporariorum (Hemiptera: Aleyrodidae).

PubMed

Zhang, Gui-Fen; Lövei, Gábor L; Hu, Man; Wan, Fang-Hao

2014-12-01

The two common whitefly species, Bemisia tabaci (Gennadius) MEAM1 and Trialeurodes vaporariorum (Westwood), often co-occur on their host plants. The effect of host plant occupation by one species on later-arriving conspecific individuals or on the other competing species was examined. Resource preoccupied by T. vaporariorum had mostly negative effects on the life history parameters of later-arriving conspecifics. Red-eyed nymph and immature survival of T. vaporariorum decreased when resource was preoccupied by conspecifics, irrespective of the previous occupation scenario. However, resource preoccupied by T. vaporariorum had only minor detrimental effects on the performance of later-arriving B. tabaci MEAM1. In the opposite colonisation sequence, previous occupation by B. tabaci MEAM1 had no significant effects on the life history parameters of later-arriving conspecifics, but severe detrimental effects were observed on the performance of later-arriving T. vaporariorum. Total immature survival of T. vaporariorum decreased in both weak and strong previous occupation situations by B. tabaci MEAM1. The interspecific interactions between B. tabaci MEAM1 and T. vaporariorum were asymmetric, with B. tabaci MEAM1 being the superior competitor. This superiority could partially explain the rapid spread of B. tabaci MEAM1 in China. © 2013 Society of Chemical Industry.

Sensitivity of Bemisia tabaci (Hemiptera: Aleyrodidae) to several new insecticides in China: effects of insecticide type and whitefly species, strain, and stage.

PubMed

Xie, Wen; Liu, Yang; Wang, Shaoli; Wu, Qingjun; Pan, Huipeng; Yang, Xin; Guo, Litao; Zhang, Youjun

2014-01-01

Whitefly biotypes B and Q are the two most damaging members of the Bemisia tabaci (Hemiptera: Aleyrodidae) species complex. Control of B. tabaci (and especially of Q) has been impaired by resistance to commonly used insecticides. To find new insecticides for B. tabaci management in China, we investigated the sensitivity of eggs, larvae, and adults of laboratory strains of B and Q (named Lab-B and Lab-Q) and field strains of Q to several insecticides. For eggs, larvae, and adults of B. tabaci and for six insecticides (cyantraniliprole, chlorantraniliprole, pyriproxyfen, buprofezin, acetamiprid, and thiamethoxam), LC50 values were higher for Lab-Q than for Lab-B; avermectin LC50 values, however, were low for adults of both Lab-Q and Lab-B. Based on the laboratory results, insecticides were selected to test against eggs, larvae, and adults of four field strains of B. tabaci Q. Although the field strains differed in their sensitivity to the insecticides, the eggs and larvae of all strains were highly sensitive to cyantraniliprole, and the adults of all strains were highly sensitive to avermectin. The eggs, larvae, and adults of B. tabaci Q were generally more resistant than those of B. tabaci B to the tested insecticides. B. tabaci Q eggs and larvae were sensitive to cyantraniliprole and pyriproxyfen, whereas B. tabaci Q adults were sensitive to avermectin. Field trials should be conducted with cyantraniliprole, pyriproxyfen, and avermectin for control of B. tabaci Q and B in China. © The Author 2014. Published by Oxford University Press on behalf of the Entomological Society of America.

Members of Bemisia tabaci (Hemiptera: Aleyrodidae) cryptic species and the status of two invasive alien species in the Yunnan Province (China).

PubMed

Hu, Jian; Jiang, Zhi-Lin; Nardi, Francesco; Liu, Yuan-Yuan; Luo, Xiao-Rong; Li, Hong-Xiang; Zhang, Zhong-Kai

2014-01-01

Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex that includes some of the most significant pests of agriculture and horticulture worldwide. To understand the diversity and distribution of B. tabaci cryptic species in Yunnan, a famous biodiversity hotspot in China, a large-scale sampling was conducted from year 2010 to 2013 in 10 prefectures. Mitochondrial cytochrome oxidase I gene sequences were used to identify different cryptic species. Phylogenetic analyses were performed using Bayesian methods to assess the position of a new B. tabaci cryptic species in the context of the B. tabaci diversity in Asia. The survey indicates at least eight B. tabaci cryptic species are present in Yunnan, two invasive (MEAM1 and MED) and six indigenous (China 2, China3, China 4, Asia I, Asia II 1, and Asia II 6), MEAM1, MED, and Asia I being the three predominant cryptic species in Yunnan. Compared with MEAM1, MED has a wider distribution. Based on molecular data, a new cryptic species, here named China 4, was identified that appears to be related to China 1, China 2, and China 3. Future efforts should focus on the interactions between predominant B. tabaci cryptic species and begomoviruses and on the development of effective control strategies. © The Author 2014. Published by Oxford University Press on behalf of the Entomological Society of America.

New putative cryptic species detection and genetic network analysis of Bemisia tabaci (Hempitera: Aleyrodidae) in China based on mitochondrial COI sequences.

PubMed

Hu, Jian; Zhang, Xiaoyun; Jiang, Zhilin; Zhang, Feifei; Liu, Yuanyuan; Li, Zhan; Zhang, Zhongkai

2018-04-01

The whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex and widely distributed throughout tropical and subtropical regions. To understand the B. tabaci cryptic species diversity in China more comprehensively, in the year 2014 and 2016, a large-scale sampling was conducted from the famous biodiversity hotspot of China, Yunnan province. Mitochondrial cytochrome oxidase I gene sequences were used to identify new putative cryptic species. Phylogenetic analyses were performed using Bayesian methods to evaluate the position of new cryptic species in the context of the B. tabaci diversity in Asia. Two new cryptic species, China 5 and Asia V were identified. In total, 19 B. tabaci cryptic species are present in China, two invasive (MED and MEAM1) and 17 indigenous. A new sibling species of B. tabaci was first defined and reported. Based on the mtCOI sequences and haplotype network analyses, the genetic diversity of MED was far higher than MEAM1. We confirmed the exotic MED was originated from the western Mediterranean regions and first invaded into Yunnan, China. The genetic structures of other four indigenous species (Asia I, Asia II 1, Asia II 6, and China 1) with relatively wide distribution ranges in China were also discussed.

The Trouble with MEAM2: Implications of Pseudogenes on Species Delimitation in the Globally Invasive Bemisia tabaci (Hemiptera: Aleyrodidae) Cryptic Species Complex.

PubMed

Tay, Wee Tek; Elfekih, Samia; Court, Leon N; Gordon, Karl H J; Delatte, Hélène; De Barro, Paul J

2017-10-01

Molecular species identification using suboptimal PCR primers can over-estimate species diversity due to coamplification of nuclear mitochondrial (NUMT) DNA/pseudogenes. For the agriculturally important whitefly Bemisia tabaci cryptic pest species complex, species identification depends primarily on characterization of the mitochondrial DNA cytochrome oxidase I (mtDNA COI) gene. The lack of robust PCR primers for the mtDNA COI gene can undermine correct species identification which in turn compromises management strategies. This problem is identified in the B. tabaci Africa/Middle East/Asia Minor clade which comprises the globally invasive Mediterranean (MED) and Middle East Asia Minor I (MEAM1) species, Middle East Asia Minor 2 (MEAM2), and the Indian Ocean (IO) species. Initially identified from the Indian Ocean island of Réunion, MEAM2 has since been reported from Japan, Peru, Turkey and Iraq. We identified MEAM2 individuals from a Peruvian population via Sanger sequencing of the mtDNA COI gene. In attempting to characterize the MEAM2 mitogenome, we instead characterized mitogenomes of MEAM1. We also report on the mitogenomes of MED, AUS, and IO thereby increasing genomic resources for members of this complex. Gene synteny (i.e., same gene composition and orientation) was observed with published B. tabaci cryptic species mitogenomes. Pseudogene fragments matching MEAM2 partial mtDNA COI gene exhibited low frequency single nucleotide polymorphisms that matched low copy number DNA fragments (<3%) of MEAM1 genomes, whereas presence of internal stop codons, loss of expected stop codons and poor primer annealing sites, all suggested MEAM2 as a pseudogene artifact and so not a real species. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Inoculation of tomato plants with rhizobacteria enhances the performance of the phloem-feeding insect Bemisia tabaci

PubMed Central

Shavit, Roee; Ofek-Lalzar, Maya; Burdman, Saul; Morin, Shai

2013-01-01

In their natural environment, plants experience multiple biotic interactions and respond to this complexity in an integrated manner. Therefore, plant responses to herbivory are flexible and depend on the context and complexity in which they occur. For example, plant growth promoting rhizobacteria (PGPR) can enhance plant growth and induce resistance against microbial pathogens and herbivorous insects by a phenomenon termed induced systemic resistance (ISR). In the present study, we investigated the effect of tomato (Solanum lycopersicum) pre-inoculation with the PGPR Pseudomonas fluorescens WCS417r, on the performance of the generalist phloem-feeding insect Bemisia tabaci. Based on the ability of P. fluorescens WCS417r to prime for ISR against generalists chewing insects and necrotrophic pathogens, we hypothesized that pre-inoculated plants will strongly resist B. tabaci infestation. In contrast, we discovered that the pre-inoculation treatment increased the tomato plant suitability for B. tabaci which was emphasized both by faster developmental rate and higher survivability of nymph stages on pre-inoculated plants. Our molecular and chemical analyses suggested that the phenomenon is likely to be related to: (I) the ability of the bacteria to reduce the activity of the plant induced defense systems; (II) a possible manipulation by P. fluorescens of the plant quality (in terms of suitability for B. tabaci) through an indirect effect on the rhizosphere bacterial community. The contribution of our study to the pattern proposed for other belowground rhizobacteria and mycorrhizal fungi and aboveground generalist phloem-feeders is discussed. PMID:23964283

Pre shipping dip treatments using soap, natural oils, and Isaria fumosorosea: potential biopesticides for mitigating the spread of whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) invasive insects on ornamental plants

USDA-ARS?s Scientific Manuscript database

The whitefly Bemisia tabaci (Hemiptera: Aleyodidae) is an invasive insect pest affecting different crops including vegetables, fruits, cereals, and ornamentals. The efficacy of some products such as commercial soap, natural oils and Preferal® (based on the entomopathogenic fungus Isaria fumosorosea ...

Multilocus approach to clarify species status and the divergence history of the Bemisia tabaci (Hemiptera: Aleyrodidae) species complex.

PubMed

Hsieh, Chia-Hung; Ko, Chiun-Cheng; Chung, Cheng-Han; Wang, Hurng-Yi

2014-07-01

The sweet potato whitefly, Bemisia tabaci, is a highly differentiated species complex. Despite consisting of several morphologically indistinguishable entities and frequent invasions on all continents with important associated economic losses, the phylogenetic relationships, species status, and evolutionary history of this species complex is still debated. We sequenced and analyzed one mitochondrial and three single-copy nuclear genes from 9 of the 12 genetic groups of B. tabaci and 5 closely related species. Bayesian species delimitation was applied to investigate the speciation events of B. tabaci. The species statuses of the different genetic groups were strongly supported under different prior settings and phylogenetic scenarios. Divergence histories were estimated by a multispecies coalescence approach implemented in (*)BEAST. Based on mitochondrial locus, B. tabaci was originated 6.47 million years ago (MYA). Nevertheless, the time was 1.25MYA based on nuclear loci. According to the method of approximate Bayesian computation, this difference is probably due to different degrees of migration among loci; i.e., although the mitochondrial locus had differentiated, gene flow at nuclear loci was still possible, a scenario similar to parapatric mode of speciation. This is the first study in whiteflies using multilocus data and incorporating Bayesian coalescence approaches, both of which provide a more biologically realistic framework for delimiting species status and delineating the divergence history of B. tabaci. Our study illustrates that gene flow during species divergence should not be overlooked and has a great impact on divergence time estimation. Copyright © 2014 Elsevier Inc. All rights reserved.

Transovarial Transmission of Rickettsia spp. and Organ-Specific Infection of the Whitefly Bemisia tabaci

PubMed Central

Brumin, Marina; Levy, Maggie

2012-01-01

The whitefly Bemisia tabaci is a cosmopolitan insect pest that harbors Portiera aleyrodidarum, the primary obligatory symbiotic bacterium, and several facultative secondary symbionts. Secondary symbionts in B. tabaci are generally associated with the bacteriome, ensuring their vertical transmission; however, Rickettsia is an exception and occupies most of the body cavity, except the bacteriome. The mode of Rickettsia transfer between generations and its subcellular localization in insect organs have not been investigated. Using electron and fluorescence microscopy, we show that Rickettsia infects the digestive, salivary, and reproductive organs of the insect; however, it was not observed in the bacteriome. Rickettsia invades the oocytes during early developmental stages and resides in follicular cells and cytoplasm; it is mostly excluded when the egg matures; however, some bacterial cells remain in the egg, ensuring their transfer to subsequent generations. Rickettsia was localized to testicles and the spermatheca, suggesting a horizontal transfer between males and females during mating. The bacterium was further observed at large amounts in midgut cells, concentrating in vacuole-like structures, and was located in the hemolymph, specifically at exceptionally large amounts around bacteriocytes and in fat bodies. Organs further infected by Rickettsia included the primary salivary glands and stylets, sites of possible secretion of the bacterium outside the whitefly body. The close association between Rickettsia and the B. tabaci digestive system might be important for digestive purposes. The vertical transmission of Rickettsia to subsequent generations occurs via the oocyte and not, like other secondary symbionts, the bacteriome. PMID:22660706

Effect of starvation on vein preference of whitefly (Bemisia tabaci) on chilli as host plant

NASA Astrophysics Data System (ADS)

Siti Sakinah, A.; Mohamad Roff M., N.; Idris, A. B.

2014-09-01

The whitefly, Bemisia tabaci (Gennadius), is a cosmopolitan pest of horticultural crops. It caused serious damaged to the plants by feeding on plant saps as direct damage and transmit virus as indirect damage. Vein preferences of both female and male whitefly (WF) on chilli plant were recorded using Dinolite, a portable microscope, under laboratory conditions. WF adults of both sexes were starved for 2 and 4 hours before used for observation while no starvation for control individual (treatment). Results showed that both female and male preferred to feed on secondary veins rather than lamina, midrib and vein. From the result of whitefly preferred target site, hopefully this information will help to improve control tactics in WF management.

Elevated O3 and TYLCV Infection Reduce the Suitability of Tomato as a Host for the Whitefly Bemisia tabaci

PubMed Central

Cui, Hongying; Sun, Yucheng; Chen, Fajun; Zhang, Youjun; Ge, Feng

2016-01-01

The effects of elevated atmospheric ozone (O3) levels on herbivorous insects have been well studied, but little is known about the combined effects of elevated O3 and virus infection on herbivorous insect performance. Using open-top chambers in the field, we determined the effects of elevated O3 and Tomato yellow leaf curl virus (TYLCV) infection on wild-type (Wt) tomato and 35S tomato (jasmonic acid (JA) defense-enhanced genotype) in association with whitefly, Bemisia tabaci Gennadius biotype B. Elevated O3 and TYLCV infection, alone and in combination, significantly reduced the contents of soluble sugars and free amino acids, increased the contents of total phenolics and condensed tannins, and increased salicylic acid (SA) content and the expression of SA-related genes in leaves. The JA signaling pathway was upregulated by elevated O3, but downregulated by TYLCV infection and O3 + TYLCV infection. Regardless of plant genotype, elevated O3, TYLCV infection, or O3 + TYLCV infection significantly decreased B. tabaci fecundity and abundance. These results suggest that elevated O3 and TYLCV infection, alone and in combination, reduce the nutrients available for B. tabaci, increase SA content and SA-related gene expression, and increase secondary metabolites, resulting in decreases in fecundity and abundance of B. tabaci in both tomato genotypes. PMID:27916792

Single basal application of thiacloprid for the integrated management of Meloidogyne incognita and Bemisia tabaci in tomato crops

NASA Astrophysics Data System (ADS)

Dong, Sa; Ren, Xiaofen; Zhang, Dianli; Ji, Xiaoxue; Wang, Kaiyun; Qiao, Kang

2017-01-01

Tomato growers commonly face heavy nematode (Meloidogyne incognita) and whitefly (B-biotype Bemisia tabaci) infestations, and previous studies demonstrated that thiacloprid could be used to control M. incognita and B. tabaci in cucumber. However, the efficacy of a single basal application of thiacloprid to control both pests and its effect on yield in tomato remains unknown. In this study, the potential of thiacloprid application to the soil for the integrated control of M. incognita and B. tabaci in tomato was evaluated in the laboratory and the field. Laboratory tests showed that thiacloprid was highly toxic to whitefly adults and eggs with an average lethal concentration 50 (LC50) of 14.7 and 62.2 mg ai L-1, respectively, and the LC50 of thiacloprid for nematode J2s and eggs averaged 36.2 and 70.4 mg ai L-1, respectively. In field trials, when thiacloprid was applied to the soil at 7.5, 15 and 30 kg ha-1 in two consecutive years, whitefly adults decreased by 37.8-75.4% within 60 days of treatment, and the root-galling index was reduced by 31.8-85.2%. Optimum tomato plant growth and maximum yields were observed in the 15 kg ha-1 treatment. The results indicated that a single basal application of thiacloprid could control M. incognita and B. tabaci and enhance tomato growth and yield.

Single basal application of thiacloprid for the integrated management of Meloidogyne incognita and Bemisia tabaci in tomato crops

PubMed Central

Dong, Sa; Ren, Xiaofen; Zhang, Dianli; Ji, Xiaoxue; Wang, Kaiyun; Qiao, Kang

2017-01-01

Tomato growers commonly face heavy nematode (Meloidogyne incognita) and whitefly (B-biotype Bemisia tabaci) infestations, and previous studies demonstrated that thiacloprid could be used to control M. incognita and B. tabaci in cucumber. However, the efficacy of a single basal application of thiacloprid to control both pests and its effect on yield in tomato remains unknown. In this study, the potential of thiacloprid application to the soil for the integrated control of M. incognita and B. tabaci in tomato was evaluated in the laboratory and the field. Laboratory tests showed that thiacloprid was highly toxic to whitefly adults and eggs with an average lethal concentration 50 (LC50) of 14.7 and 62.2 mg ai L−1, respectively, and the LC50 of thiacloprid for nematode J2s and eggs averaged 36.2 and 70.4 mg ai L−1, respectively. In field trials, when thiacloprid was applied to the soil at 7.5, 15 and 30 kg ha−1 in two consecutive years, whitefly adults decreased by 37.8–75.4% within 60 days of treatment, and the root-galling index was reduced by 31.8–85.2%. Optimum tomato plant growth and maximum yields were observed in the 15 kg ha−1 treatment. The results indicated that a single basal application of thiacloprid could control M. incognita and B. tabaci and enhance tomato growth and yield. PMID:28120937

Salicylic acid is required for Mi-1-mediated resistance of tomato to whitefly Bemisia tabaci, but not for basal defense to this insect pest.

PubMed

Rodríguez-Álvarez, C I; López-Climent, M F; Gómez-Cadenas, A; Kaloshian, I; Nombela, G

2015-10-01

Plant defense to pests or pathogens involves global changes in gene expression mediated by multiple signaling pathways. A role for the salicylic acid (SA) signaling pathway in Mi-1-mediated resistance of tomato (Solanum lycopersicum) to aphids was previously identified and its implication in the resistance to root-knot nematodes is controversial, but the importance of SA in basal and Mi-1-mediated resistance of tomato to whitefly Bemisia tabaci had not been determined. SA levels were measured before and after B. tabaci infestation in susceptible and resistant Mi-1-containing tomatoes, and in plants with the NahG bacterial transgene. Tomato plants of the same genotypes were also screened with B. tabaci (MEAM1 and MED species, before known as B and Q biotypes, respectively). The SA content in all tomato genotypes transiently increased after infestation with B. tabaci albeit at variable levels. Whitefly fecundity or infestation rates on susceptible Moneymaker were not significantly affected by the expression of NahG gene, but the Mi-1-mediated resistance to B. tabaci was lost in VFN NahG plants. Results indicated that whiteflies induce both SA and jasmonic acid accumulation in tomato. However, SA has no role in basal defense of tomato against B. tabaci. In contrast, SA is an important component of the Mi-1-mediated resistance to B. tabaci in tomato.

Use of fluorescence, a novel technique to determine reduction in Bemisia tabaci (Hemiptera: Aleyrodidae) nymph feeding when exposed to Benevia and other insecticides.

PubMed

Cameron, Rachel; Lang, Edward B; Annan, I Billy; Portillo, Hector E; Alvarez, Juan M

2013-04-01

The sweet potato whitefly, Bemisia tabaci (Gennadius), is an economically important pest in the United States and other countries. Growers in many places rely on the use of insecticides to reduce populations of B. tabaci. However, insecticides may take a few days to cause B. tabaci mortality and some do not reduce feeding before death. Earlier reduction of feeding of whiteflies would decrease the physiological effects on plants, reduce the production of sooty mold and potentially reduce the transmission of viruses. Measuring the reduction in feeding after the exposure of B. tabaci to an insecticide has proven difficult. This series of laboratory experiments demonstrate the usefulness of fluorescence in determining B. tabaci feeding cessation. Fluorescein sodium salt is systemically transported in the xylem from the roots to the plant leaves and absorbed by B. tabaci nymphs feeding on these plants. Nymphs start fluorescing shortly after the cotton plant root system is submerged in the fluorescein sodium salt. Using this novel technique, the effect of three insecticides with different modes of action, cyantraniliprole, imidacloprid, and spirotetramat on B. tabaci was evaluated and compared to determine reduction in feeding. Results indicate that B. tabaci nymphs feeding on a plant treated with Benevia have a significant reduction of feeding when compared with nymphs feeding on plants treated with imidacloprid or spirotetramat. Both Benevia and spirotetramat caused significant nymphal mortality by 48 h after exposure. This novel technique will be useful to demonstrate the feeding cessation or reduction in feeding produced by different insecticides in several sucking insect groups.

Qualitative and Quantitative Differences in Herbivore-Induced Plant Volatile Blends from Tomato Plants Infested by Either Tuta absoluta or Bemisia tabaci.

PubMed

Silva, Diego B; Weldegergis, Berhane T; Van Loon, Joop J A; Bueno, Vanda H P

2017-01-01

Plants release a variety of volatile organic compounds that play multiple roles in the interactions with other plants and animals. Natural enemies of plant-feeding insects use these volatiles as cues to find their prey or host. Here, we report differences between the volatile blends of tomato plants infested with the whitefly Bemisia tabaci or the tomato borer Tuta absoluta. We compared the volatile emission of: (1) clean tomato plants; (2) tomato plants infested with T. absoluta larvae; and (3) tomato plants infested with B. tabaci adults, nymphs, and eggs. A total of 80 volatiles were recorded of which 10 occurred consistently only in the headspace of T. absoluta-infested plants. Many of the compounds detected in the headspace of the two herbivory treatments were emitted at different rates. Plants damaged by T. absoluta emitted at least 10 times higher levels of many compounds compared to plants damaged by B. tabaci and intact plants. The multivariate separation of T. absoluta-infested plants from those infested with B. tabaci was due largely to the chorismate-derived compounds as well as volatile metabolites of C 18 -fatty acids and branched chain amino acids that had higher emission rates from T. absoluta-infested plants, whereas the cyclic sesquiterpenes α- and β-copaene, valencene, and aristolochene were emitted at significantly higher levels from B. tabaci-infested plants. Our findings imply that feeding by T. absoluta and B. tabaci induced emission of volatile blends that differ quantitatively and qualitatively, providing a chemical basis for the recently documented behavioral discrimination by two generalist predatory mirid species, natural enemies of T. absoluta and B. tabaci employed in biological control.

Monitoring changes in Bemisia tabaci (Hemiptera: Aleyrodidae) susceptibility to neonicotinoid insecticides in Arizona and California.

PubMed

Castle, S J; Prabhaker, N

2013-06-01

Bemisia tabaci (Gennadius) biotype B is a highly prolific and polyphagous whitefly that established in much of North America during the 1980s. Neonicotinoid insecticides have been fundamental in regaining control over outbreak populations of B. tabaci, but resistance threatens their sustainability. Susceptibility of B. tabaci in the southwestern United States to four neonicotinoid insecticides varied considerably across populations within each year over a 3 yr period. Using a variability ratio of highest LC50 to lowest LC50 in field-collected whitefly adults from Arizona and California, the ranges of LC50(s) across all tests within compounds were highest to imidacloprid and lowest to thiamethoxam. Patterns of susceptibility were similar among all four neonicotinoid insecticides, but the greater variability in responses to imidacloprid and significantly higher LC50(s) attained indicated higher resistance levels to imidacloprid in all field populations. Further evidence of differential toxicities of neonicotinoids was observed in multiple tests of dinotefuran against imidacloprid-resistant lab strains that yielded significant differences in the LC50(s) of dinotefuran and imidacloprid in simultaneous bioassays. To test the possibility that resistance expression in field-collected insects was sometimes masked by stressful conditions, field strains cultured in a greenhouse without insecticide exposure produced significantly higher LC50(s) to all neonicotinoids compared with LC50(s) attained directly from the field. In harsh climates such as the American southwest, resistance expression in field-collected test insects may be strongly influenced by environmental stresses such as high temperatures, overcrowding, and declining host plant quality.

Role of the Insect Supervectors Bemisia tabaci and Frankliniella occidentalis in the Emergence and Global Spread of Plant Viruses.

PubMed

Gilbertson, Robert L; Batuman, Ozgur; Webster, Craig G; Adkins, Scott

2015-11-01

Emergence of insect-transmitted plant viruses over the past 10-20 years has been disproportionately driven by two so-called supervectors: the whitefly, Bemisia tabaci, and the Western flower thrips, Frankliniella occidentalis. High rates of reproduction and dispersal, extreme polyphagy, and development of insecticide resistance, together with human activities, have made these insects global pests. These supervectors transmit a diversity of plant viruses by different mechanisms and mediate virus emergence through local evolution, host shifts, mixed infections, and global spread. Associated virus evolution involves reassortment, recombination, and component capture. Emergence of B. tabaci-transmitted geminiviruses (begomoviruses), ipomoviruses, and torradoviruses has led to global disease outbreaks as well as multiple paradigm shifts. Similarly, F. occidentalis has mediated tospovirus host shifts and global dissemination and the emergence of pollen-transmitted ilarviruses. The plant virus-supervector interaction offers exciting opportunities for basic research and global implementation of generalized disease management strategies to reduce economic and environmental impacts.

Fitness costs associated with infections of secondary endosymbionts in the cassava whitefly species Bemisia tabaci.

PubMed

Ghosh, Saptarshi; Bouvaine, Sophie; Richardson, Simon C W; Ghanim, Murad; Maruthi, M N

2018-01-01

We investigated the dual effects of bacterial infections and diseased cassava plants on the fitness and biology of the Bemisia tabaci infesting cassava in Africa. Isofemale B. tabaci colonies of sub-Saharan Africa 1-subgroup 3 (SSA1-SG3), infected with two secondary endosymbiotic bacteria Arsenophonus and Rickettsia (AR+) and those free of AR infections (AR-), were compared for fitness parameters on healthy and East African cassava mosaic virus -Uganda variant (EACMV-UG)-infected cassava plants. The whitefly fecundity and nymph development was not affected by bacterial infections or the infection of cassava by the virus. However, emergence of adults from nymphs was 50 and 17% higher by AR- on healthy and virus-infected plants, respectively, than AR+ flies. Development time of adults also was 10 days longer in AR+ than AR-. The whiteflies were further compared for acquisition and retention of EACMV-UG. Higher proportion of AR- acquired (91.8%) and retained (87.6%) the virus than AR+ (71.8, 61.2%, respectively). Similarly, the AR- flies retained higher quantities of virus (~ninefold more) than AR+. These results indicated that bacteria-free whiteflies were superior and better transmitters of EACMV-UG, as they had higher adult emergence, quicker life cycle and better virus retention abilities than those infected with bacteria.

Biological Invasions of Geminiviruses: Case Study of TYLCV and Bemisia tabaci in Reunion Island

PubMed Central

Péréfarres, Frédéric; Thierry, Magali; Becker, Nathalie; Lefeuvre, Pierre; Reynaud, Bernard; Delatte, Hélène; Lett, Jean-Michel

2012-01-01

In the last 20 years, molecular ecology approaches have proven to be extremely useful to identify and assess factors associated with viral emerging diseases, particularly in economically and socially important tropical crops such as maize (maize streak disease) and cassava (cassava mosaic disease). Molecular ecology approaches were applied in Reunion Island to analyze the epidemic of tomato yellow leaf curl disease, which has been affecting the island since the end of the 1990s. Before the invasive biotype B (currently known as Middle East-Asia Minor 1 cryptic species) of Bemisia tabaci spread across the world, Reunion Island (South West Indian Ocean) only hosted an indigenous biotype of B. tabaci, Ms (currently known as Indian Ocean cryptic species). Wild hybrids between invasive and indigenous species were subsequently characterized over multiple generations. Endosymbiont analysis of the hybrid population indicated that matings were non-random. Similarly, while no indigenous begomoviruses have ever been reported on Reunion Island, the two main strains of one of the most damaging and emerging plant viruses in the world, the Mild and Israel strains of the Tomato yellow leaf curl virus (TYLCV-Mld and TYLCV-IL), were introduced in 1997 and 2004 respectively. While these introductions extensively modified the agricultural landscape of Reunion Island, they also provided an invaluable opportunity to study the ecological and genetic mechanisms involved in biological invasion and competition. PMID:23235470

Challenges with managing insecticide resistance in agricultural pests, exemplisfied by the whitefly Bemisia tabaci

PubMed Central

Denholm, I.

1998-01-01

For many key agricultural pests, successful management of insecticide resistance depends not only on modifying the way that insecticides are deployed, but also on reducing the total number of treatments applied. Both approaches benefit from a knowledge of the biological characteristics of pests that promote or may retard the development of resistance. For the whitefly Bemisia tabaci (Gennadius), these factors include a haplodiploid breeding system that encourages the rapid selection and fixation of resistance genes, its breeding cycle on a succession of treated or untreated hosts, and its occurrence on and dispersal from high-value crops in greenhouses and glasshouses. These factors, in conjunction with often intensive insecticide use, have led to severe and widespread resistance that now affects several novel as well as conventional control agents. Resistance-management strategies implemented on cotton in Israel, and subsequently in south-western USA, have nonetheless so far succeeded in arresting the resistance treadmill in B. tabaci through a combination of increased chemical diversity, voluntary or mandatory restrictions on the use of key insecticides, and careful integration of chemical control with other pest-management options. In both countries, the most significant achievement has been a dramatic reduction in the number of insecticide treatments applied against whiteflies on cotton, increasing the prospect of sustained use of existing and future insecticides.

Diversity and Distribution of Cryptic Species of the Bemisia tabaci (Hemiptera: Aleyrodidae) complex in Pakistan.

PubMed

Masood, Mariyam; Amin, Imran; Hassan, Ishtiaq; Mansoor, Shahid; Brown, Judith K; Briddon, Rob W

2017-12-05

Bemisia tabaci (Gennadius; Hempitera: Aleyrodidae) is considered to be a cryptic (sibling) species complex, the members of which exhibit morphological invariability while being genetically and behaviorally distinct. Members of the complex are agricultural pests that cause direct damage by feeding on plants, and indirectly by transmitting viruses that cause diseases leading to reduced crop yield and quality. In Pakistan, cotton leaf curl disease, caused by multiple begomovirus species, is the most economically important viral disease of cotton. In the study outlined here, the diversity and geographic distribution of B. tabaci cryptic species was investigated by analyzing a taxonomically informative fragment of the mitochondrial cytochrome c oxidase 1 gene (mtCOI-3'). The mtCOI-3' sequence was determined for 285 adult whiteflies and found to represent six cryptic species, the most numerous being Asia II-1 and Middle East Asia Minor 1 (MEAM-1), the later also referred to as the B-biotype, which was previously thought to be confined to Sindh province but herein, was also found to be present in the Punjab province. The endemic Asia I was restricted to Sindh province, while an individual in the Asia II-8 was identified in Pakistan for the first time. Also for the first time, samples were collected from northwestern Pakistan and Asia II-1 was identified. Results indicate that in Pakistan the overall diversity of B. tabaci cryptic species is high and, based on comparisons with findings from previous studies, the distribution is dynamic. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

DNA Barcoding of Bemisia tabaci Complex (Hemiptera: Aleyrodidae) Reveals Southerly Expansion of the Dominant Whitefly Species on Cotton in Pakistan

PubMed Central

Ashfaq, Muhammad; Hebert, Paul D. N.; Mirza, M. Sajjad; Khan, Arif M.; Mansoor, Shahid; Shah, Ghulam S.; Zafar, Yusuf

2014-01-01

Background Although whiteflies (Bemisia tabaci complex) are an important pest of cotton in Pakistan, its taxonomic diversity is poorly understood. As DNA barcoding is an effective tool for resolving species complexes and analyzing species distributions, we used this approach to analyze genetic diversity in the B. tabaci complex and map the distribution of B. tabaci lineages in cotton growing areas of Pakistan. Methods/Principal Findings Sequence diversity in the DNA barcode region (mtCOI-5′) was examined in 593 whiteflies from Pakistan to determine the number of whitefly species and their distributions in the cotton-growing areas of Punjab and Sindh provinces. These new records were integrated with another 173 barcode sequences for B. tabaci, most from India, to better understand regional whitefly diversity. The Barcode Index Number (BIN) System assigned the 766 sequences to 15 BINs, including nine from Pakistan. Representative specimens of each Pakistan BIN were analyzed for mtCOI-3′ to allow their assignment to one of the putative species in the B. tabaci complex recognized on the basis of sequence variation in this gene region. This analysis revealed the presence of Asia II 1, Middle East-Asia Minor 1, Asia 1, Asia II 5, Asia II 7, and a new lineage “Pakistan”. The first two taxa were found in both Punjab and Sindh, but Asia 1 was only detected in Sindh, while Asia II 5, Asia II 7 and “Pakistan” were only present in Punjab. The haplotype networks showed that most haplotypes of Asia II 1, a species implicated in transmission of the cotton leaf curl virus, occurred in both India and Pakistan. Conclusions DNA barcodes successfully discriminated cryptic species in B. tabaci complex. The dominant haplotypes in the B. tabaci complex were shared by India and Pakistan. Asia II 1 was previously restricted to Punjab, but is now the dominant lineage in southern Sindh; its southward spread may have serious implications for cotton plantations in this region. PMID

DNA barcoding of Bemisia tabaci complex (Hemiptera: Aleyrodidae) reveals southerly expansion of the dominant whitefly species on cotton in Pakistan.

PubMed

Ashfaq, Muhammad; Hebert, Paul D N; Mirza, M Sajjad; Khan, Arif M; Mansoor, Shahid; Shah, Ghulam S; Zafar, Yusuf

2014-01-01

Although whiteflies (Bemisia tabaci complex) are an important pest of cotton in Pakistan, its taxonomic diversity is poorly understood. As DNA barcoding is an effective tool for resolving species complexes and analyzing species distributions, we used this approach to analyze genetic diversity in the B. tabaci complex and map the distribution of B. tabaci lineages in cotton growing areas of Pakistan. Sequence diversity in the DNA barcode region (mtCOI-5') was examined in 593 whiteflies from Pakistan to determine the number of whitefly species and their distributions in the cotton-growing areas of Punjab and Sindh provinces. These new records were integrated with another 173 barcode sequences for B. tabaci, most from India, to better understand regional whitefly diversity. The Barcode Index Number (BIN) System assigned the 766 sequences to 15 BINs, including nine from Pakistan. Representative specimens of each Pakistan BIN were analyzed for mtCOI-3' to allow their assignment to one of the putative species in the B. tabaci complex recognized on the basis of sequence variation in this gene region. This analysis revealed the presence of Asia II 1, Middle East-Asia Minor 1, Asia 1, Asia II 5, Asia II 7, and a new lineage "Pakistan". The first two taxa were found in both Punjab and Sindh, but Asia 1 was only detected in Sindh, while Asia II 5, Asia II 7 and "Pakistan" were only present in Punjab. The haplotype networks showed that most haplotypes of Asia II 1, a species implicated in transmission of the cotton leaf curl virus, occurred in both India and Pakistan. DNA barcodes successfully discriminated cryptic species in B. tabaci complex. The dominant haplotypes in the B. tabaci complex were shared by India and Pakistan. Asia II 1 was previously restricted to Punjab, but is now the dominant lineage in southern Sindh; its southward spread may have serious implications for cotton plantations in this region.

Bemisia tabaci MED Population Density as Affected by Rootstock-Modified Leaf Anatomy and Amino Acid Profiles in Hydroponically Grown Tomato

PubMed Central

Žanić, Katja; Dumičić, Gvozden; Mandušić, Marija; Vuletin Selak, Gabriela; Bočina, Ivana; Urlić, Branimir; Ljubenkov, Ivica; Bučević Popović, Viljemka; Goreta Ban, Smiljana

2018-01-01

Bemisia tabaci is one of the most devastating pests in tomato greenhouse production. Insecticide resistance management for B. tabaci requires a novel approach that maximizes non-chemical methods for pest control. The aim of this study was to test the effects of rootstocks on B. tabaci populations in hydroponically grown tomato plants. In order to contribute to the better understanding of the mechanisms defining the attractiveness of plant to the aerial pest, the effects of rootstocks on leaf anatomy and the amino acid composition of phloem sap were assessed. A two-factorial experimental design was adopted using cultivars (rootstock cultivars and Clarabella) grown as either non-grafted or grafted with cultivar Clarabella as a scion. The rootstock cultivars included Arnold, Buffon, Emperador, and Maxifort. A reduction in B. tabaci density was observed using all rootstock cultivars. The number of adult individuals per leaf was 2.7–5.4 times lower on rootstock cultivars than on Clarabella. The number of large nymphs per square centimeter was at least 24% higher on non–grafted Clarabella compared with all other treatments. The leaf lamina thickness and mesophyll thickness were lower in self-grafted Clarabella than in non-grafted or in one grafted on rootstock cultivars; however, the extent of this reduction depended on the rootstock. The leaves with thinner laminae were generally less attractive to B. tabaci. Eighteen amino acids were detected in the exudates of phloem sap. In all treatments, the most abundant amino acid was γ-aminobutyric acid (GABA), followed by proline, serine, alanine, and histidine. The scion cultivar Clarabella was the most attractive to B. tabaci and had a higher content of leucine than did rootstock cultivars, and a higher content of lysine compared to Buffon and Maxifort. The features modified by rootstock such are changes in leaf anatomy can affect the attractiveness of plants to B. tabaci. Thus, the grafting of tomato could constitute a

Analysis of Species, Subgroups, and Endosymbionts of Bemisia tabaci (Hemiptera: Aleyrodidae) From Southwestern Cotton Fields in Turkey.

PubMed

Karut, Kamil; Mete Karaca, M; Döker, Ismail; Kazak, Cengiz

2017-08-01

Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is one of the most important insect pests worldwide including Turkey. Although there are substantial data regarding species composition of Turkish B. tabaci populations, the situation is still not clear and further investigations are needed. Therefore, in this study, species and subgroups of B. tabaci collected from cotton fields in southwestern part of Turkey (Antalya, Aydın, Denizli, and Muğla) were determined using microsatellite analysis, AluI-based mtCOI polymerase chain reaction-random length polymorphism, and sequencing. Secondary endosymbionts were also determined using diagnostic species-specific PCR. Middle East Asia Minor 1 (MEAM1), Mediterranean (MED) Q1, and MED Q2 were the species and subgroups found in this study. The MED species (85.3%) were found to be more dominant than MEAM1. Species status of B. tabaci varied depending on the location. Although all samples collected from Aydın were found to be Q1, three species and subgroups were found in Muğla. Secondary endosymbionts varied according to species and subgroups. Arsenophonus was found only from Q2, while Hamiltonella was detected in MEAM1 and Q1. In addition, high Rickettsia and low Wolbachia infections were detected in MEAM1 and Q1 populations, respectively. In conclusion, for the first time, we report the presence and symbiotic communities of Q1 from Turkey. We also found that the symbiont complement of the Q1 is more congruent with Q1 from Greece than other regions of the world, which may have some interesting implications for movement of this invasive subgroup. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Implication of the Whitefly Bemisia tabaci Cyclophilin B Protein in the Transmission of Tomato yellow leaf curl virus

PubMed Central

Kanakala, Surapathrudu; Ghanim, Murad

2016-01-01

Tomato yellow leaf curl virus (TYLCV) is a single-stranded (ssDNA) begomoviruses that causes severe damage to tomato and several other crops worldwide. TYLCV is exclusively transmitted by the sweetpotato whitefly, Bemisia tabaci in a persistent circulative and propagative manner. Previous studies have shown that the transmission, retention, and circulation of TYLCV in its vector involves interaction with insect and endosymbiont proteins, which aid in the transmission of the virus, or have a protective role in response to the presence of the virus in the insect body. However, only a low number of such proteins have been identified. Here, the role of B. tabaci Cyclophilin B (CypB) in the transmission of TYLCV protein was investigated. Cyclophilins are a large family of cellular prolyl isomerases that have many molecular roles including facilitating protein-protein interactions in the cell. One cyclophilin protein has been implicated in aphid-luteovirus interactions. We demonstrate that the expression of CypB from B. tabaci is altered upon TYLCV acquisition and retention. Further experiments used immunocapture-PCR and co-immunolocalization and demonstrated a specific interaction and colocalization between CypB and TYLCV in the the midgut, eggs, and salivary glands. Membrane feeding of anti-CypB antibodies and TYLCV-infected plants showed a decrease in TYLCV transmission, suggesting a critical role that CypB plays in TYLCV transmission. Further experiments, which used membrane feeding with the CypB inhibitor Cyclosporin A showed decrease in CypB-TYLCV colocalization in the midgut and virus transmission. Altogether, our results indicate that CypB plays an important role in TYLCV transmission by B. tabaci. PMID:27895657

Implication of the Whitefly Bemisia tabaci Cyclophilin B Protein in the Transmission of Tomato yellow leaf curl virus.

PubMed

Kanakala, Surapathrudu; Ghanim, Murad

2016-01-01

Tomato yellow leaf curl virus (TYLCV) is a single-stranded (ssDNA) begomoviruses that causes severe damage to tomato and several other crops worldwide. TYLCV is exclusively transmitted by the sweetpotato whitefly, Bemisia tabaci in a persistent circulative and propagative manner. Previous studies have shown that the transmission, retention, and circulation of TYLCV in its vector involves interaction with insect and endosymbiont proteins, which aid in the transmission of the virus, or have a protective role in response to the presence of the virus in the insect body. However, only a low number of such proteins have been identified. Here, the role of B. tabaci Cyclophilin B (CypB) in the transmission of TYLCV protein was investigated. Cyclophilins are a large family of cellular prolyl isomerases that have many molecular roles including facilitating protein-protein interactions in the cell. One cyclophilin protein has been implicated in aphid-luteovirus interactions. We demonstrate that the expression of CypB from B. tabaci is altered upon TYLCV acquisition and retention. Further experiments used immunocapture-PCR and co-immunolocalization and demonstrated a specific interaction and colocalization between CypB and TYLCV in the the midgut, eggs, and salivary glands. Membrane feeding of anti-CypB antibodies and TYLCV-infected plants showed a decrease in TYLCV transmission, suggesting a critical role that CypB plays in TYLCV transmission. Further experiments, which used membrane feeding with the CypB inhibitor Cyclosporin A showed decrease in CypB-TYLCV colocalization in the midgut and virus transmission. Altogether, our results indicate that CypB plays an important role in TYLCV transmission by B. tabaci .

Only a minority of broad-range detoxification genes respond to a variety of phytotoxins in generalist Bemisia tabaci species

PubMed Central

Halon, Eyal; Eakteiman, Galit; Moshitzky, Pnina; Elbaz, Moshe; Alon, Michal; Pavlidi, Nena; Vontas, John; Morin, Shai

2015-01-01

Generalist insect can utilize two different modes for regulating their detoxification genes, the constitutive mode and the induced mode. Here, we used the Bemisia tabaci sibling species MEAM1 and MED, as a model system for studying constitutive and induced detoxification resistance and their associated tradeoffs. B. tabaci adults were allowed to feed through membranes for 24 h on diet containing only sucrose or sucrose with various phytotoxins. Quantitative real-time PCR analyses of 18 detoxification genes, indicated that relatively few transcripts were changed in both the MEAM1 and MED species, in response to the addition of phytotoxins to the diet. Induced transcription of detoxification genes only in the MED species, in response to the presence of indole-3-carbinol in the insect’s diet, was correlated with maintenance of reproductive performance in comparison to significant reduction in performance of the MEAM1 species. Three genes, COE2, CYP6-like 5 and BtGST2, responded to more than one compound and were highly transcribed in the insect gut. Furthermore, functional assays showed that the BtGST2 gene encodes a protein capable of interacting with both flavonoids and glucosinolates. In conclusion, several detoxification genes were identified that could potentially be involved in the adaptation of B. tabaci to its host plants. PMID:26655836

Assessment of Potential Sublethal Effects of Various Insecticides on Key Biological Traits of The Tobacco Whitefly, Bemisia tabaci

PubMed Central

He, Yuxian; Zhao, Jianwei; Zheng, Yu; Weng, Qiyong; Biondi, Antonio; Desneux, Nicolas; Wu, Kongming

2013-01-01

The tobacco whitefly Bemisia tabaci is one of the most devastating pests worldwide. Current management of B. tabaci relies upon the frequent applications of insecticides. In addition to direct mortality by typical acute toxicity (lethal effect), insecticides may also impair various key biological traits of the exposed insects through physiological and behavioral sublethal effects. Identifying and characterizing such effects could be crucial for understanding the global effects of insecticides on the pest and therefore for optimizing its management in the crops. We assessed the effects of sublethal and low-lethal concentrations of four widely used insecticides on the fecundity, honeydew excretion and feeding behavior of B. tabaci adults. The probing activity of the whiteflies feeding on treated cotton seedlings was recorded by an Electrical Penetration Graph (EPG). The results showed that imidacloprid and bifenthrin caused a reduction in phloem feeding even at sublethal concentrations. In addition, the honeydew excretions and fecundity levels of adults feeding on leaf discs treated with these concentrations were significantly lower than the untreated ones. While, sublethal concentrations of chlorpyrifos and carbosulfan did not affect feeding behavior, honeydew excretion and fecundity of the whitefly. We demonstrated an antifeedant effect of the imidacloprid and bifenthrin on B. tabaci, whereas behavioral changes in adults feeding on leaves treated with chlorpyrifos and carbosulfan were more likely caused by the direct effects of the insecticides on the insects' nervous system itself. Our results show that aside from the lethal effect, the sublethal concentration of imidacloprid and bifenthrin impairs the phloem feeding, i.e. the most important feeding trait in a plant protection perspective. Indeed, this antifeedant property would give these insecticides potential to control insect pests indirectly. Therefore, the behavioral effects of sublethal concentrations of

The suitability of biotypes Q and B of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) at different nymphal instars as hosts for Encarsia formosa Gahan (Hymenoptera: Aphelinidae).

PubMed

Liu, Xin; Zhang, Youjun; Xie, Wen; Wu, Qingjun; Wang, Shaoli

2016-01-01

Encarsia formosa Gahan (Hymenoptera: Aphelinidae) is a solitary endoparasitoid that is commercially reared and released for augmentative biological control of whiteflies infesting greenhouse crops. In most areas in China, the invasive and destructive whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) biotype Q has replaced B. tabaci biotype B and has become dominant between the two. A better understanding of the suitability of different nymphal instars of B. tabaci biotypes Q and B as hosts for E. formosa is needed to improve the use of this parasitoid for biological control. Parasitism of the four nymphal instars of B. tabaci biotypes Q and B by the commercial strain of E. formosa mass reared on Trialeurodes vaporariorum (Westwood) (Hemiptera: Aleyrodidae) was assessed in the laboratory. The results indicated that E. formosa parasitized and successfully developed on all instars of both biotypes but performed best on the 3rd instar of B. tabaci biotype B and on the 2nd, 3rd, and 4th instars of B. tabaci biotype Q. The host-feeding rate of the adult parasitoid was generally higher on nymphal instars of B. tabaci biotype Q than on the corresponding nymphal instars of biotype B and was significantly higher on the 2nd and 3rd instars. For both whitefly biotypes, the parasitoid's immature developmental period was the longest on the 1st instar, intermediate on the 2nd and 3rd instars, and the shortest on the 4th instar. The parasitoid emergence rate was significantly lower on the 1st instar than on the other three instars and did not significantly differ between B. tabaci biotype B and biotype Q. Offspring longevity was greater on the 3rd and 4th instars than on the 1st instar and did not significantly differ between the two B. tabaci biotypes. The results indicate that commercially-produced E. formosa can parasitize all instars of B. tabaci biotypes B and Q, making this parasitoid a promising tool for the management of the two biotypes of B. tabaci present in

[Genetic variability of the Bemisia tabaci (Gennadius) biotype B (Hemiptera: Aleyrodidae) in vegetable crops in São Luís, state of Maranhão, Brazil].

PubMed

Da Silva, Maria C; De Lemos, Raimunda N S; Lima, Luzia H C; Gourlart Filho, Luiz R; Pereira, Silma R F

2009-01-01

The RAPD technique is widely used to investigate the distinct genetic characteristics of the complex Bemisia tabaci (Gennadius), which is currently constituted of approximately 41 biotypes. The objective of this research was to characterize populations of whitefly collected in crops of agricultural producing areas in São Luís, MA, like okra, beans and pepper, using RAPD molecular markers. Females from nine whitefly populations were analyzed and compared with B. tabaci biotype B taken from poinsettia culture of Embrapa Genetic Resources and Biotechnology (Brasília, DF). Twelve out of the 20 primers tested produced specific band patterns suitable to confirm that the evaluated specimens belong to the biotype B of B. tabaci, despite the high percentage of detected polymorphism. The analysis of the 96 RAPD molecular markers generated indicated that the populations on okra, beans and pepper were grouped according to the host cultures, sharing 80, 76 and 45% of genetic similarity, respectively, when compared with the control population of B. tabaci biotype B. A lower selective pressure was observed with the population of whitefly collected on pepper and minor genetic variability in the whitefly populations collected on okra and bean, when compared with the control population.

Insecticide resistance status in the whitefly, Bemisia tabaci genetic groups Asia-I, Asia-II-1 and Asia-II-7 on the Indian subcontinent

PubMed Central

Naveen, N. C.; Chaubey, Rahul; Kumar, Dinesh; Rebijith, K. B.; Rajagopal, Raman; Subrahmanyam, B.; Subramanian, S.

2017-01-01

The present study is a summary of the current level of the insecticide resistance to selected organophosphates, pyrethroids, and neonicotinoids in seven Indian field populations of Bemisia tabaci genetic groups Asia-I, Asia-II-1, and Asia-II-7. Susceptibility of these populations was varied with Asia-II-7 being the most susceptible, while Asia-I and Asia-II-1 populations were showing significant resistance to these insecticides. The variability of the LC50 values was 7x for imidacloprid and thiamethoxam, 5x for monocrotophos and 3x for cypermethrin among the Asia-I, while, they were 7x for cypermethrin, 6x for deltamethrin and 5x for imidacloprid within the Asia-II-1 populations. When compared with the most susceptible, PUSA population (Asia-II-7), a substantial increase in resistant ratios was observed in both the populations of Asia-I and Asia-II-1. Comparative analysis during 2010–13 revealed a decline in susceptibility in Asia-I and Asia-II-1 populations of B. tabaci to the tested organophosphate, pyrethroid, and neonicotinoid insecticides. Evidence of potential control failure was detected using probit analysis estimates for cypermethrin, deltamethrin, monocrotophos and imidacloprid. Our results update resistance status of B. tabaci in India. The implications of insecticide resistance management of B. tabaci on Indian subcontinent are discussed. PMID:28098188

Resistance of Collard Green Genotypes to Bemisia tabaci Biotype B: Characterization of Antixenosis.

PubMed

Domingos, G M; Baldin, E L L; Canassa, V F; Silva, I F; Lourenção, A L

2018-08-01

Bemisia tabaci (Genn.) biotype B (Hemiptera: Aleyrodidae) is an important pest of vegetable crops, including collard greens Brassica oleracea var. acephala (Brassicaceae). The use of resistant genotypes is an interesting option to reduce insect populations and can be used as an important tool for integrated pest management (IPM). This study evaluated 32 genotypes of collard greens against the attack of silver leaf whitefly, with the aim to characterize antixenosis. Initially, a multiple-choice trial was conducted using all genotypes, in which the adult attractiveness was assessed on two leaves per genotype at 24 and 48 h after infestation. After 48 h, one leaf of each genotype was randomly selected for the determination of the number of eggs per square centimeter. From the results of the multiple-choice trial, 13 genotypes were selected for a no-choice oviposition test, following the same method of the previous test. Colorimetric analyses were also performed to establish possible correlations between leaf color and insect colonization. Genotypes HS-20, OE, and VA were less attractive, demonstrating antixenosis. Genotypes LG, VE, J, MG, MOP, HS-20, VA, and MT had less oviposition in the multiple-choice test, which indicated expression of antixenosis. In the no-choice test, genotypes VE, P1C, CCB, RI-919, H, and J had less oviposition, which also characterized antixenosis. Therefore, genotypes VE and J showed the highest resistance stability because both had less oviposition in both test modalities. Thus, the resistance to B. tabaci biotype B indicates the genotypes HS-20, OE, VA, VE, and J are promising for use in breeding programs to develop resistance to whitefly.

O3-Induced Leaf Senescence in Tomato Plants Is Ethylene Signaling-Dependent and Enhances the Population Abundance of Bemisia tabaci

PubMed Central

Guo, Honggang; Sun, Yucheng; Yan, Hongyu; Li, Chuanyou; Ge, Feng

2018-01-01

Elevated ozone (O3) can alter the phenotypes of host plants particularly in induction of leaf senescence, but few reports examine the involvement of phytohormone in O3-induced changes in host phenotypes that influence the foraging quality for insects. Here, we used an ethylene (ET) receptor mutant Nr and its wild-type to determine the function of the ET signaling pathway in O3-induced leaf senescence, and bottom-up effects on the performance of Bemisia tabaci in field open-top chambers (OTCs). Our results showed that elevated O3 reduced photosynthetic efficiency and chlorophyll content and induced leaf senescence of plant regardless of plant genotype. Leaf senescence in Nr plants was alleviated relative to wild-type under elevated O3. Further analyses of foliar quality showed that elevated O3 had little effect on phytohormone-mediated defenses, but significantly increased the concentration of amino acids in two plant genotypes. Furthermore, Nr plants had lower amino acid content relative to wild-type under elevated O3. These results provided an explanation of O3-induced increase in abundance of B. tabaci. We concluded that O3-induced senescence of plant was ET signal-dependent, and positive effects of O3-induced leaf senescence on the performance of B. tabaci largely resulted from changes of nutritional quality of host plants. PMID:29946327

The Whitefly Bemisia tabaci Knottin-1 Gene Is Implicated in Regulating the Quantity of Tomato Yellow Leaf Curl Virus Ingested and Transmitted by the Insect

PubMed Central

Hariton Shalev, Aliza; Sobol, Iris; Ghanim, Murad; Liu, Shu-Sheng; Czosnek, Henryk

2016-01-01

The whitefly Bemisia tabaci is a major pest to agricultural crops. It transmits begomoviruses, such as Tomato yellow leaf curl virus (TYLCV), in a circular, persistent fashion. Transcriptome analyses revealed that B. tabaci knottin genes were responsive to various stresses. Upon ingestion of tomato begomoviruses, two of the four knottin genes were upregulated, knot-1 (with the highest expression) and knot-3. In this study, we examined the involvement of B. tabaci knottin genes in relation to TYLCV circulative transmission. Knottins were silenced by feeding whiteflies with knottin dsRNA via detached tomato leaves. Large amounts of knot-1 transcripts were present in the abdomen of whiteflies, an obligatory transit site of begomoviruses in their circulative transmission pathway; knot-1 silencing significantly depleted the abdomen from knot-1 transcripts. Knot-1 silencing led to an increase in the amounts of TYLCV ingested by the insects and transmitted to tomato test plants by several orders of magnitude. This effect was not observed following knot-3 silencing. Hence, knot-1 plays a role in restricting the quantity of virions an insect may acquire and transmit. We suggest that knot-1 protects B. tabaci against deleterious effects caused by TYLCV by limiting the amount of virus associated with the whitefly vector. PMID:27455309

Detection of Cucurbit chlorotic yellows virus from Bemisia tabaci captured on sticky traps using reverse transcription loop-mediated isothermal amplification (RT-LAMP) and simple template preparation.

PubMed

Okuda, Mitsuru; Okuda, Shiori; Iwai, Hisashi

2015-09-01

Cucurbit chlorotic yellows virus (CCYV) of the genus Crinivirus within the family Closteroviridae is an emerging infectious agent of cucurbits leading to severe disease and significant economic losses. Effective detection and identification methods for this virus are urgently required. In this study, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to detect CCYV from its vector Bemisia tabaci. LAMP primer sets to detect CCYV were evaluated for their sensitivity and specificity, and a primer set designed from the HSP70h gene with corresponding loop primers were selected. The RT-LAMP assay was applied to detect CCYV from viruliferous B. tabaci trapped on sticky traps. A simple extraction procedure using RNAsecure™ was developed for template preparation. CCYV was detected in all of the B. tabaci 0, 1, 7 and 14 days after they were trapped. Although the rise of turbidity was delayed in reactions using RNA from B. tabaci trapped for 7 and 14 days compared with those from 0 and 1 day, the DNA amplification was sufficient to detect CCYV in all of the samples. These findings therefore present a simple template preparation method and an effective RT-LAMP assay, which can be easily and rapidly performed to monitor CCYV-viruliferous B. tabaci in the field. Copyright © 2015 Elsevier B.V. All rights reserved.

Leaf Morphological Characters Can Be a Factor for Intra-Varietal Preference of Whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) among Eggplant Varieties.

PubMed

Hasanuzzaman, Abu Tayeb Mohammad; Islam, Md Nazrul; Zhang, Yi; Zhang, Chen-Yang; Liu, Tong-Xian

2016-01-01

The sweetpotato whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae) MEAM1, is considered a serious pest of horticultural and many other crops. While eggplant (Solanum melongena) is one of the most favored host plants, the whiteflies exhibit preferences among different varieties. We hypothesized that certain morphological leaf characteristics of different varieties, like leaf trichome density, trichome length, leaf lamina thickness and leaf color, may affect whitefly landing, feeding and oviposition. In this study, we investigated the variation in leaf morphological characters among selected eggplant varieties and evaluated the effect of these leaf characteristics in rendering eggplant varieties either susceptible or resistant to B. tabaci. We evaluated eight eggplant varieties in choice feeding tests, and we found that the varieties JinSheng Zilongchangqie (JSZ) and H149 were the highly preferred varieties with the highest numbers of whitefly adults and eggs. Significantly lower numbers of whitefly adult eggs were found on the resistant variety Tuo Lu Bamu (TLB). The varieties JinGuangbo Luqie (JGL), JinGuangbo Ziquanqie (JGZ), DaYang Ziguanqie (DYZ), QinXing Ziguanqie (QXZ), and QinXing Niuxinqie (QXN) were moderately favored by B. tabaci. Leaf trichome density, trichome length and leaf lamina thickness were positively correlated with numbers of whitefly adults and eggs. B. tabaci was less attracted to the leaves that reflect long and middle wavelength light (higher R and G values) than to the bright green leaves (medium G value), but the short wavelength light (higher B value) had no significant effect on whitefly preference. The degree of hue had a positive effect, and saturation and brightness had a negative effect on whitefly attraction.

Silicon influence on resistance induction against Bemisia tabaci biotype B (Genn.) (Hemiptera: Aleyrodidae) and on vegetative development in two soybean cultivars.

PubMed

Ferreira, R S; Moraes, J C; Antunes, C S

2011-01-01

The potential of populations of Bemisia tabaci (Genn.) to become resistant to insecticides has stimulated research into alternative tactics of integrated pest management such as the induction of host-plant resistance. Recent data have shown that silicon can increase the degree of resistance of host plants to insect pests. Therefore the aim of our work was to study the effects of silicon application on the vegetative development of soybean plants and on the induction of resistance to the silverleaf whitefly, B. tabaci biotype B. We performed choice and no-choice tests of oviposition preference on two soybean cultivars, IAC-19 (moderately resistant to B. tabaci biotype B) and MONSOY-8001 (susceptible), with and without application of silicon. Silicon did not affect silverleaf whitefly oviposition preferences, but caused significant mortality in nymphs. Thus, silicon increased the degree of resistance to silverleaf whitefly. Silicon decreased the production of phenolic compounds, but did not affect lignin production. However, when applied to cultivar IAC-19, it increased the production of non-protein organic nitrogen. Silicon had no effect on the vegetative development of soybean plants, but it increased the degree of resistance to the silverleaf whitefly. We conclude that silicon applications combined with cultivar IAC-19 can significantly decrease silverleaf whitefly populations, having a positive impact both on the soybean plant and on the environment.

Bioactivity of indigenous medicinal plants against the cotton whitefly, Bemisia tabaci

PubMed Central

Hammad, E. Abou-Fakhr; Zeaiter, A.; Saliba, N.; Talhouk, S.

2014-01-01

Abstract Forty-one methanol extracts of 28 indigenous medicinal plant species were tested for their insecticidal bioactivity against cotton whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), adults and second nymphal instars under controlled conditions. This study is within a bioprospection context, in the form of utilizing local plant species as an alternative in sustainable agriculture development. Eighteen and nine plant extracts caused a significant decrease in number of live adult and nymphal whiteflies, respectively, compared to the control. This is the first report for the potential effect on survival of insects for 22 out of 28 tested medicinal plant species. Whole plant extracts of Ranunculus myosuroudes Boiss. and Kotschy (Ranunculaceae), Achillea damascena L. (Asteraceae), and Anthemis hebronica Boiss. and Kotschy (Asteraceae) and leaf extracts of Verbascum leptostychum DC. (Scrophulariaceae) and Heliotropium rotundifolium Boiss. (Borangiaceae) caused both repellent and toxic effects against the adult and second nymphal instars, respectively. Extracts of leaves and stems of Anthemis scariosa Boiss. (Asteraceae) and Calendula palestina Pers. (Asteraceae) were found to be more bioactive against the adult and nymphal instars, respectively, than extracts of other plant parts, such as flowers. Thus, the bioactive extracts of these medicinal plants have the potential to lower whitefly populations in a comprehensive pest management program in local communities, pending cultivation of these medicinal plant species. PMID:25204756

The role of the whitefly, Bemisia tabaci (Gennadius), and farmer practices in the spread of cassava brown streak ipomoviruses.

PubMed

Maruthi, Midatharahally N; Jeremiah, Simon C; Mohammed, Ibrahim U; Legg, James P

2017-12-01

Cassava brown streak disease (CBSD) is arguably the most dangerous current threat to cassava, which is Africa's most important food security crop. CBSD is caused by two RNA viruses: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). The roles of the whitefly Bemisia tabaci (Gennadius) and farmer practices in the spread of CBSD were investigated in a set of field and laboratory experiments. The virus was acquired and transmitted by B. tabaci within a short time (5-10 min each for virus acquisition and inoculation), and was retained for up to 48 hr. Highest virus transmission (60%) was achieved using 20-25 suspected viruliferous whiteflies per plant that were given acquisition and inoculation periods of 24 and 48 hr, respectively. Experiments mimicking the agronomic practices of cassava leaf picking or the use of contaminated tools for making cassava stem cuttings did not show the transmission of CBSV or UCBSV. Screenhouse and field experiments in Tanzania showed that the spread of CBSD next to spreader rows was high, and that the rate of spread decreased with increasing distance from the source of inoculum. The disease spread in the field up to a maximum of 17 m in a cropping season. These results collectively confirm that CBSV and UCBSV are transmitted by B. tabaci semipersistently, but for only short distances in the field. This implies that spread over longer distances is due to movements of infected stem cuttings used for planting material. These findings have important implications for developing appropriate management strategies for CBSD.

Distribution of Bemisia tabaci (Hemiptera: Aleyrodidae) biotypes in North America after the Q invasion.

PubMed

McKenzie, Cindy L; Bethke, James A; Byrne, Frank J; Chamberlin, Joseph R; Dennehy, Timothy J; Dickey, Aaron M; Gilrein, Dan; Hall, Paula M; Ludwig, Scott; Oetting, Ronald D; Osborne, Lance S; Schmale, Lin; Shatters, Robert G

2012-06-01

After the 2004 discovery of the Bemisia tabaci (Gennadius) (Hemiptera Aleyrodidae) Q biotype in the United States, there was a vital need to determine the geographical and host distribution as well as its interaction with the resident B biotype because of its innate ability to rapidly develop high-level insecticide resistance that persists in the absence of exposure. As part of a coordinated country-wide effort, an extensive survey of B. tabaci biotypes was conducted in North America, with the cooperation of growers, industry, local, state, and federal agencies, to monitor the introduction and distribution of the Q biotype. The biotype status of submitted B. tabaci samples was determined either by polymerase chain reaction amplification and sequencing of a mitochondrial cytochrome oxidase I small subunit gene fragment and characterization of two biotype discriminating nuclear microsatellite markers or esterase zymogram analysis. Two hundred and eighty collections were sampled from the United States, Bermuda, Canada, and Mexico during January 2005 through December 2011. Host plants were split between ornamental plant and culinary herb (67%) and vegetable and field crop (33%) commodities. The New World biotype was detected on field-grown tomatoes (Solanum lycopersicum L.) in Mexico (two) and in commercial greenhouses in Texas (three) and represented 100% of these five collections. To our knowledge, the latter identification represents the first report of the New World biotype in the United States since its rapid displacement in the late 1980s after the introduction of biotype B. Seventy-one percent of all collections contained at least one biotype B individual, and 53% of all collections contained only biotype B whiteflies. Biotype Q was detected in 23 states in the United States, Canada (British Columbia and Ontario territories), Bermuda, and Mexico. Forty-five percent of all collections were found to contain biotype Q in samples from ornamentals, herbs and a single

Lethal and Sublethal Effects of Clothianidin on the Development and Reproduction of Bemisia tabaci (Hemiptera: Aleyrodidae) MED and MEAM1

PubMed Central

Fang, Yong; Wang, Jinda; Luo, Chen; Wang, Ran

2018-01-01

Abstract The Bemisia tabaci (Gennadius) cryptic species complex includes important crop pests, and among them, the cryptic species Mediterranean (MED) and Middle East-Asia Minor 1 (MEAM1) cause substantial crop losses in China. The second-generation neonicotinoid clothianidin acts as an agonist of the nicotinic acetylcholine receptor in the insect nervous system and has both stomach and contact activity. In this study, the toxicity of clothianidin and five other insecticides to MED and MEAM1 was examined. The sublethal effects of clothianidin on the development and reproduction of MED and MEAM1 were also investigated. Among the six insecticides tested, clothianidin showed toxicities to both MED and MEAM1 adults with LC50 values of 5.23 and 5.18 mg/liter, respectively. The sublethal effects of clothianidin were assessed by treating MED and MEAM1 adults with the LC25 of 1.58 and 1.13 mg/liter, respectively. The LC25 treatments accelerated the development of the F1 generation but reduced survival and fecundity of both species. Our results indicate that clothianidin could be useful for the management of B. tabaci MED and MEAM1. PMID:29718499

Biochemical evaluation of interactions between synergistic molecules and phase I enzymes involved in insecticide resistance in B- and Q-type Bemisia tabaci (Hemiptera: Aleyrodidae).

PubMed

Panini, Michela; Tozzi, Francesco; Zimmer, Christoph T; Bass, Chris; Field, Linda; Borzatta, Valerio; Mazzoni, Emanuele; Moores, Graham

2017-09-01

Metabolic resistance is an important consideration in the whitefly Bemisia tabaci, where an esterase-based mechanism has been attributed to pyrethroid resistance and over-expression of the cytochrome P450, CYP6CM1, has been correlated to resistance to imidacloprid and other neonicotinoids. In vitro interactions between putative synergists and CYP6CM1, B and Q-type esterases were investigated, and structure-activity relationship analyses allowed the identification of chemical structures capable of acting as inhibitors of esterase and oxidase activities. Specifically, methylenedioxyphenyl (MDP) moieties with a polyether chain were preferable for optimum inhibition of B-type esterase, whilst corresponding dihydrobenzofuran structures were potent for the Q-esterase variation. Potent inhibition of CYP6CM1 resulted from structures which contained an alkynyl chain with a terminal methyl group. Synergist candidates could be considered for field control of B. tabaci, especially to abrogate neonicotinoid resistance. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Survey of indigenous entomopathogenic fungi and evaluation of their pathogenicity against the carmine spider mite, Tetranychus cinnabarinus (Boisd.), and the whitefly, Bemisia tabaci (Genn.) biotype B.

PubMed

Topuz, Emine; Erler, Fedai; Gumrukcu, Emine

2016-12-01

The carmine spider mite, Tetranychus cinnabarinus, and the silverleaf whitefly, Bemisia tabaci, are serious pests of both field- and greenhouse-grown crops in south-western Turkey. Control of these pests has been heavily dependent upon chemical pesticides. The objectives of this study were to investigate the occurrence of indigenous entomopathogenic fungi (EPF) in field populations of T. cinnabarinus and B. tabaci, and to evaluate their pathogenicity against these pests. For this purpose, a survey of EPF isolated from field-collected samples of both pests was carried out in Antalya in 2010 and 2011 using the dilution plating method. Four indigenous Beauveria bassiana isolates (TUR1-B, TUR2-B, FIN1-B, FIN2-B) were recovered. In pathogenicity bioassays with T. cinnabarinus and B. tabaci biotype B, all the isolates tested were pathogenic to some of the biological stages of both pests to varying degrees. FIN1-B and TUR1-B caused mortalities of up to 50 and 45%, respectively, in adults of T. cinnabarinus, and of over 79 and 37%, respectively, in pupae of B. tabaci with 10 7 conidia mL -1 suspensions under laboratory conditions 10 days after inoculation. FIN2-B and TUR2-B had mortalities of 19.45 and 12.28%, respectively, in adults of T. cinnabarinus, and of 6.78 and 8.18%, respectively, in pupae of B. tabaci. None of the isolates had an effect on eggs of either species and larvae of the mite. Overall results suggest that isolates FIN1-B and TUR1-B have potential for management of T. cinnabarinus and B. tabaci. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Aqueous Extracts of Some Medicinal Plants are as Toxic as Lmidacloprid to the Sweet Potato Whitefly, Bemisia tabaci

PubMed Central

Ateyyat, Mazen A.; Al-Mazra'awi, Mohammad; Abu-Rjai, Talal; Shatnawi, Mohamad A.

2009-01-01

Aqueous extracts of nine plants, known to have medicinal activity, were tested for their toxicity against the sweet potato whitefly, Bemisia tabaci Genn. (Homoptera: Aleurodidae) compared to the toxicity of the insecticide, Imidacloprid. Extracts of Lepidiuim sativum L. (Brassicales: Brassicaceae) killed 71 % of early stage nymphs, which was not significantly different from mortality caused by Imidacloprid. Treatment of pupae with three plant extracts, L. sativum, Achillea biebersteinii L. (Asterales: Asteraceae), or Retama raetam (Forssk.) Webb and Berthel (Fabales: Fabaceae) prevented adult development, and treatment with R. raetam extract killed adults, at levels that were not significantly different from Imidacloprid. None of the other plants showed significant toxicity. However extracts of four plants, Pimpinella anisum L. (Apiales: Apiaceae), Galium longifolium (Sibth. and SM.) (Gentianales: Rubiaceae), R. raetam and Ballota undulata Bentham (Lamiales: Lamiaceae) had a repellent effect. PMID:19613450

Reproduction of the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) B biotype in maize fields (Zea mays L.) in Brazil.

PubMed

Quintela, Eliane D; Abreu, Aluana G; Lima, Julyana F Dos S; Mascarin, Gabriel M; Santos, Jardel B Dos; Brown, Judith K

2016-11-01

Bemisia tabaci (Genn.) (Hemiptera: Aleyrodidae) was observed to have completed its reproductive cycle from the egg to the adult on maize (Zea mays L.). Field and screenhouse studies were carried out to investigate the durability of this putative and unprecedented adaptation to a grass host. Analysis of the mitochondrial COI gene sequence identified the maize-associated B. tabaci as the exotic B biotype (major clade North Africa-Mediterranean-Middle East). Results showed that whiteflies migrated from soybean crops and successfully established in maize plants. Females exhibited a preference for oviposition primarily on the first and second leaves of maize, but were also able to colonise developing leaves. A high, natural infestation on maize (193.3 individuals, all developmental stages) was observed within a 7.1 cm 2 designated 'observation area'. Whiteflies collected from naturally infested maize leaves and allowed to oviposit on maize seedlings grown in a screenhouse developed from egg to adulthood in 28.6 ± 0.2 days. This is the first report of the B biotype completing its development on maize plants. This surprising anomaly indicates that the B biotype is capable of adapting to monocotyledonous host plants, and importantly, broadens the host range to include at least one species in the Poaceae. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Further insight into reproductive incompatibility between putative cryptic species of the Bemisia tabaci whitefly complex.

PubMed

Qin, Li; Pan, Li-Long; Liu, Shu-Sheng

2016-04-01

The whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), with its global distribution and extensive genetic diversity, is now known to be a complex of over 35 cryptic species. However, a satisfactory resolution of the systematics of this species complex is yet to be achieved. Here, we designed experiments to examine reproductive compatibility among species with different levels of mitochondrial cytochrome oxidase I (mtCOI) divergence. The data show that putative species with mtCOI divergence of >8% between them consistently exhibited complete reproductive isolation. However, two of the putative species, Asia II 9 and Asia II 3, with mtCOI divergence of 4.47% between them, exhibited near complete reproductive compatibility in one direction of their cross, and partial reproductive compatibility in the other direction. Together with some recent reports on this topic from the literature, our data indicates that, while divergence in the mtCOI sequences provides a valid molecular marker for species delimitation in most clades, more genetic markers and more sophisticated molecular phylogeny will be required to achieve adequate delimitation of all species in this whitefly complex. While many attempts have been made to examine the reproductive compatibility among genetic groups of the B. tabaci complex, our study represents the first effort to conduct crossing experiments with putative species that were chosen with considerations of their genetic divergence. In light of the new data, we discuss the best strategy and protocols to conduct further molecular phylogenetic analysis and crossing trials, in order to reveal the overall pattern of reproductive incompatibility among species of this whitefly complex. © 2015 Institute of Zoology, Chinese Academy of Sciences.

Gene Expression Profiling in the Thiamethoxam Resistant and Susceptible B-biotype Sweetpotato Whitefly, Bemisia tabaci

PubMed Central

Xie, Wen; Yang, Xin; Wang, Shao-Ii; Wu, Qing-jun; Yang, Ni-na; Li, Ru-mei; Jiao, Xiaoguo; Pan, Hui-peng; Liu, Bai-ming; Feng, Yun-tao; Xu, Bao-yun; Zhou, Xu-guo; Zhang, You-jun

2012-01-01

Thiamethoxam has been used as a major insecticide to control the B-biotype sweetpotato whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae). Due to its excessive use, a high level of resistance to thiamethoxam has developed worldwide over the past several years. To better understand the molecular mechanisms underlying this resistance in B. tabaci, gene profiles between the thiamethoxam-resistant and thiamethoxam-susceptible strains were investigated using the suppression subtractive hybridization (SSH) library approach. A total of 72 and 52 upand down-regulated genes were obtained from the forward and reverse SSH libraries, respectively. These expressed sequence tags (ESTs) belong to several functional categories based on their gene ontology annotation. Some categories such as cell communication, response to abiotic stimulus, lipid particle, and nuclear envelope were identified only in the forward library of thiamethoxam-resistant strains. In contrast, categories such as behavior, cell proliferation, nutrient reservoir activity, sequence-specific DNA binding transcription factor activity, and signal transducer activity were identified solely in the reverse library. To study the validity of the SSH method, 16 differentially expressed genes from both forward and reverse SSH libraries were selected randomly for further analyses using quantitative realtime PCR (qRT-PCR). The qRT-PCR results were fairly consistent with the SSH results; however, only 50% of the genes showed significantly different expression profiles between the thiamethoxam-resistant and thiamethoxam-susceptible whiteflies. Among these genes, a putative NAD-dependent methanol dehydrogenase was substantially over-expressed in the thiamethoxamresistant adults compared to their susceptible counterparts. The distributed profiles show that it was highly expressed during the egg stage, and was most abundant in the abdomen of adult females. PMID:22957505

Naturally occurring bioactive compounds from four repellent essential oils against Bemisia tabaci whiteflies.

PubMed

Deletre, Emilie; Chandre, Fabrice; Barkman, Barbara; Menut, Chantal; Martin, Thibaud

2016-01-01

In tropical countries, netting is an effective sustainable tool for protecting horticultural crops against Lepidoptera, although not against small pests such as Bemisia tabaci, while smaller mesh netting can be used in temperate regions. A solution is to combine a net with a repellent. Previously we identified repellent essential oils: lemongrass (Cymbopogon citratus), cinnamon (Cinnamomum zeylanicum), cumin (Cuminum cyminum) and citronella (Cymbopogon winternarius). The present study was designed to identify the active compounds of these essential oils, characterise their biological activity and examine their potential for coating nets. We investigated the efficiency and toxicity of nets dipped in different solutions. We then studied the repellent effect with an olfactometer and the irritant effect by videotracking. Geraniol and citronellol were the most promising net coatings owing to their repellent effect. The repellency, irritancy or toxicity varied with the product and concentration, and these features were independent, indicating that the repellent and the irritant/toxic mechanisms were not the same. The combined effects of these different compounds account for the bioactivity of the mixture, suggesting interactions between the compounds. This new sustainable strategy for protecting vegetable crops against whiteflies is discussed, in addition to the use of companion plants that could produce such bioactive compounds. © 2015 Society of Chemical Industry.

RNAi-mediated resistance to whitefly (Bemisia tabaci) in genetically engineered lettuce (Lactuca sativa).

PubMed

Ibrahim, Abdulrazak B; Monteiro, Tatiane R; Cabral, Glaucia B; Aragão, Francisco J L

2017-10-01

RNA interference (RNAi)-based transgenic technologies have evolved as potent biochemical tools for silencing specific genes of plant pathogens and pests. The approach has been demonstrated to be useful in silencing genes in insect species. Here, we report on the successful construction of RNAi-based plasmid containing an interfering cassette designed to generate dsRNAs that target a novel v-ATPase transcript in whitefly (Bemisia tabaci), an important agricultural pest in tropical and sub-tropical regions. The presence of the transgene was confirmed in T 0 and T 1 generations of transgenic lettuce lines, segregating in a Mendelian fashion. Seven lines were infested with whiteflies and monitored over a period of 32 days. Analysis of mortality showed that within five days of feeding, insects on transgenic plants showed a mortality rate of 83.8-98.1%. In addition, a reduced number of eggs (95 fold less) was observed in flies feeding on transgenic lettuce plants than insects on control lines. Quantitative reverse transcription PCR showed decreased expression level of endogenous v-ATPase gene in whiteflies feeding on transgenic plants. This technology is a foundation for the production of whitefly-resistant commercial crops, improving agricultural sustainability and food security, reducing the use of more environmentally aggressive methods of pest control.

Attraction of Three Mirid Predators to Tomato Infested by Both the Tomato Leaf Mining Moth Tuta absoluta and the Whitefly Bemisia tabaci.

PubMed

Silva, Diego B; Bueno, Vanda H P; Van Loon, Joop J A; Peñaflor, Maria Fernanda G V; Bento, José Maurício S; Van Lenteren, Joop C

2018-01-01

Plants emit volatile compounds in response to insect herbivory, which may play multiple roles as defensive compounds and mediators of interactions with other plants, microorganisms and animals. Herbivore-induced plant volatiles (HIPVs) may act as indirect plant defenses by attracting natural enemies of the attacking herbivore. We report here the first evidence of the attraction of three Neotropical mirid predators (Macrolophus basicornis, Engytatus varians and Campyloneuropsis infumatus) toward plants emitting volatiles induced upon feeding by two tomato pests, the leaf miner Tuta absoluta and the phloem feeder Bemisia tabaci, in olfactometer bioassays. Subsequently, we compared the composition of volatile blends emitted by insect-infested tomato plants by collecting headspace samples and analyzing them with GC-FID and GC-MS. Egg deposition by T. absoluta did not make tomato plants more attractive to the mirid predators than uninfested tomato plants. Macrolophus basicornis is attracted to tomato plants infested with either T. absoluta larvae or by a mixture of B. tabaci eggs, nymphs and adults. Engytatus varians and C. infumatus responded to volatile blends released by tomato plants infested with T. absoluta larvae over uninfested plants. Also, multiple herbivory by T. absoluta and B. tabaci did not increase the attraction of the mirids compared to infestation with T. absoluta alone. Terpenoids represented the most important class of compounds in the volatile blends and there were significant differences between the volatile blends emitted by tomato plants in response to attack by T. absoluta, B. tabaci, or by both insects. We, therefore, conclude that all three mirids use tomato plant volatiles to find T. absoluta larvae. Multiple herbivory did neither increase, nor decrease attraction of C. infumatus, E. varians and M. basicornis. By breeding for higher rates of emission of selected terpenes, increased attractiveness of tomato plants to natural enemies may

Is agriculture driving the diversification of the Bemisia tabaci species complex (Hemiptera: Sternorrhyncha: Aleyrodidae)?: Dating, diversification and biogeographic evidence revealed.

PubMed

Boykin, Laura M; Bell, Charles D; Evans, Gregory; Small, Ian; De Barro, Paul J

2013-10-18

Humans and insect herbivores are competing for the same food crops and have been for thousands of years. Despite considerable advances in crop pest management, losses due to insects remain considerable. The global homogenisation of agriculture has supported the range expansion of numerous insect pests and has been driven in part by human-assisted dispersal supported through rapid global trade and low-cost air passenger transport. One of these pests, is the whitefly, Bemisia tabaci, a cryptic species complex that contains some of the world's most damaging pests of agriculture. The complex shows considerable genetic diversity and strong phylogeographic relationships. One consequence of the considerable impact that members of the B. tabaci complex have on agriculture, is the view that human activity, particularly in relation to agricultural practices, such as use of insecticides, has driven the diversification found within the species complex. This has been particularly so in the case of two members of the complex, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED), which have become globally distributed invasive species. An alternative hypothesis is that diversification is due to paleogeographic and paleoclimatological changes. The idea that human activity is driving speciation within the B. tabaci complex has never been tested, but the increased interest in fossil whiteflies and the growth in molecular data have enabled us to apply a relaxed molecular clock and so estimate divergence dates for the major lineages within the B. tabaci species complex. The divergence estimates do not support the view that human activity has been a major driver of diversification. Our analysis suggests that the major lineages within the complex arose approximately 60-30 mya and the highly invasive MED and MEAM1 split from the rest of the species complex around 12 mya well before the evolution of Homo sapiens and agriculture. Furthermore, the divergence dates coincide with a period

Status of Resistance of Bemisia tabaci (Hemiptera: Aleyrodidae) to Neonicotinoids in Iran and Detoxification by Cytochrome P450-Dependent Monooxygenases.

PubMed

Basij, M; Talebi, K; Ghadamyari, M; Hosseininaveh, V; Salami, S A

2017-02-01

Nine Bemisia tabaci (Gennadius) populations were collected from different regions of Iran. In all nine populations, only one biotype (B biotype) was detected. Susceptibilities of these populations to imidacloprid and acetamiprid were assayed. The lethal concentration 50 values (LC 50 ) for different populations showed a significant discrepancy in the susceptibility of B. tabaci to imidacloprid (3.76 to 772.06 mg l -1 ) and acetamiprid (4.96 to 865 mg l -1 ). The resistance ratio of the populations ranged from 9.72 to 205.20 for imidacloprid and 6.38 to 174.57 for acetamiprid. The synergistic effects of piperonylbutoxide (PBO) and S,S,S-tributylphosphorotrithioate (DEF) were evaluated for the susceptible (RF) and resistant (JR) populations for the determination of the involvement of cytochrome P450-dependent monooxygenase and carboxylesterase, respectively, in their resistance mechanisms. The results showed that PBO overcame the resistance of the JR population to both imidacloprid and acetamiprid, with synergistic ratios of 72.7 and 106.9, respectively. Carboxylesterase, glutathione S-transferase and cytochrome P450-dependent monooxygenase were studied biochemically, for the purpose of measuring the activity of the metabolizing enzymes in order to determine which enzymes are directly involved in neonicotinoid resistance. There was an increase in the activity of cytochrome P450-dependent monooxygenase up to 17-fold in the resistant JR population (RR = 205.20). The most plausible activity of cytochrome P450-dependent monooxygenase correlated with the resistances of imidacloprid and acetamiprid, and this suggests that cytochrome P450-dependent monooxygenase is the only enzyme system responsible for neonicotinoid resistance in the nine populations of B. tabaci.

A Primary Screening and Applying of Plant Volatiles as Repellents to Control Whitefly Bemisia tabaci (Gennadius) on Tomato

NASA Astrophysics Data System (ADS)

Du, Wenxiao; Han, Xiaoqing; Wang, Yubo; Qin, Yuchuan

2016-02-01

With the goal of finding a new way to reduce population densities of Bemisia tabaci biotype Q in greenhouses, seven repellent volatile chemicals and their combinations were screened. The mixture of DLCO (D-limonene, citral and olive oil (63:7:30)) had a better cost performance(SC50 = 22.59 mg/ml)to repel whiteflies from settling than the other mixtures or single chemicals. In the greenhouse, in both the choice test and the no-choice tests, the number of adult whiteflies that settled on 1% DLCO-treated tomato plants was significantly lower than those settling on the control plants for the different exposure periods (P < 0.01). In the choice test, the egg amount on the treated tomato plants was significantly lower (P < 0.01) than that on the control plants, but there was no significant difference (P > 0.05) between the number of eggs on treated and control plants in the no-choice test. Compared with the controls, 1% DLCO did not cause significantly statistic mortality rates (P > 0.05) out of different living stages of B. tabaci. The tests for evaluating the repellent efficacy, showed that a slow-releasing bottle containing the mixture had a period of efficacy of 29 days, and the application of this mixture plus a yellow board used as a push-pull strategy in the greenhouse was also effective.

A Primary Screening and Applying of Plant Volatiles as Repellents to Control Whitefly Bemisia tabaci (Gennadius) on Tomato

PubMed Central

Du, Wenxiao; Han, Xiaoqing; Wang, Yubo; Qin, Yuchuan

2016-01-01

With the goal of finding a new way to reduce population densities of Bemisia tabaci biotype Q in greenhouses, seven repellent volatile chemicals and their combinations were screened. The mixture of DLCO (D-limonene, citral and olive oil (63:7:30)) had a better cost performance(SC50 = 22.59 mg/ml)to repel whiteflies from settling than the other mixtures or single chemicals. In the greenhouse, in both the choice test and the no-choice tests, the number of adult whiteflies that settled on 1% DLCO-treated tomato plants was significantly lower than those settling on the control plants for the different exposure periods (P < 0.01). In the choice test, the egg amount on the treated tomato plants was significantly lower (P < 0.01) than that on the control plants, but there was no significant difference (P > 0.05) between the number of eggs on treated and control plants in the no-choice test. Compared with the controls, 1% DLCO did not cause significantly statistic mortality rates (P > 0.05) out of different living stages of B. tabaci. The tests for evaluating the repellent efficacy, showed that a slow-releasing bottle containing the mixture had a period of efficacy of 29 days, and the application of this mixture plus a yellow board used as a push-pull strategy in the greenhouse was also effective. PMID:26907368

Effect of Zohar LQ-215, a biorational surfactant, on the sweetpotato whitefly Bemisia tabaci (biotype b).

PubMed

Ishaaya, I; Khasdan, V; Horowitz, A Rami

2006-01-01

Zohar LQ-215, a surfactant based on plant oils, able to control nymphs of the whitefly, Bemisia tabaci (Gennadius), under laboratory and field conditions. To evaluate the effects of the surfactant on the nymph stages of whitefly under laboratory conditions, potted cotton seedlings infested with 1st- or 3rd-instars were treated with the compound aqueous solutions. LC90 values of Zohar LQ-215 on 1st and 3rd-nymphs, based on mortality curves, were 0.78% and 1.14%, respectively. Adult mortality of 12% and 19% was obtained at concentrations of 0.5% and 1%, respectively. Under both laboratory and, in some cases, under field conditions, greater mortality was achieved when combining Zohar LQ-215 with the insect growth regulator buprofezin than when either insecticide was applied separately. Our results indicate that Zohar LQ-215 could serve as a potential compound for controlling whiteflies under light to moderate infestation and could be used in combination with other rational insecticides such as buprofezin for controlling whiteflies in integrated pest management programs.

[Phagodeterrent activity of the plants Tithonia diversifolia and Montanoa hibiscifolia (Asteraceae) on adults of the pest insect Bemisia tabaci (Homoptera: Aleyrodidae)].

PubMed

Bagnarello, Gina; Hilje, Luko; Bagnarello, Vanessa; Cartín, Victor; Calvo, Marco

2009-12-01

Bemisia tabaci (Gennadius) is a polyphagous, cosmopolitan and worldwide relevant pest, mainly acting as a virus vector on many crops. A sound preventive approach to deal with it would be the application of repellent or deterrent substances hopefully present in tropical plants, which in turn may contribute to take advantage of the remarkable rich Mesoamerican biodiversity. Therefore, extracts of two wild plants belonging to family Asteraceae, titonia (Tithonia diversifolia) and "tora" (Montanoa hibiscifolia), were tested for phagodeterrence to B. tabaci adults. The crude leaf extract of each one, as well as four fractions thereof (hexane, dichlorometane, ethyl acetate, and methanol) were tested under greenhouse conditions; in addition, the extracts were submitted to a phytochemical screening to determine possible metabolites causing phagodeterrence. Both restricted-choice and unrestricted-choice experiments were conducted. In the former ones, each fraction was tested at four doses (0.1, 0.5, 1.0 and 1.5% v/v), which were compared with four control treatments: distilled water, endosulfan, an agricultural oil (Aceite Agricola 81 SC), and the emulsifier Citowett. Tomato plants were sprayed and placed inside sleeve cages, where 50 B. tabaci adults were released. The criterion to appraise phagodeterrence was the number of landed adults on plants at 48h. For the unrestricted-choice experiments, only the two highest doses (1.0 and 1.5%) of the crude extracts of each species were tested, and compared to distilled water and the agricultural oil. The titonia and "tora" crude extracts caused phagodeterrence, and for both plant species the methanol fraction stood out. Results suggest that metabolites causing phagodeterrence are several sesquiterpenic lactones, polyphenolic compounds (flavonoids and tannins) and saponins.

Bemisia tabaci females from the Mediterranean (Q) species detect and avoid laying eggs in the presence of pyriproxyfen, a juvenile hormone analogue.

PubMed

Moshitzky, Pnina; Morin, Shai

2014-10-01

Pyriproxyfen, a juvenile hormone analogue, disrupts embryogenesis, metamorphosis and adult formation in Bemisia tabaci, but does not directly affect adult females. The effect of pyriproxyfen on egg-laying preference and performance of B. tabaci females and the influence of resistance to pyriproxyfen on these reproductive behaviours were studied. Choice experiments utilising cotton plants treated and not treated with pyriproxyfen revealed a significant preference for egg laying on non-treated plants both by resistant and susceptible females. No-choice assays indicated a reduction of ∼60% in the number of eggs laid on pyriproxyfen-treated plants by both resistant and susceptible females. The reduction in oviposition on treated plants was not accompanied with reduced expression of the vitellogenin gene or a delay in oocyte maturation, but significant accumulation of mature oocytes in the ovaries was observed, and could be reversed by transferring the females to non-treated plants. Pyriproxyfen caused reduced oviposition and enhanced mature oocyte accumulation in pyriproxyfen-resistant and pyriproxyfen-susceptible females. These findings can be explained by two alternative mechanisms: pyriproxyfen-regulated physiological arrest of oviposition, involving hormonal regulation of myotrophic factors, or the hierarchy-threshold behavioural theory of host choice, in which pyriproxyfen-treated plants are defined as low-quality hosts. Aspects of application are discussed. © 2013 Society of Chemical Industry.

Susceptibility of MED-Q1 and MED-Q3 Biotypes of Bemisia tabaci (Hemiptera: Aleyrodidae) Populations to Essential and Seed Oils.

PubMed

Samuel Fogné, Drabo; Olivier, Gnankine; Bassolé, Imael H N; Nébié, Roger Charles; Laurence, Mouton

2017-06-01

Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a major pest of many agricultural and ornamental crops in tropical and subtropical regions causing damages that result in important economic losses. Insecticides are commonly used in greenhouses or fields to control B. tabaci populations leading to rapid evolution of resistance that render treatments inefficient. Therefore, and for environmental and human health concerns, other approaches must be developed for this pest management. In the present study, we compare, using the leaf dip method, the toxicity of three essential oils (Cymbopogon citratus, Ocimum americanum, and Hyptis spicigera) and three seed oils (Lannea microcarpa, Lannea acida, and Carapa procera) with three chemical insecticides (acetamiprid, deltamethrin, and chlorpyrifos-ethyl) on adults. Two B. tabaci biotypes (MED-Q1 and MED-Q3) belonging to the Mediterranean species and collected in Burkina Faso were used. Essential oils were analyzed by gas chromatography-mass spectrometry and gas chromatography-flame ionization detector. We showed that these two biotypes have different levels of resistance to the three insecticides, MED-Q3 being more sensitive than MED-Q1. Moreover, they differ in the frequency of resistance alleles to insecticides, especially for organophosphates, as these alleles are almost fixed in MED-Q1. On the other hand, the two biotypes prove to be more susceptible to the plant extracts than to insecticides except for chlorpyrifos-ethyl, with essential oils that showed the highest insecticidal activities. Monoterpenes content were the most abundant and showed the highest insecticidal activities. Our results indicated that essential oils, but also seed oils, have the potential to constitute an alternative strategy of pest management. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Bemisia tabaci Q carrying tomato yellow leaf curl virus strongly suppresses host plant defenses

PubMed Central

Shi, Xiaobin; Pan, Huipeng; Zhang, Hongyi; Jiao, Xiaoguo; Xie, Wen; Wu, Qingjun; Wang, Shaoli; Fang, Yong; Chen, Gong; Zhou, Xuguo; Zhang, Youjun

2014-01-01

The concurrence of tomato yellow leaf curl virus (TYLCV) with the spread of its vector Bemisia tabaci Q rather than B in China suggests a more mutualistic relationship between TYLCV and Q. Here, we investigated the hypothesis that viruliferous B and Q have different effects on plant defenses. We found the fecundity of nonviruliferous B, nonviruliferous Q, viruliferous Q and viruliferous B was 11.080, 12.060, 10.760, and 11.220 respectively on plants previously attacked by the other biotype, however, on their respective noninfested control leaves fecundity was 12.000, 10.880, 9.760, and 8.020 respectively. Only viruliferous B had higher fecundity on viruliferous Q-infested plants than on control plants. The longevity of viruliferous B showed the same phenomenon. At 1 d infestion, the jasmonic acid content in leaves noninfested and in leaves infested with nonviruliferous B, nonviruliferous Q, viruliferous B and viruliferous Q was 407.000, 281.333, 301.333, 266.667 and 134.000 ng/g FW, respectively. The JA content was lowest in viruliferous Q-infested leaves. The proteinase inhibitor activity and expression of JA-related upstream gene LOX and downstream gene PI II showed the same trend. The substantial suppression of host defenses by Q carrying TYLCV probably enhances the spread of Q and TYLCV in China. PMID:24912756

Cassava whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) in East African farming landscapes: a review of the factors determining abundance.

PubMed

Macfadyen, S; Paull, C; Boykin, L M; De Barro, P; Maruthi, M N; Otim, M; Kalyebi, A; Vassão, D G; Sseruwagi, P; Tay, W T; Delatte, H; Seguni, Z; Colvin, J; Omongo, C A

2018-02-13

Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a pest species complex that causes widespread damage to cassava, a staple food crop for millions of households in East Africa. Species in the complex cause direct feeding damage to cassava and are the vectors of multiple plant viruses. Whilst significant work has gone into developing virus-resistant cassava cultivars, there has been little research effort aimed at understanding the ecology of these insect vectors. Here we assess critically the knowledge base relating to factors that may lead to high population densities of sub-Saharan African (SSA) B. tabaci species in cassava production landscapes of East Africa. We focus first on empirical studies that have examined biotic or abiotic factors that may lead to high populations. We then identify knowledge gaps that need to be filled to deliver sustainable management solutions. We found that whilst many hypotheses have been put forward to explain the increases in abundance witnessed since the early 1990s, there are little published data and these tend to have been collected in a piecemeal manner. The most critical knowledge gaps identified were: (i) understanding how cassava cultivars and alternative host plants impact population dynamics and natural enemies; (ii) the impact of natural enemies in terms of reducing the frequency of outbreaks and (iii) the use and management of insecticides to delay the development of resistance. In addition, there are several fundamental methodologies that need to be developed and deployed in East Africa to address some of the more challenging knowledge gaps.

Host Plant Effects on Alkaline Phosphatase Activity in the Whiteflies, Bemisia tabaci Biotype B and Trialeurodes vaporariorum

PubMed Central

Yan, Ying; Peng, Lu; Liu, Wan-Xue; Wan, Fang-Hao; Harris, Marvin K.

2011-01-01

Bemisia tabaci (Gennadius) B-biotype and Trialeurodes vaporariorum (Westwood) (Hemiptera: Aleyrodidae) often coexist on greenhouse-grown vegetable crops in northern China. The recent spread of B. tabaci B-biotype has largely replaced T. vaporariorum, and B-biotype now overlaps with T. vaporariorum where common hosts occur in most invaded areas. The impact of the B-biotype on the agro eco system appears to be widespread, and involves the ability to compete with and perhaps replace other phytophages like T. vaporariorum. An emerging hypothesis is that the B-biotype is physiologically superior due at least in part to an improved ability to metabolically utilize the alkaline phosphatase pathway. To test this hypothesis, alkaline phosphatase activity was studied in the B-biotype and T. vaporariorum after feeding on a number of different hosts for a range of durations, with and without host switching. Alkaline phosphatase activity in T. vaporariorum was 1.45 to 2.53-fold higher than that of the B-biotype when fed on tomato for 4 and 24 h, or switched from tomato to cotton and cabbage for the same durations. However, alkaline phosphatase activity in the B-biotype was 1.40 to 3.35-fold higher than that of T. vaporariorum when the host switching time was ∼72 and ∼120 h on the same plant. Both short-term (4 h) and long-term (72 h) switching of plant hosts can significantly affect the alkaline phosphatase activity in the two species. After ∼120 h, feeding on tomato and cotton alkaline phosphatase activity in the B-biotype was significantly higher than that of T. vaporariorum. It was shown that alkaline phosphatase aids the species feeding on different plant species, and that the B-biotype is physiologically superior to T. vaporariorum in utilizing the enzyme compared to T. vaporariorum over longer periods of feeding. PMID:21521136

Expression Profiling in Bemisia tabaci under Insecticide Treatment: Indicating the Necessity for Custom Reference Gene Selection

PubMed Central

Zhou, Xuguo; Gao, Xiwu

2014-01-01

Finding a suitable reference gene is the key for qRT-PCR analysis. However, none of the reference gene discovered thus far can be utilized universally under various biotic and abiotic experimental conditions. In this study, we further examine the stability of candidate reference genes under a single abiotic factor, insecticide treatment. After being exposed to eight commercially available insecticides, which belong to five different classes, the expression profiles of eight housekeeping genes in the sweetpotato whitefly, Bemisia tabaci, one of the most invasive and destructive pests in the world, were investigated using qRT-PCR analysis. In summary, elongation factor 1α (EF1α), α-tubulin (TUB1α) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were identified as the most stable reference genes under the insecticide treatment. The initial assessment of candidate reference genes was further validated with the expression of two target genes, a P450 (Cyp6cm1) and a glutathione S-transferase (GST). However, ranking of reference genes varied substantially among intra- and inter-classes of insecticides. These combined data strongly suggested the necessity of conducting custom reference gene selection designed for each and every experimental condition, even when examining the same abiotic or biotic factor. PMID:24498122

Inundative Field Releases and Evaluation of Three Predators for Bemisia tabasi (Hemiptera: Aleyrodidae) Management in Three Vegetable Crops

USDA-ARS?s Scientific Manuscript database

The sweetpotato whitefly, Bemisia tabaci (Gennadius), is a global pest on numerous crops, including vegetables. Weekly inundative releases of a coccinellid predator (Coccinella undecimpunctata L.), a mirid predator [Macrophillus caliginosus (Wagner)] and a neuropteran predator [Chrysoperla carnea S...

Whitefly Bemisia tabaci (Homoptera: Aleyrodidae) infestation on cassava genotypes grown at different ecozones in Nigeria.

PubMed

Ariyo, O A; Dixon, A G O; Atiri, G I

2005-04-01

Large-scale screening of cassava, Manihot esculenta Crantz, genotypes for resistance to infestation by whitefly Bemisia tabaci Gennadius, the vector of cassava mosaic geminiviruses, is limited. A range of new cassava elite clones were therefore assessed for the whitefly infestation in the 1999/2000 and 2000/2001 cropping seasons in experimental fields of International Institute of Tropical Agriculture, Ibadan, Nigeria. On each scoring day, between 0600 and 0800 hours when the whiteflies were relatively immobile, adult whitefly populations on the five topmost expanded leaves of cassava cultivars were counted. All through the 6-mo scoring period, there was a highly significant difference in whitefly infestation among the new cassava elite clones. Vector population buildup was observed in Ibadan (forest-savanna transition zone) and Onne (humid forest), 2 mo after planting (MAP). Mean infestation across cassava genotypes was significantly highest (16.6 whiteflies per plant) in Ibadan and lowest in Zaria (0.2). Generally, whitefly infestation was very low in all locations at 5 and 6 MAP. During this period, cassava genotypes 96/1439 and 91/02324 significantly supported higher infestations than other genotypes. Plants of 96/1089A and TMS 30572 supported the lowest whitefly infestation across cassava genotypes in all locations. The preferential whitefly visitation, the differences between locations in relation to whitefly population, cassava mosaic disease, and the fresh root yield of cassava genotypes are discussed.

Tomato Pathogenesis-related Protein Genes are Expressed in Response to Trialeurodes vaporariorum and Bemisia tabaci Biotype B Feeding

PubMed Central

Puthoff, David P.; Holzer, Frances M.; Perring, Thomas M.

2010-01-01

The temporal and spatial expression of tomato wound- and defense-response genes to Bemisia tabaci biotype B (the silverleaf whitefly) and Trialeurodes vaporariorum (the greenhouse whitefly) feeding were characterized. Both species of whiteflies evoked similar changes in tomato gene expression. The levels of RNAs for the methyl jasmonic acid (MeJA)- or ethylene-regulated genes that encode the basic β-1,3-glucanase (GluB), basic chitinase (Chi9), and Pathogenesis-related protein-1 (PR-1) were monitored. GluB and Chi9 RNAs were abundant in infested leaves from the time nymphs initiated feeding (day 5). In addition, GluB RNAs accumulated in apical non-infested leaves. PR-1 RNAs also accumulated after whitefly feeding. In contrast, the ethylene- and salicylic acid (SA)-regulated Chi3 and PR-4 genes had RNAs that accumulated at low levels and GluAC RNAs that were undetectable in whitefly-infested tomato leaves. The changes in Phenylalanine ammonia lyase5 (PAL5) were variable; in some, but not all infestations, PAL5 RNAs increased in response to whitefly feeding. PAL5 RNA levels increased in response to MeJA, ethylene, and abscisic acid, and declined in response to SA. Transcripts from the wound-response genes, leucine aminopeptidase (LapA1) and proteinase inhibitor 2 (pin2), were not detected following whitefly feeding. Furthermore, whitefly infestation of transgenic LapA1:GUS tomato plants showed that whitefly feeding did not activate the LapA1 promoter, although crushing of the leaf lamina increased GUS activity up to 40 fold. These studies indicate that tomato plants perceive B. tabaci and T. vaporariorum in a manner similar to baterical pathogens and distinct from tissue-damaging insects. PMID:20927641

Dissipation rate of thiacloprid and its control effect against Bemisia tabaci in greenhouse tomato after soil application.

PubMed

Dong, Sa; Qiao, Kang; Wang, Hongyan; Zhu, Yukun; Xia, Xiaoming; Wang, Kaiyun

2014-08-01

Thiacloprid is a chloronicotinyl insecticide that is quite effective against sucking insects. In this study, when thiacloprid was applied at two different rates (normal rate 15 kg ha(-1) , double rate 30 kg ha(-1) ), the systemic distribution and residue of thiacloprid as well as its control effect against whitefly (Bemisia tabaci) were investigated in greenhouse tomato after soil application. The results showed that thiacloprid was present in the tomato leaves until day 25, and then its amount was less than 0.005 mg kg(-1) and could not be detected. Thiacloprid residue in the tomato stems basically remained at a stable low level throughout the experimental period. Thiacloprid in soil had half-lives of 11.8 and 12.5 days for the normal treatment and the double treatment respectively. The control efficiency of whiteflies was about 90% from day 1 to day 10. This was followed by a slow decline, but efficiency was still higher than 50% until day 21. In addition, no significant differences were noted in the control effect of thiacloprid on whiteflies between the two different rates. Soil application of thiacloprid at the normal rate can effectively control whiteflies, with high efficiency and long persistence. © 2013 Society of Chemical Industry.

Dynamics of Bemisia tabaci biotypes and insecticide resistance in Fujian province in China during 2005–2014

PubMed Central

Yao, Feng-Luan; Zheng, Yu; Huang, Xiao-Yan; Ding, Xue-Ling; Zhao, Jian-Wei; Desneux, Nicolas; He, Yu-Xian; Weng, Qi-Yong

2017-01-01

The whitefly Bemisia tabaci (Gennadius) is an important agricultural insect pest worldwide. The B and Q biotypes are the two most predominant and devastating biotypes prevalent across China. However, there are few studies regarding the occurrence of the Q biotype in Fujian Province, China, where high insecticide resistance has been reported in the B biotype. Differences in some biological characteristics between the B and Q biotypes, especially insecticide resistance, are considered to affect the outcome of their competition. Extensive surveys in Fujian revealed that the B biotype was predominant during 2005–2014, whereas the Q biotype was first detected in some locations in 2013 and widely detected throughout the province in 2014. Resistance to neonicotinoids (that have been used for more than 10 years) exhibited fluctuations in open fields, but showed a continual increasing trend in protected areas. Resistance to lambda-cyhalothrin, chlorpyrifos, and abamectin exhibited a declining trend. Resistance to novel insecticides, such as nitenpyram, pymetrozine, sulfoxaflor, and cyantraniliprole, in 2014 was generally below a moderate level. A decline in insecticide resistance in the B biotype and the rapid buildup of protected crops under global temperature increase may have promoted the establishment of the Q biotype in Fujian. PMID:28112233

Nuclear and cytoplasmic differentiation among Mediterranean populations of Bemisia tabaci: testing the biological relevance of cytotypes.

PubMed

Terraz, Gabriel; Gueguen, Gwenaelle; Arnó, Judit; Fleury, Frédéric; Mouton, Laurence

2014-10-01

The taxonomy of the species complex Bemisia tabaci is still an unresolved issue. Recently, phylogenetic analysis based on mtCOI identified 31 cryptic species. However, mitochondrial diversity is observed within these species, associated with distinct symbiotic bacterial communities forming associations, which here are called cytotypes. The authors investigated the biological significance of two cytotypes (Q1 and Q2) belonging to the Mediterranean species, which have only been found in allopatry in the Western Mediterranean to date. Sampling was done over a few years in Western Europe, and sympatric situations were found that allowed their reproductive compatibility to be tested in the field with the use of microsatellites. The field survey indicated that, in spite of its recent introduction, Q2 is well established in France and Spain, where it coexists with Q1. Microsatellite data showed that, in allopatry, Q1 and Q2 are highly differentiated, while there is little or no genetic differentiation when they coexist in sympatry, suggesting a high rate of hybridisation. Crossing experiments in the lab confirmed their interfertility. Q1 and Q2 hybridise, which confirms that they belong to the same species, in spite of the high degree of genetic differentiation at both the cytoplasmic and nuclear levels, and also suggests that their symbiotic bacteria do not prevent hybridisation. © 2014 Society of Chemical Industry.

Effect of foliar application of Xxpire on Bemisisa tabaci (MED whitefly) and Amblyseius swirskii, 2016

USDA-ARS?s Scientific Manuscript database

Bemisia tabaci is a polyphagous pest known to feed upon over 900 plant taxa, and is an effective vector of more than 100 plant damaging viruses. Among different biotypes of this cryptic species complex, MEAM1 and MED whitefly are the two most destructive members posing threats of several crops of ec...

Comparison of transmission of Papaya leaf curl China virus among four cryptic species of the whitefly Bemisia tabaci complex

PubMed Central

Guo, Tao; Guo, Qi; Cui, Xi-Yun; Liu, Yin-Quan; Hu, Jian; Liu, Shu-Sheng

2015-01-01

Begomoviruses are transmitted by cryptic species of the whitefly Bemisia tabaci complex, often in a species-specific manner. Papaya leaf curl China virus (PaLCuCNV) has been recorded to infect several crops including papaya, tomato and tobacco in China. To help assess the risks of spread of this virus, we compared the acquisition, retention and transmission of PaLCuCNV among four species of whiteflies, Middle East-Asia Minor 1 (MEAM1), Mediterranean (MED), Asia 1 and Asia II 7. All four species of whiteflies are able to acquire, retain and transmit the virus, but with different levels of efficiency. Transmission tests using tomato as the host plant showed that MEAM1 transmitted PaLCuCNV with substantially higher efficiency than did MED, Asia 1 and Asia II 7. Furthermore, accumulation of PaLCuCNV in the whiteflies was positively associated with its efficiency of transmitting the virus. Altogether, these findings indicate that MEAM1 is the most efficient vector for PaLCuCNV in the four species of whiteflies, and suggest that risks of PaLCuCNV pandemics are high in regions where MEAM1 occurs. PMID:26486606

Comparison of transmission of Papaya leaf curl China virus among four cryptic species of the whitefly Bemisia tabaci complex.

PubMed

Guo, Tao; Guo, Qi; Cui, Xi-Yun; Liu, Yin-Quan; Hu, Jian; Liu, Shu-Sheng

2015-10-21

Begomoviruses are transmitted by cryptic species of the whitefly Bemisia tabaci complex, often in a species-specific manner. Papaya leaf curl China virus (PaLCuCNV) has been recorded to infect several crops including papaya, tomato and tobacco in China. To help assess the risks of spread of this virus, we compared the acquisition, retention and transmission of PaLCuCNV among four species of whiteflies, Middle East-Asia Minor 1 (MEAM1), Mediterranean (MED), Asia 1 and Asia II 7. All four species of whiteflies are able to acquire, retain and transmit the virus, but with different levels of efficiency. Transmission tests using tomato as the host plant showed that MEAM1 transmitted PaLCuCNV with substantially higher efficiency than did MED, Asia 1 and Asia II 7. Furthermore, accumulation of PaLCuCNV in the whiteflies was positively associated with its efficiency of transmitting the virus. Altogether, these findings indicate that MEAM1 is the most efficient vector for PaLCuCNV in the four species of whiteflies, and suggest that risks of PaLCuCNV pandemics are high in regions where MEAM1 occurs.

Effectiveness of two insect growth regulators against Bemisia tabaci (Gennadius) (Homoptera: Aleyrodidae) and Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) and their impact on population densities of arthropod predators in cotton in Pakistan.

PubMed

Gogi, Muhammad D; Sarfraz, Rana M; Dosdall, Lloyd M; Arif, Muhammad J; Keddie, Andrew B; Ashfaq, Muhammad

2006-10-01

Field efficacies of two insect growth regulators (IGRs) at two recommended application rates, buprofezin at 370 and 555 g AI ha(-1) and lufenuron at 37 and 49 g AI ha(-1), were determined against the sweet potato whitefly, Bemisia tabaci (Gennadius), and the cotton bollworm, Helicoverpa armigera (Hübner), in experimental plots of cotton at the Directorate of Cotton Research, Faisalabad, Pakistan. Adverse effects of the IGRs on populations of associated arthropod predators, namely geocorids, chrysopids, coccinellids, formicids and arachnids, were also assessed. Both IGRs significantly reduced populations of B. tabaci at each application rate 24, 48 and 72 h after treatment, and higher doses were more effective than lower doses. Buprofezin was not effective against H. armigera at any tested dose for any time of treatment in any spray. Lufenuron applied at 37 and 49 g AI ha(-1) effectively suppressed H. armigera populations, resulting in significant reductions in crop damage. At lower doses, both IGRs appeared safe to predator populations, which did not differ significantly in IGR-treated versus untreated control plots. Population densities of formicids and coccinellids were significantly lower at high concentrations of both IGRs in treatment plots, possibly as a result of reduced prey availability. The potential role of buprofezin and lufenuron for control of B. tabaci and H. armigera in a spray programme and the likelihood of direct toxic effects of IGRs on predatory fauna of cotton are discussed.

Insecticide resistance in Bemisia tabaci Gennadius (Homoptera: Aleyrodidae) and Anopheles gambiae Giles (Diptera: Culicidae) could compromise the sustainability of malaria vector control strategies in West Africa.

PubMed

Gnankiné, Olivier; Bassolé, Imael H N; Chandre, Fabrice; Glitho, Isabelle; Akogbeto, Martin; Dabiré, Roch K; Martin, Thibaud

2013-10-01

Insecticides from the organophosphate (OP) and pyrethroid (PY) chemical families, have respectively, been in use for 50 and 30 years in West Africa, mainly against agricultural pests, but also against vectors of human disease. The selection pressure, with practically the same molecules year after year (mainly on cotton), has caused insecticide resistance in pest populations such as Bemisia tabaci, vector of harmful phytoviruses on vegetables. The evolution toward insecticide resistance in malaria vectors such as Anopheles gambiae sensus lato (s.l.) is probably related to the current use of these insecticides in agriculture. Thus, successful pest and vector control in West Africa requires an investigation of insect susceptibility, in relation to the identification of species and sub species, such as molecular forms or biotypes. Identification of knock down resistance (kdr) and acetylcholinesterase gene (Ace1) mutations modifying insecticide targets in individual insects and measure of enzymes activity typically involved in insecticide metabolism (oxidase, esterase and glutathion-S-transferase) are indispensable in understanding the mechanisms of resistance. Insecticide resistance is a good example in which genotype-phenotype links have been made successfully. Insecticides used in agriculture continue to select new resistant populations of B. tabaci that could be from different biotype vectors of plant viruses. As well, the evolution of insecticide resistance in An. gambiae threatens the management of malaria vectors in West Africa. It raises the question of priority in the use of insecticides in health and/or agriculture, and more generally, the question of sustainability of crop protection and vector control strategies in the region. Here, we review the susceptibility tests, biochemical and molecular assays data for B. tabaci, a major pest in cotton and vegetable crops, and An. gambiae, main vector of malaria. The data reviewed was collected in Benin and Burkina

Genetic networking of the Bemisia tabaci cryptic species complex reveals pattern of biological invasions.

PubMed

De Barro, Paul; Ahmed, Muhammad Z

2011-01-01

A challenge within the context of cryptic species is the delimitation of individual species within the complex. Statistical parsimony network analytics offers the opportunity to explore limits in situations where there are insufficient species-specific morphological characters to separate taxa. The results also enable us to explore the spread in taxa that have invaded globally. Using a 657 bp portion of mitochondrial cytochrome oxidase 1 from 352 unique haplotypes belonging to the Bemisia tabaci cryptic species complex, the analysis revealed 28 networks plus 7 unconnected individual haplotypes. Of the networks, 24 corresponded to the putative species identified using the rule set devised by Dinsdale et al. (2010). Only two species proposed in Dinsdale et al. (2010) departed substantially from the structure suggested by the analysis. The analysis of the two invasive members of the complex, Mediterranean (MED) and Middle East - Asia Minor 1 (MEAM1), showed that in both cases only a small number of haplotypes represent the majority that have spread beyond the home range; one MEAM1 and three MED haplotypes account for >80% of the GenBank records. Israel is a possible source of the globally invasive MEAM1 whereas MED has two possible sources. The first is the eastern Mediterranean which has invaded only the USA, primarily Florida and to a lesser extent California. The second are western Mediterranean haplotypes that have spread to the USA, Asia and South America. The structure for MED supports two home range distributions, a Sub-Saharan range and a Mediterranean range. The MEAM1 network supports the Middle East - Asia Minor region. The network analyses show a high level of congruence with the species identified in a previous phylogenetic analysis. The analysis of the two globally invasive members of the complex support the view that global invasion often involve very small portions of the available genetic diversity.

Detection of resistance, cross-resistance, and stability of resistance to new chemistry insecticides in Bemisia tabaci (Homoptera: Aleyrodidae).

PubMed

Basit, Muhammad; Saeed, Shafqat; Saleem, Mushtaq Ahmad; Denholm, Ian; Shah, Maqbool

2013-06-01

Resistance levels in whitefly, Bemisia tabaci (Gennadius) collections from cotton and sunflower (up to four districts) for five neonicotinoids and two insect growth regulators (IGRs) were investigated for two consecutive years. Based on the LC50(s), all collections showed slight to moderate levels of resistance for the tested insecticides compared with the laboratory susceptible population. The data also indicated that cotton and sunflower collections had similar resistance levels. In comparison (four collections), Vehari collections showed higher resistance for acetamiprid, thiacloprid, and nitenpyram compared with those of others. Average resistance ratios for acetamiprid, thiacloprid, and nitenpyram ranged from 5- to 13-, 4- to 8-, and 9- to 13-fold, respectively. Multan and Vehari collections also exhibited moderate levels (9- to 16-fold) of resistance to buprofezin. Furthermore, toxicity of neonicotinoids against immature stages was equal to that of insect growth regulators. The data also suggested that resistance in the field populations was stable. After selection for four generations with bifenthrin (G1 to G4), resistance to bifenthrin increased to 14-fold compared with the laboratory susceptible population. Selection also increased resistance to fenpropathrin, lambdacyhalothrin, imidacloprid, acetamiprid, and diafenthuron. Cross-resistance and stability of resistance in the field populations is of some concern. Rotation of insecticides having no cross-resistance and targeting the control against immature stages may control the resistant insects, simultaneously reducing the selection pressure imposed.

Molecular characterizations of DNA methyltransferase 3 and its roles in temperature tolerance in the whitefly, Bemisia tabaci Mediterranean.

PubMed

Dai, T-M; Lü, Z-C; Wang, Y-S; Liu, W-X; Hong, X-Y; Wan, F-H

2018-02-01

The Bemisia tabaci Mediterranean (MED) cryptic species is an invasive pest, distributed worldwide, with high ecological adaptability and thermotolerance. DNA methylation (a reversible chromatin modification) is one possible change that may occur within an organism subjected to environmental stress. To assess the effects of temperature stress on DNA methyltransferase 3 (Dnmt3) in MED, we cloned and sequenced BtDnmt3 and identified its functions in response to high and low temperatures. The full-length cDNA of BtDnmt3 was 3913 bp, with an open reading frame of 1962 bp, encoding a 73.89 kDa protein. In situ hybridization showed that BtDnmt3 was expressed mainly in the posterior region. BtDnmt3 messenger RNA expression levels were significantly down-regulated after exposure to heat shock and significantly up-regulated after exposure to cold shock. Furthermore, after feeding on double-stranded RNA specific for BtDnmt3, both heat resistance and cold resistance were significantly decreased, suggesting that BtDnmt3 is associated with thermal stress response and indicating a differential response to high- and low-temperature stress in MED. Together, these results highlight a potential role for DNA methylation in thermal resistance, which is a process important to successful invasion and colonization of an alien species in various environments. © 2017 The Royal Entomological Society.

Spectral separability and mapping potential of cassava leaf damage symptoms caused by whiteflies (Bemisia tabaci)

PubMed Central

De Barro, Paul; Newnham, Glenn J; Kalyebi, Andrew; Macfadyen, Sarina; Malthus, Tim J

2017-01-01

Abstract BACKGROUND This study examines whether leaf spectra can be used to measure damage to cassava plants from whitefly (Bemisia tabaci), and the potential to translate measurements from leaf to landscape scale in eastern Africa. Symptoms of the cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) viruses, and sooty mould (SM) blackening of lower leaves from whiteflies feeding on the upper leaves, were measured at the leaf scale with a high‐resolution spectroradiometer and a single photon avalanche diode (SPAD) meter, which retrieves relative chlorophyll concentration. Spectral measurements were compared to the five‐level visual scores used to assess the severity of each of the three damaging agents in the field, and also to leaf chemistry data. RESULTS Leaves exhibiting severe CBSD and CMD were spectrally indistinguishable from leaves without any symptoms. Severe SM was spectrally distinctive but is likely to be difficult to map because of its occurrence in the lower crown. SPAD measurements were highly correlated with most foliar chemistry measurements and field scores of disease severity. Regression models between simulated Sentinel 2 bands, field scores and SPAD measurements were strongest using wavelengths with high importance weightings in random forest models. CONCLUSION SPAD measurements are highly correlated to many foliar chemistry parameters, and should be considered for use in mapping disease severity over larger areas. Remaining challenges for mapping relate to the subtle expression of symptoms, the spatial distribution of disease severity within fields, and the small size and complex structure of the cassava fields themselves. © 2017 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. PMID:28851022

Spectral separability and mapping potential of cassava leaf damage symptoms caused by whiteflies (Bemisia tabaci).

PubMed

Sims, Neil C; De Barro, Paul; Newnham, Glenn J; Kalyebi, Andrew; Macfadyen, Sarina; Malthus, Tim J

2018-01-01

This study examines whether leaf spectra can be used to measure damage to cassava plants from whitefly (Bemisia tabaci), and the potential to translate measurements from leaf to landscape scale in eastern Africa. Symptoms of the cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) viruses, and sooty mould (SM) blackening of lower leaves from whiteflies feeding on the upper leaves, were measured at the leaf scale with a high-resolution spectroradiometer and a single photon avalanche diode (SPAD) meter, which retrieves relative chlorophyll concentration. Spectral measurements were compared to the five-level visual scores used to assess the severity of each of the three damaging agents in the field, and also to leaf chemistry data. Leaves exhibiting severe CBSD and CMD were spectrally indistinguishable from leaves without any symptoms. Severe SM was spectrally distinctive but is likely to be difficult to map because of its occurrence in the lower crown. SPAD measurements were highly correlated with most foliar chemistry measurements and field scores of disease severity. Regression models between simulated Sentinel 2 bands, field scores and SPAD measurements were strongest using wavelengths with high importance weightings in random forest models. SPAD measurements are highly correlated to many foliar chemistry parameters, and should be considered for use in mapping disease severity over larger areas. Remaining challenges for mapping relate to the subtle expression of symptoms, the spatial distribution of disease severity within fields, and the small size and complex structure of the cassava fields themselves. © 2017 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. © 2017 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Transcriptome analysis of the whitefly, Bemisia tabaci MEAM1 during feeding on tomato infected with the crinivirus, Tomato chlorosis virus, identifies a temporal shift in gene expression and differential regulation of novel orphan genes.

PubMed

Kaur, Navneet; Chen, Wenbo; Zheng, Yi; Hasegawa, Daniel K; Ling, Kai-Shu; Fei, Zhangjun; Wintermantel, William M

2017-05-11

Whiteflies threaten agricultural crop production worldwide, are polyphagous in nature, and transmit hundreds of plant viruses. Little is known how whitefly gene expression is altered due to feeding on plants infected with a semipersistently transmitted virus. Tomato chlorosis virus (ToCV; genus Crinivirus, family Closteroviridae) is transmitted by the whitefly (Bemisia tabaci) in a semipersistent manner and infects several globally important agricultural and ornamental crops, including tomato. To determine changes in global gene regulation in whiteflies after feeding on tomato plants infected with a crinivirus (ToCV), comparative transcriptomic analysis was performed using RNA-Seq on whitefly (Bemisia tabaci MEAM1) populations after 24, 48, and 72 h acquisition access periods on either ToCV-infected or uninfected tomatoes. Significant differences in gene expression were detected between whiteflies fed on ToCV-infected tomato and those fed on uninfected tomato among the three feeding time periods: 447 up-regulated and 542 down-regulated at 24 h, 4 up-regulated and 7 down-regulated at 48 h, and 50 up-regulated and 160 down-regulated at 72 h. Analysis revealed differential regulation of genes associated with metabolic pathways, signal transduction, transport and catabolism, receptors, glucose transporters, α-glucosidases, and the uric acid pathway in whiteflies fed on ToCV-infected tomatoes, as well as an abundance of differentially regulated novel orphan genes. Results demonstrate for the first time, a specific and temporally regulated response by the whitefly to feeding on a host plant infected with a semipersistently transmitted virus, and advance the understanding of the whitefly vector-virus interactions that facilitate virus transmission. Whitefly transmission of semipersistent viruses is believed to require specific interactions between the virus and its vector that allow binding of virus particles to factors within whitefly mouthparts. Results provide a

Selection and validation of reference genes for qRT-PCR analysis during biological invasions: The thermal adaptability of Bemisia tabaci MED.

PubMed

Dai, Tian-Mei; Lü, Zhi-Chuang; Liu, Wan-Xue; Wan, Fang-Hao

2017-01-01

The Bemisia tabaci Mediterranean (MED) cryptic species has been rapidly invading to most parts of the world owing to its strong ecological adaptability, which is considered as a model insect for stress tolerance studies under rapidly changing environments. Selection of a suitable reference gene for quantitative stress-responsive gene expression analysis based on qRT-PCR is critical for elaborating the molecular mechanisms of thermotolerance. To obtain accurate and reliable normalization data in MED, eight candidate reference genes (β-act, GAPDH, β-tub, EF1-α, GST, 18S, RPL13A and α-tub) were examined under various thermal stresses for varied time periods by using geNorm, NormFinder and BestKeeper algorithms, respectively. Our results revealed that β-tub and EF1-α were the best reference genes across all sample sets. On the other hand, 18S and GADPH showed the least stability for all the samples studied. β-act was proved to be highly stable only in case of short-term thermal stresses. To our knowledge this was the first comprehensive report on validation of reference genes under varying temperature stresses in MED. The study could expedite particular discovery of thermotolerance genes in MED. Further, the present results can form the basis of further research on suitable reference genes in this invasive insect and will facilitate transcript profiling in other invasive insects.

Host-parasitoid interactions relating to penetration of the whitefly, Bemisia tabaci, by the parasitoid wasp, Eretmocerus mundus

PubMed Central

Gelman, Dale B.; Gerling, Dan; Blackburn, Michael A.

2005-01-01

It has been reported that the aphelinid wasp Eertmocerus mundus parasitizes all four nymphal instars of the sweet potato whitefly, Bemisia tabaci (Biotype B), with 3rd instars being the preferred hosts. The parasitoid lays its egg on the leaf underneath the host nymph. First instars hatch and later penetrate the whitefly. Previous studies have shown that the initiation of parasitoid penetration induces the host to form a cellular capsule around the parasitoid. As described here, females never oviposited once the 4th instar whitefly nymph had initiated adult development. First instar E. mundus larvae were observed under 2nd, 3rd and 4th instar whitefly nymphs, however, penetration did not occur until the whitefly had reached the 4th instar. The non-penetrating E. mundus larva almost always induced permanent developmental arrest in its 4th instar whitefly host and also caused a reduction in whole body host ecdysteroid titers. Therefore, unless there is a peak in molting hormone titer in the area local to penetration, it appears that the induction of capsule formation is not due to an increase in ecdysteroid titer. As the capsule formed around the penetrating parasitoid, host epidermal cells multiplied and became cuboidal and columnar, and relatively thick layers of new cuticle were deposited within the developing capsule, particularly near its ventral opening. The newly formed host cuticle was thinner in the dorsal part of the capsule and appeared to be absent at its apex. These results provide new information regarding the timing and dynamics of parasitoid oviposition and egg hatch as related to larval penetration, parasitoid-induced changes in whitefly development, molting hormone titers and the process of capsule formation. PMID:17119628

A landscape genetic analysis of important agricultural pest species in Tunisia: The whitefly Bemisia tabaci

PubMed Central

Fakhfakh, Hatem; Belkadhi, Mohamed Sadok

2017-01-01

Combining landscape ecology and genetics provides an excellent framework to appreciate pest population dynamics and dispersal. The genetic architectures of many species are always shaped by environmental constraints. Because little is known about the ecological and genetic traits of Tunisian whitefly populations, the main objective of this work is to highlight patterns of biodiversity, genetic structure and migration routes of this pest. We used nuclear microsatellite loci to analyze B. tabaci populations collected from various agricultural areas across the country and we determine their biotype status. Molecular data were subsequently interpreted in an ecological context supplied from a species distribution model to infer habitat suitability and hereafter the potential connection paths between sampling localities. An analysis of landscape resistance to B. tabaci genetic flow was thus applied to take into account habitat suitability, genetic relatedness and functional connectivity of habitats within a varied landscape matrix. We shed light on the occurrence of three geographically delineated genetic groups with high levels of genetic differentiation within each of them. Potential migration corridors of this pest were then established providing significant advances toward the understanding of genetic features and the dynamic dispersal of this pest. This study supports the hypothesis of a long-distance dispersal of B. tabaci followed by infrequent long-term isolations. The Inference of population sources and colonization routes is critical for the design and implementation of accurate management strategies against this pest. PMID:28972992

A landscape genetic analysis of important agricultural pest species in Tunisia: The whitefly Bemisia tabaci.

PubMed

Ben Abdelkrim, Ahmed; Hattab, Tarek; Fakhfakh, Hatem; Belkadhi, Mohamed Sadok; Gorsane, Faten

2017-01-01

Combining landscape ecology and genetics provides an excellent framework to appreciate pest population dynamics and dispersal. The genetic architectures of many species are always shaped by environmental constraints. Because little is known about the ecological and genetic traits of Tunisian whitefly populations, the main objective of this work is to highlight patterns of biodiversity, genetic structure and migration routes of this pest. We used nuclear microsatellite loci to analyze B. tabaci populations collected from various agricultural areas across the country and we determine their biotype status. Molecular data were subsequently interpreted in an ecological context supplied from a species distribution model to infer habitat suitability and hereafter the potential connection paths between sampling localities. An analysis of landscape resistance to B. tabaci genetic flow was thus applied to take into account habitat suitability, genetic relatedness and functional connectivity of habitats within a varied landscape matrix. We shed light on the occurrence of three geographically delineated genetic groups with high levels of genetic differentiation within each of them. Potential migration corridors of this pest were then established providing significant advances toward the understanding of genetic features and the dynamic dispersal of this pest. This study supports the hypothesis of a long-distance dispersal of B. tabaci followed by infrequent long-term isolations. The Inference of population sources and colonization routes is critical for the design and implementation of accurate management strategies against this pest.

Metabolic coevolution in the bacterial symbiosis of whiteflies and related plant sap-feeding insects

USDA-ARS?s Scientific Manuscript database

In animals dependent on intracellular bacteria with very small genomes, the host cell is adapted to support the function of its bacterial symbionts, but the molecular basis of these adaptations is poorly understood. We investigated the metabolic coevolution between the whitefly Bemisia tabaci and th...

Differential gene expression in whitefly Bemisia tabaci-infested tomato (Solanum lycopersicum) plants at progressing developmental stages of the insect's life cycle.

PubMed

Estrada-Hernández, María Gloria; Valenzuela-Soto, José Humberto; Ibarra-Laclette, Enrique; Délano-Frier, John Paul

2009-09-01

A suppression-subtractive-hybridization (SSH) strategy was used to identify genes whose expression was modified in response to virus-free whitefly Bemisia tabaci (Bt, biotype A) infestation in tomato (Solanum lycopersicum) plants. Thus, forward and reverse SSH gene libraries were generated at four points in the whitefly's life cycle, namely at (1) 2 days (adult feeding and oviposition: phase I); (2) 7 days (mobile crawler stage: phase II); (3) 12 days (second to third instar nymphal transition: phase III) and (4) 18 days (fourth instar nymphal stage: phase IV). The 169 genes with altered expression (up and downregulated) that were identified in the eight generated SSH libraries, together with 75 additional genes that were selected on the basis of their involvement in resistance responses against phytofagous insects and pathogens, were printed on a Nexterion(®) Slide MPX 16 to monitor their pattern of expression at the above phases. The results indicated that Bt infestation in tomato led to distinctive phase-specific expression/repression patterns of several genes associated predominantly with photosynthesis, senescence, secondary metabolism and (a)biotic stress. Most of the gene expression modifications were detected in phase III, coinciding with intense larval feeding, whereas fewer changes were detected in phases I and IV. These results complement previously reported gene expression profiles in Bt-infested tomato and Arabidopisis, and support and expand the opinion that Bt infestation leads to the downregulation of specific defense responses in addition to those controlled by jasmonic acid. Copyright © Physiologia Plantarum 2009.

Thermotolerance and Heat-Shock Protein Gene Expression Patterns in Bemisia tabaci (Hemiptera: Aleyrodidae) Mediterranean in Relation to Developmental Stage.

PubMed

Jiang, Rui; Qi, Lan-Da; Du, Yu-Zhou; Li, Yuan-Xi

2017-10-01

Temperature plays an important role in the growth, development, and geographic distribution of insects. There is convincing evidence that heat-shock proteins (HSPs) play important roles in helping organisms adapt to thermal stress. To better understand the physiological and ecological influence of thermal stress on the different development stages of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) Mediterranean species (MED), nymphs and adults were shocked with temperatures of 35, 38, and 41℃ for 1 and 2 h, respectively, and the survival rate, fecundity, and developmental duration were investigated in the laboratory. The expression levels of the hsp40, hsp70, and hsp90 genes were assessed using real-time PCR. The results indicate that the survival rates of the nymphs and adults decreased with increased temperature. A 2-h heat shock at 41℃ induced a significant reduction in fecundity in adults and an increase in developmental duration in young nymphs. Hsp90 showed higher temperature responses to thermal stress than hsp40 or hsp70. The expression levels of the hsps in the adults were significantly down-regulated by a 2-h heat shock at 41℃ compared with that by a 1-h treatment. A significant decrease in the expression levels of the hsps also occurred in the adults when the temperature increased from 38 to 41℃ for the 2-h treatment, whereas no significant decrease occurred in the nymphs. Compared with previous studies, we provide some evidence indicating that MED has the potential to adapt to a wider temperature range than the Middle East-Asia Minor 1 species. © The Author 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Susceptibility of Bemisia tabaci MEAM1 (Hemiptera: Aleyrodidae) to imidacloprid, thiamethoxam, dinotefuran and flupyradifurone in south Florida

USDA-ARS?s Scientific Manuscript database

Populations of Bemisa tabaci Middle East Asia Minor 1 (MEAM 1) were established from nineteen locations in south Florida, primarily from commercial tomato fields, and were tested using a cotton leaf petiole systemic uptake method for susceptibility to the nicotinic acetylcholine agonist insecticides...

The invasive MED/Q Bemisia tabaci genome: a tale of gene loss and gene gain

USDA-ARS?s Scientific Manuscript database

Whiteflies are a group of invasive crop pests that impact global agriculture. An analysis was conducted to compare draft genomes of two whitefly strains, which demonstrated the relative conserved gene order, but a number of genes were either novel (added) or omitted (deleted) between genomes. This...

Increased survival and prolonged longevity mainly contribute to the temperature-adaptive evolutionary strategy in invasive Bemisia tabaci (Hemiptera: Aleyrodidae) Middle East Asia Minor 1.

PubMed

Lü, Zhi-Chuang; Gao, Qing-Lei; Wan, Fang-Hao; Yu, Hao; Guo, Jian-Ying

2014-10-15

With increasing global climate change, analyses of stress-inducing conditions have important significance in ecological adaptation and the biological distribution of species. To reveal the difference in temperature-adaptive strategy between Turpan and Beijing populations of Bemisia tabaci (Gennadius) Middle East Asia Minor 1 (MEAM1) under high-temperature stress conditions, we compared thermal tolerance and life history traits between Beijing and Turpan populations of MEAM1 after exposure to different heat shock treatments for different times. The experimental design reflected the nature of heat stress conditions suffered by MEAM1. The results showed that eggs, red-eyed pupae, and adults of the Turpan population were more heat tolerant than those of the Beijing population under the same stress conditions. Additionally, it was found that longevity and F1 adult survival rate were significantly higher in the Turpan population than in the Beijing population after heat shock stress, but egg number and F1 female ratio were not significantly different between Turpan population and Beijing population. Overall, it was suggested that heat tolerance and longevity traits were the most relevant for climate characteristics and not reproductive traits, and improved heat tolerance and prolonged longevity were important adaptive strategies that helped MEAM1 to survive in harsh high-temperature conditions such as Turpan arid desert climate. The present results provided further insight into the modes of heat tolerance and the ways in which survival and longevity traits respond to environmental selection pressures. © The Author 2014. Published by Oxford University Press on behalf of the Entomological Society of America.

Resistance Mechanisms to Chlorpyrifos and F392W Mutation Frequencies in the Acetylcholine Esterase Ace1 Allele of Field Populations of the Tobacco Whitefly, Bemisia tabaci in China

PubMed Central

Zhang, Ning-ning; Liu, Cai-feng; Yang, Fang; Dong, Shuang-lin; Han, Zhao-jun

2012-01-01

The tobacco whitefly B-biotype Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae) is a worldwide pest of many crops. In China, chlorpyrifos has been used to control this insect for many years and is still being used despite the fact that some resistance has been reported. To combat resistance and maintain good control efficiency of chlorpyrifos, it is essential to understand resistance mechanisms. A chlorpyrifos resistant tobacco whitefly strain (NJ-R) and a susceptible strain (NJ-S) were derived from a field-collected population in Nanjing, China, and the resistance mechanisms were investigated. More than 30-fold resistance was achieved after selected by chlorpyrifos for 13 generations in the laboratory. However, the resistance dropped significantly to about 18-fold in only 4 generations without selection pressure. Biochemical assays indicated that increased esterase activity was responsible for this resistance, while acetylcholine esterase, glutathione S-transferase, and microsomal-O-demethylase played little or no role. F392W mutations in acel were prevalent in NJ-S and NJ-R strains and 6 field-collected populations of both B and Q-biotype from locations that cover a wide geographical area of China. These findings provide important information about tobacco whitefly chlorpyrifos resistance mechanisms and guidance to combat resistance and optimize use patterns of chlorpyrifos and other organophosphate and carbamate insecticides. PMID:22954331

Genome Evolution in the Primary Endosymbiont of Whiteflies Sheds Light on Their Divergence

PubMed Central

Santos-Garcia, Diego; Vargas-Chavez, Carlos; Moya, Andrés; Latorre, Amparo; Silva, Francisco J.

2015-01-01

Whiteflies are important agricultural insect pests, whose evolutionary success is related to a long-term association with a bacterial endosymbiont, Candidatus Portiera aleyrodidarum. To completely characterize this endosymbiont clade, we sequenced the genomes of three new Portiera strains covering the two extant whitefly subfamilies. Using endosymbiont and mitochondrial sequences we estimated the divergence dates in the clade and used these values to understand the molecular evolution of the endosymbiont coding sequences. Portiera genomes were maintained almost completely stable in gene order and gene content during more than 125 Myr of evolution, except in the Bemisia tabaci lineage. The ancestor had already lost the genetic information transfer autonomy but was able to participate in the synthesis of all essential amino acids and carotenoids. The time of divergence of the B. tabaci complex was much more recent than previous estimations. The recent divergence of biotypes B (MEAM1 species) and Q (MED species) suggests that they still could be considered strains of the same species. We have estimated the rates of evolution of Portiera genes, synonymous and nonsynonymous, and have detected significant differences among-lineages, with most Portiera lineages evolving very slowly. Although the nonsynonymous rates were much smaller than the synonymous, the genomic dN/dS ratios were similar, discarding selection as the driver of among-lineage variation. We suggest variation in mutation rate and generation time as the responsible factors. In conclusion, the slow evolutionary rates of Portiera may have contributed to its long-term association with whiteflies, avoiding its replacement by a novel and more efficient endosymbiont. PMID:25716826

Development of a lateral flow test to detect metabolic resistance in Bemisia tabaci mediated by CYP6CM1, a cytochrome P450 with broad spectrum catalytic efficiency.

PubMed

Nauen, Ralf; Wölfel, Katharina; Lueke, Bettina; Myridakis, Antonis; Tsakireli, Dimitra; Roditakis, Emmanouil; Tsagkarakou, Anastasia; Stephanou, Euripides; Vontas, John

2015-06-01

Cotton whitefly, Bemisia tabaci (Genn.) (Homoptera: Aleyrodidae) is a major sucking pest in many agricultural and horticultural cropping systems globally. The frequent use of insecticides of different mode of action classes resulted in populations resisting treatments used to keep numbers under economic damage thresholds. Recently it was shown that resistance to neonicotinoids such as imidacloprid is linked to the over-expression of CYP6CM1, a cytochrome P450 monooxygenase detoxifying imidacloprid and other neonicotinoid insecticides when recombinantly expressed in insect cells. However over-expression of CYP6CM1 is also known to confer cross-resistance to pymetrozine, an insecticide not belonging to the chemical class of neonicotinoids. In addition we were able to demonstrate by LC-MS/MS analysis the metabolisation of pyriproxyfen by recombinantly expressed CYP6CM1. Based on our results CYP6CM1 is one of the most versatile detoxification enzymes yet identified in a pest of agricultural importance, as it detoxifies a diverse range of chemical classes used to control whiteflies. Therefore we developed a field-diagnostic antibody-based lateral flow assay which detects CYP6CM1 protein at levels providing resistance to neonicotinoids and other insecticides. The ELISA based test kit can be used as a diagnostic tool to support resistance management strategies based on the alternation of different modes of action of insecticides. Copyright © 2014 Elsevier Inc. All rights reserved.

Identification of a whitefly species by genomic and behavioral studies

USGS Publications Warehouse

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

1993-01-01

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

A massive incorporation of microbial genes into the genome of Tetranychus urticae, a polyphagous arthropod herbivore.

PubMed

Wybouw, N; Van Leeuwen, T; Dermauw, W

2018-06-01

A number of horizontal gene transfers (HGTs) have been identified in the spider mite Tetranychus urticae, a chelicerate herbivore. However, the genome of this mite species has at present not been thoroughly mined for the presence of HGT genes. Here, we performed a systematic screen for HGT genes in the T. urticae genome using the h-index metric. Our results not only validated previously identified HGT genes but also uncovered 25 novel HGT genes. In addition to HGT genes with a predicted biochemical function in carbohydrate, lipid and folate metabolism, we also identified the horizontal transfer of a ketopantoate hydroxymethyltransferase and a pantoate β-alanine ligase gene. In plants and bacteria, both genes are essential for vitamin B5 biosynthesis and their presence in the mite genome strongly suggests that spider mites, similar to Bemisia tabaci and nematodes, can synthesize their own vitamin B5. We further show that HGT genes were physically embedded within the mite genome and were expressed in different life stages. By screening chelicerate genomes and transcriptomes, we were able to estimate the evolutionary histories of these HGTs during chelicerate evolution. Our study suggests that HGT has made a significant and underestimated impact on the metabolic repertoire of plant-feeding spider mites. © 2018 The Royal Entomological Society.

Herbivory by Thrips tabaci

Treesearch

Deborah M. Kendall

1991-01-01

Herbivory by Thrips tabaci (Lindeman) affects both the bulb yield and phytohormone balance in its major host plant, the onion (Alium cepa L.). Seasonal changes in the susceptibility of onion yield to T. tabaci feeding were examined during the three growth stages of onion; prebulbing, bulbing and sizing (Kendall...

Evaluating plant and plant oil repellency against the sweetpotato whitefly

USDA-ARS?s Scientific Manuscript database

The sweetpotato whitefly, Bemisia tabaci is a major insect pest of vegetables world-wide. We evaluated the effect of commercial plant oils – garlic oil, hot pepper wax, and mustard oil against B. tabaci. Cucumber plants served as the control. Additional treatments included no plants or oil (clear ai...

Metabolic Coevolution in the Bacterial Symbiosis of Whiteflies and Related Plant Sap-Feeding Insects.

PubMed

Luan, Jun-Bo; Chen, Wenbo; Hasegawa, Daniel K; Simmons, Alvin M; Wintermantel, William M; Ling, Kai-Shu; Fei, Zhangjun; Liu, Shu-Sheng; Douglas, Angela E

2015-09-15

Genomic decay is a common feature of intracellular bacteria that have entered into symbiosis with plant sap-feeding insects. This study of the whitefly Bemisia tabaci and two bacteria (Portiera aleyrodidarum and Hamiltonella defensa) cohoused in each host cell investigated whether the decay of Portiera metabolism genes is complemented by host and Hamiltonella genes, and compared the metabolic traits of the whitefly symbiosis with other sap-feeding insects (aphids, psyllids, and mealybugs). Parallel genomic and transcriptomic analysis revealed that the host genome contributes multiple metabolic reactions that complement or duplicate Portiera function, and that Hamiltonella may contribute multiple cofactors and one essential amino acid, lysine. Homologs of the Bemisia metabolism genes of insect origin have also been implicated in essential amino acid synthesis in other sap-feeding insect hosts, indicative of parallel coevolution of shared metabolic pathways across multiple symbioses. Further metabolism genes coded in the Bemisia genome are of bacterial origin, but phylogenetically distinct from Portiera, Hamiltonella and horizontally transferred genes identified in other sap-feeding insects. Overall, 75% of the metabolism genes of bacterial origin are functionally unique to one symbiosis, indicating that the evolutionary history of metabolic integration in these symbioses is strongly contingent on the pattern of horizontally acquired genes. Our analysis, further, shows that bacteria with genomic decay enable host acquisition of complex metabolic pathways by multiple independent horizontal gene transfers from exogenous bacteria. Specifically, each horizontally acquired gene can function with other genes in the pathway coded by the symbiont, while facilitating the decay of the symbiont gene coding the same reaction. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Geraniol encapsulated in chitosan/gum arabic nanoparticles: a promising system for pest management in sustainable agriculture.

PubMed

de Oliveira, Jhones Luiz; Campos, Estefania Vangelie Ramos; Pereira, Anderson E S; Nunes, Lucas E S; da Silva, Camila C L; Pasquoto, Tatiane; Lima, Renata; Smaniotto, Giovani; Polanczyk, Ricardo Antonio; Fraceto, Leonardo F

2018-05-07

The nanoencapsulation of botanical compounds (such as geraniol) is an important strategy that can be used to increase the stability and efficiency of these substances in integrated pest management. In this study, chitosan/gum arabic nanoparticles containing geraniol were prepared and characterized. In addition, evaluation was made of the biological activity of geraniol encapsulated in chitosan/gum arabic nanoparticles towards whitefly (Bemisia tabaci). The optimized formulation showed a high encapsulation efficiency (>90%) and remained stable for about 120 days. The formulation protected the geraniol against degradation by UV radiation, and the in vitro release was according to a diffusion mechanism that was influenced by temperature. An attraction effect was observed for Bemisia tabaci, indicating the potential of this type of system for use in pest management, especially in trap devices.

Effects of selected defoliants in combination with insecticides on sweetpotato whitefly (Hemiptera: Aleyrodidae) and its parasitoids in cotton

USDA-ARS?s Scientific Manuscript database

Effects of two defoliants, Def (S, S, Stributylphosphorotrithioate) and Dropp (thidiazuron) alone and in combination with two commonly used insecticides, a pyrethroid, Karate (lambda-cyhalothrin) and an organophosphate, Guthion (azinphosmethyl) on sweetpotato whitefly, Bemisia tabaci Gennadius Bioty...

Virus infection of a weed increases vector attraction to and vector fitness on the weed.

PubMed

Chen, Gong; Pan, Huipeng; Xie, Wen; Wang, Shaoli; Wu, Qingjun; Fang, Yong; Shi, Xiaobin; Zhang, Youjun

2013-01-01

Weeds are important in the ecology of field crops, and when crops are harvested, weeds often become the main hosts for plant viruses and their insect vectors. Few studies, however, have examined the relationships between plant viruses, vectors, and weeds. Here, we investigated how infection of the weed Datura stramonium L. by tomato yellow leaf curl virus (TYLCV) affects the host preference and performance of the TYLCV vector, Bemisia tabaci (Gennadius) Q. The results of a choice experiment indicated that B. tabaci Q preferentially settled and oviposited on TYLCV-infected plants rather than on healthy plants. In addition, B. tabaci Q performed better on TYLCV-infected plants than on healthy plants. These results demonstrate that TYLCV is indirectly mutualistic to B. tabaci Q. The mutually beneficial interaction between TYLCV and B. tabaci Q may help explain the concurrent outbreaks of TYLCV and B. tabaci Q in China.

Susceptibility of ornamental pepper banker plant candidates to common greenhouse pests

USDA-ARS?s Scientific Manuscript database

Susceptibility of four potential ornamental pepper banker plant candidates [Black Pearl (BP), Explosive Ember (EE), Masquerade (MA), Red Missile (RM), and a commercial pepper cultivar Blitz (BL)] were evaluated against three common greenhouse pests - Bemisia tabaci, Polyphagotarsonemus latus and Fra...

Comparative toxicities of newer and conventional insecticides against four generalist predator species

USDA-ARS?s Scientific Manuscript database

Generalist insect predators play an essential role at regulating populations of Bemisia tabaci and other pests in agricultural systems, but face depredations due to insecticide applications. Evaluation of insecticide compatibility with specific predator species can provide a basis for making treatme...

Potential sources of whitefly (Hemiptera: Aleyrodidae) resistance in desert watermelon (Citrullus colocynthis) germplasm

USDA-ARS?s Scientific Manuscript database

Selection for host plant resistance and incorporation of natural resistance into cultivars is a fundamental strategy to control insects and diseases in an environmentally-sensitive manner, and may help reduce reliance on synthetic pesticides. The sweetpotato whitefly, Bemisia tabaci (Gennadius), is...

Transcriptomics-guided development of RNA interference strategies to manage whiteflies: a globally distributed vector of crop viruses

USDA-ARS?s Scientific Manuscript database

Over 300 viruses are transmitted by the whitefly, Bemisia tabaci, with 90% of them belonging to the genus, Begomovirus. Begomoviruses are exclusively transmitted by whiteflies to a range of agriculture crops, resulting in billions of dollars lost annually, while jeopardizing food security worldwide....

Whitefly transmission of Sweet potato leaf curl virus in sweetpotato germplasm

USDA-ARS?s Scientific Manuscript database

Sweetpotato, Ipomoea batatas (L.) Lam., is among an extensive number of plant species attacked by Bemisia tabaci (Gennadius). Because this important world food crop is vegetatively propagated, it can conveniently accumulate infections by several viruses. Sweet potato leaf curl virus (SPLCV) (ssDNA...

Persistent, circulative transmission of begomoviruses by whitefly vectors

USDA-ARS?s Scientific Manuscript database

Begomoviruses comprise an emerging and economically important group of plant viruses exclusively transmitted by the sweetpotato whitefly Bemisia tabaci in many regions of the world. The past twenty years have witnessed significant progress in studying the molecular interactions between members of th...

Partial leaf chemical profiles of a desert watermelon species (Citrullus colocynthis) and heirloom watermelon cultivars (Citrullus lanatus var. lanatus)

USDA-ARS?s Scientific Manuscript database

Whiteflies [Bemisia tabaci (Gennadius)] and aphids [Aphis gossypii Glover and Myzus persicae (Sulzer)] are serious threats to watermelon by direct feeding and by transmitting viruses of important virus diseases. The desert watermelon Citrullus colocynthis (L.) has been shown to exhibit resistance t...

RNAi-mediated mortality of the whitefly through transgenic expression of double-stranded RNA homologous to acetylcholinesterase and ecdysone receptor in tobacco plants

USDA-ARS?s Scientific Manuscript database

The whitefly Bemisia tabaci (Genn.) is a pest and vector of plant viruses affecting plants worldwide. Using RNA interference (RNAi) to downregulate whitefly genes by expressing their homologous double stranded RNAs in plants has great potential for management of whiteflies to reduce plant virus dise...

Developing ribonucleic acid interference technology to manage whitefly-transmitted begomoviruses

USDA-ARS?s Scientific Manuscript database

Of nearly 300 viruses transmitted by the whitefly (Bemisia tabaci), 90% of them belong to the genus Begomovirus. Begomoviruses are efficiently transmitted by whiteflies to a range of agricultural crops. This results in billions of dollars lost annually, while jeopardizing food security worldwide. Se...

Isaria poprawskii sp. nov. (Hypocreales: Cordycipitacae), a new entomopathogenic fungus from Texas affecting sweet potato whitefly

USDA-ARS?s Scientific Manuscript database

Isaria poprawskii is described as a new entomopathogenic species similar to Isaria javanica (=Paecilomyces javanicus). It was discovered ont he sweet potato whitefly, Bemisia tabaci biotype B in the Lower Rio Grande Valley of Texas (LRGV), USA. Morphological and DNA examinations indicated the dist...

Intra- and Interspecific Competition Between Western Flower Thrips and Sweetpotato Whitefly

PubMed Central

Wu, Qing-Jun; Hou, Wen-Jie; Li, Fei; Xu, Bao-Yun; Xie, Wen; Wang, Shao-Li; Zhang, You-Jun

2014-01-01

Abstract The western flower thrips, Frankliniella occidentalis (Pergande), and the sweetpotato whitefly, Bemisia tabaci (Gennadius), are both invasive insect pests and are present in most of the same agricultural crops without a clear dominance of either species. Here, intra- and interspecific competition in B. tabaci and F. occidentalis was determined under controlled experiments. The results showed that intraspecific competition was distinct in F. occidentalis and that the co-occurrence of B. tabaci had a strong effect on F. occidentalis , resulting in a decrease in oviposition. Significant intraspecific competition was found in B. tabaci , and the coexistence of F. occidentalis had limited effect on the oviposition of B. tabaci . In a selective host plant preference experiment, both F. occidentalis and B. tabaci preferred eggplants most, followed by cucumbers and tomatoes. On cucumber plants, B. tabaci was predominant, whereas on eggplant and tomato plants, F. occidentalis and B. tabaci exhibited comparative competitive abilities during the initial stage. However, over time, higher numbers of B. tabaci than that of F. occidentalis were found on the two host plants. Our in vitro and potted plant experiments indicate that B. tabaci is competitively superior to F. occidentalis , which might help to explain their differential distribution patterns in China. PMID:25480973

Companion and refuge plants to control insect pests

USDA-ARS?s Scientific Manuscript database

Introduction: The sweetpotato whitefly, Bemisia tabaci and aphids are major pests of crops in the southeast USA. An environmentally-friendly management strategy is “push-pull” technology which combines the use of repellent (“push”) and trap crops (“pull”) for insect pest control. The repellent crop,...

Effects of a foliar neem formulation on colonization and mortality of whiteflies (Hemiptera: Aleyrodidae) on collard plants

USDA-ARS?s Scientific Manuscript database

A study was conducted to determine the effects of foliar sprays of a selected neem (Azadirachta indica A. Juss) product (GOS Neem 7-Way) on colonization and development by the Middle-East Asia Minor-1 (= B-biotype sweetpotato whitefly) Bemisia tabaci (Gennadius) on collard (Brassica oleracea variety...

Detection of Gene Flow from Sexual to Asexual Lineages in Thrips tabaci (Thysanoptera: Thripidae)

PubMed Central

Li, Xiao-Wei; Wang, Ping; Fail, Jozsef; Shelton, Anthony M.

2015-01-01

Populations of Thrips tabaci are known to have two sympatric but genetically isolated reproductive modes, arrhenotoky (sexual reproduction) and thelytoky (asexual reproduction). Herein, we report behavioral, ecological and genetic studies to determine whether there is gene flow between arrhenotokous and thelytokous T. tabaci. We did not detect significant preference by arrhenotokous males to mate with females of a particular reproductive mode, nor did we detect significant behavioral differences between arrhenotokous males mated with arrhenotokous or thelytokous females in their pre-copulation, copulation duration and mating frequency. Productive gene transfer resulting from the mating between the two modes was experimentally confirmed. Gene transfer from arrhenotokous T. tabaci to thelytokous T. tabaci was further validated by confirmation of the passage of the arrhenotokous male-originated nuclear gene (histone H3 gene) allele to the F2 generation. These behavioral, ecological and genetic studies confirmed gene transfer from the sexual arrhenotokous mode to the asexual thelytokous mode of T. tabaci in the laboratory. These results demonstrate that asexual T. tabaci populations may acquire genetic variability from sexual populations, which could offset the long-term disadvantage of asexual reproduction. PMID:26375283

Recessive resistance to Cucurbit yellow stunting disorder virus in melon

USDA-ARS?s Scientific Manuscript database

Cucurbit yellow stunting disorder virus (CYSDV) reduces melon (Cucumis melo L.) fruit quality and yield in many parts of the world. CYSDV and its vector, sweetpotato whitefly (MEAM1 cryptic species of Bemisia tabaci; SPWF) are a devastating combination in the Sonoran Desert areas of California and A...

Papaya is not a host for Tomato Yellow Leaf Curl Virus

USDA-ARS?s Scientific Manuscript database

The economic value of tomato production is threatened by tomato yellow leaf-curl virus TYLCV and its vector, the silverleaf whitefly Bemisia tabaci biotype B (Gennadius) (Hemiptera: Aleyrodidae). Use of papaya Carica papaya L. as a banker plant for a whitefly parasitoid shows promise as a whitefly m...

Breeding for cotton leaf curl disease (CLCuD) resistance

USDA-ARS?s Scientific Manuscript database

Cotton leaf curl disease (CLCuD) is caused by a whitefly (Bemisia tabaci) transmitted geminivirus. It is a major disease of cotton in Africa and South Asia, and has spread to other countries through ornamental plants. It can potentially devastate U.S. cotton where commercial varieties have no resi...

Tracking disease and insect pests using Smartphone technology: a new approach for regional (and local) pest management

USDA-ARS?s Scientific Manuscript database

Tomato yellow leaf curl virus (TYLCV) is vectored by the silverleaf whitefly (Bemisia tabaci biotype B) and was first detected in south Florida in 1997. The virus has spread widely in Florida and is responsible for millions of dollars of lost production. Anlaysis of data from a comprehensive, multi-...

Epidemiology of Cucurbit yellow stunting disorder virus in the US Southwest and development of virus resistant melon

USDA-ARS?s Scientific Manuscript database

Cucurbit yellow stunting disorder virus (CYSDV), emerged in the Southwest USA in 2006, where it is transmitted by the MEAM1 cryptic species of Bemisia tabaci. The virus results in late-season infection of spring melon crops with limited economic impact; however, all summer and fall cucurbits become ...

A new and potentially damaging whitefly-transmitted virus of cucurbits was found this fall 2014 in Imperial County, CA

USDA-ARS?s Scientific Manuscript database

A new virus that appears to be related to but distinct from Squash vein yellowing virus (SqVYV), a Bemisia tabaci-transmitted ipomovirus (family Potyviridae) that occurs in Florida was found in fall 2014 in Imperial County, CA infecting pumpkin and melon plants and exhibiting symptoms of stunting an...

Intra- and interspecific competition between western flower thrips and sweetpotato whitefly.

PubMed

Wu, Qing-Jun; Hou, Wen-Jie; Li, Fei; Xu, Bao-Yun; Xie, Wen; Wang, Shao-Li; Zhang, You-Jun

2014-01-01

The western flower thrips, Frankliniella occidentalis (Pergande), and the sweetpotato whitefly, Bemisia tabaci (Gennadius), are both invasive insect pests and are present in most of the same agricultural crops without a clear dominance of either species. Here, intra- and interspecific competition in B. tabaci and F. occidentalis was determined under controlled experiments. The results showed that intraspecific competition was distinct in F. occidentalis and that the co-occurrence of B. tabaci had a strong effect on F. occidentalis, resulting in a decrease in oviposition. Significant intraspecific competition was found in B. tabaci, and the coexistence of F. occidentalis had limited effect on the oviposition of B. tabaci. In a selective host plant preference experiment, both F. occidentalis and B. tabaci preferred eggplants most, followed by cucumbers and tomatoes. On cucumber plants, B. tabaci was predominant, whereas on eggplant and tomato plants, F. occidentalis and B. tabaci exhibited comparative competitive abilities during the initial stage. However, over time, higher numbers of B. tabaci than that of F. occidentalis were found on the two host plants. Our in vitro and potted plant experiments indicate that B. tabaci is competitively superior to F. occidentalis, which might help to explain their differential distribution patterns in China. © The Author 2014. Published by Oxford University Press on behalf of the Entomological Society of America.

Emergence and epidemiology of Cucurbit yellow stunting disorder virus in the American desert southwest, and development of host plant resistance in melon

USDA-ARS?s Scientific Manuscript database

Cucurbit yellow stunting disorder virus (CYSDV), emerged in the Sonoran Desert region of the southwestern USA in 2006 and has become established. The virus is transmitted by the MEAM1 cryptic species of Bemisia tabaci, which has been present in the region since the early 1990s. CYSDV results in lat...

Six New Record Species of Whiteflies (Hemiptera: Aleyrodidae) Infesting Morus alba in China

PubMed Central

Wang, Ji-Rui; Song, Zao-Qin; Du, Yu-Zhou

2014-01-01

Abstract To determine the species of whiteflies occurring on mulberry, Morus alba L. (Rosales: Moraceae) in China, we collected samples in more than 87 sites in 16 provinces of China from 2008 to 2011. In total, 10 species, representing seven genera of the subfamily Aleyrodinae, were identified. Of these, six species are newly recorded on mulberry in China, namely, Aleuroclava ficicola Takahashi, Aleuroclava gordoniae (Takahashi), Aleurotrachelus camelliae (Kuwana), Bemisia afer (Priesner & Hosny), Bemisia tabaci Gennadius, and Pealius machili Takahashi. Information on the taxonomy, distribution, and host plants of the whitefly species found on mulberry in China, along with a brief description and illustrations of each species are provided. PMID:25368095

RNA viral metagenome of whiteflies leads to the discovery and characterization of a whitefly-transmitted carlavirus in North America.

PubMed

Rosario, Karyna; Capobianco, Heather; Ng, Terry Fei Fan; Breitbart, Mya; Polston, Jane E

2014-01-01

Whiteflies from the Bemisia tabaci species complex have the ability to transmit a large number of plant viruses and are some of the most detrimental pests in agriculture. Although whiteflies are known to transmit both DNA and RNA viruses, most of the diversity has been recorded for the former, specifically for the Begomovirus genus. This study investigated the total diversity of DNA and RNA viruses found in whiteflies collected from a single site in Florida to evaluate if there are additional, previously undetected viral types within the B. tabaci vector. Metagenomic analysis of viral DNA extracted from the whiteflies only resulted in the detection of begomoviruses. In contrast, whiteflies contained sequences similar to RNA viruses from divergent groups, with a diversity that extends beyond currently described viruses. The metagenomic analysis of whiteflies also led to the first report of a whitefly-transmitted RNA virus similar to Cowpea mild mottle virus (CpMMV Florida) (genus Carlavirus) in North America. Further investigation resulted in the detection of CpMMV Florida in native and cultivated plants growing near the original field site of whitefly collection and determination of its experimental host range. Analysis of complete CpMMV Florida genomes recovered from whiteflies and plants suggests that the current classification criteria for carlaviruses need to be reevaluated. Overall, metagenomic analysis supports that DNA plant viruses carried by B. tabaci are dominated by begomoviruses, whereas significantly less is known about RNA viruses present in this damaging insect vector.

Evidence For Rapid Spatiotemporal Changes in Genetic Structure of an Alien Whitefly During Initial Invasion

PubMed Central

Chu, Dong; Guo, Dong; Tao, Yunli; Jiang, Defeng; Li, Jie; Zhang, Youjun

2014-01-01

The sweetpotato whitefly Bemisia tabaci Q species is a recent invader and important pest of agricultural crops in China. This research tested the hypothesis that the Q populations that establish in agricultural fields in northern China each year are derived from multiple secondary introductions and/or local populations that overwinter in greenhouses (the pest cannot survive winters in the field in northern China). Here, we report the evidence that the Q populations in agricultural fields mainly derive from multiple secondary introductions. In addition, the common use of greenhouses during the winter in certain locations in northern China helps increase the genetic diversity and the genetic structure of the pest. The genetic structure information generated from this long-term and large-scale field analysis increases our understanding of B. tabaci Q as an invasive pest and has important implications for B. tabaci Q management. PMID:24637851

Effects of Three Insect Growth Regulators on Encarsia formosa (Hymenoptera: Aphelinidae), an Endoparasitoid of Bemisia tabaci (Hemiptera: Aleyrodidae).

PubMed

Wang, Q L; Liu, T-X

2016-12-01

Insect growth regulators (IGRs) disrupt the normal activity of the endocrine or hormone system of insects, affecting the development, reproduction, or metamorphosis of the target insects, and normally causing less detrimental effects to beneficial insects. The effects of three IGRs (pyriproxyfen, fenoxycarb, and buprofezin) on Encarsia formosa Gahan, an endoparasitoid of whiteflies, were determined using B. tabaci as a host. We assessed the effects of the IGRs on parasitoid's larval development, pupation, emergence, and contact effects of the dry residues on plant leaf and glass vial surface on adult mortality and parasitism. When the three IGRs were applied at larval stage, no or few larvae pupated in the pyriproxyfen treatments and the highest concentration of fenoxycarb, and a majority of larvae pupated in the buprofezin treatments; of those pupated, 62.3-88.1% became adults. When the IGRs were applied at the pupal stage, 2.3-17.5% developed to adults in the pyriproxyfen treatments, 59.7-89.0% in the fenoxycarb treatments, and 58.4-83.6% in the buprofezin treatments. The leaf residues of the IGRs had no appreciable effects on adults, whereas the residues on glass vial caused significantly lower adult survival than on plant leaves. The residues of pyriproxyfen and fenoxycarb slightly reduced parasitism as compared with buprofezin and controls. However, the rates of parasitoids that became adults were significantly lower, especially in the pyriproxyfen treatments. According to the standards of International Organization of Biological Control (IOBC), pyriproxyfen was harmful, while fenoxycarb and buprofezin were slightly or moderately harmful to larvae and harmless to E. formosa pupae. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Modeling trophic dependencies and exchanges among insects' bacterial symbionts in a host-simulated environment.

PubMed

Opatovsky, Itai; Santos-Garcia, Diego; Ruan, Zhepu; Lahav, Tamar; Ofaim, Shany; Mouton, Laurence; Barbe, Valérie; Jiang, Jiandong; Zchori-Fein, Einat; Freilich, Shiri

2018-05-25

Individual organisms are linked to their communities and ecosystems via metabolic activities. Metabolic exchanges and co-dependencies have long been suggested to have a pivotal role in determining community structure. In phloem-feeding insects such metabolic interactions with bacteria enable complementation of their deprived nutrition. The phloem-feeding whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) harbors an obligatory symbiotic bacterium, as well as varying combinations of facultative symbionts. This well-defined bacterial community in B. tabaci serves here as a case study for a comprehensive and systematic survey of metabolic interactions within the bacterial community and their associations with documented occurrences of bacterial combinations. We first reconstructed the metabolic networks of five common B. tabaci symbionts genera (Portiera, Rickettsia, Hamiltonella, Cardinium and Wolbachia), and then used network analysis approaches to predict: (1) species-specific metabolic capacities in a simulated bacteriocyte-like environment; (2) metabolic capacities of the corresponding species' combinations, and (3) dependencies of each species on different media components. The predictions for metabolic capacities of the symbionts in the host environment were in general agreement with previously reported genome analyses, each focused on the single-species level. The analysis suggests several previously un-reported routes for complementary interactions and estimated the dependency of each symbiont in specific host metabolites. No clear association was detected between metabolic co-dependencies and co-occurrence patterns. The analysis generated predictions for testable hypotheses of metabolic exchanges and co-dependencies in bacterial communities and by crossing them with co-occurrence profiles, contextualized interaction patterns into a wider ecological perspective.

Complete nucleotide sequences of a new bipartite begomovirus from Malvastrum sp. plants with bright yellow mosaic symptoms in South Texas.

PubMed

Alabi, Olufemi J; Villegas, Cecilia; Gregg, Lori; Murray, K Daniel

2016-06-01

Two isolates of a novel bipartite begomovirus, tentatively named malvastrum bright yellow mosaic virus (MaBYMV), were molecularly characterized from naturally infected plants of the genus Malvastrum showing bright yellow mosaic disease symptoms in South Texas. Six complete DNA-A and five DNA-B genome sequences of MaBYMV obtained from the isolates ranged in length from 2,608 to 2,609 nucleotides (nt) and 2,578 to 2,605 nt, respectively. Both genome segments shared a 178- to 180-nt common region. In pairwise comparisons, the complete DNA-A and DNA-B sequences of MaBYMV were most similar (87-88 % and 79-81 % identity, respectively) and phylogenetically related to the corresponding sequences of sida mosaic Sinaloa virus-[MX-Gua-06]. Further analysis revealed that MaBYMV is a putative recombinant virus, thus supporting the notion that malvaceous hosts may be influencing the evolution of several begomoviruses. The design of new diagnostic primers enabled the detection of MaBYMV in cohorts of Bemisia tabaci collected from symptomatic Malvastrum sp. plants, thus implicating whiteflies as potential vectors of the virus.

A molecular insight into papaya leaf curl-a severe viral disease.

PubMed

Varun, Priyanka; Ranade, S A; Saxena, Sangeeta

2017-11-01

Papaya leaf curl disease (PaLCuD) caused by papaya leaf curl virus (PaLCuV) not only affects yield but also plant growth and fruit size and quality of papaya and is one of the most damaging and economically important disease. Management of PaLCuV is a challenging task due to diversity of viral strains, the alternate hosts, and the genomic complexities of the viruses. Several management strategies currently used by plant virologists to broadly control or eliminate the viruses have been discussed. In the absence of such strategies in the case of PaLCuV at present, the few available options to control the disease include methods like removal of affected plants from the field, insecticide treatments against the insect vector (Bemisia tabaci), and gene-specific control through transgenic constructs. This review presents the current understanding of papaya leaf curl disease, genomic components including satellite DNA associated with the virus, wide host and vector range, and management of the disease and suggests possible generic resistance strategies.

Transmission of Pantoea ananatis and P. agglomerans, causal agents of center rot of onion (Allium cepa), by onion thrips (Thrips tabaci) through feces.

PubMed

Dutta, B; Barman, A K; Srinivasan, R; Avci, U; Ullman, D E; Langston, D B; Gitaitis, R D

2014-08-01

Frankliniella fusca, the tobacco thrips, has been shown to acquire and transmit Pantoea ananatis, one of the causal agents of the center rot of onion. Although Thrips tabaci, the onion thrips, is a common pest of onions, its role as a vector of P. ananatis has been unknown. The bacterium, P. agglomerans, is also associated with the center rot of onion, but its transmission by thrips has not been previously investigated. In this study, we investigated the relationship of T. tabaci with P. ananatis and P. agglomerans. Surface-sterilized T. tabaci were provided with various acquisition access periods (AAP) on onion leaves inoculated with either P. ananatis or P. agglomerans. A positive exponential relationship was observed between thrips AAP duration and P. ananatis (R² = 0.967; P = 0.023) or P. agglomerans acquisition (R² = 0.958; P = 0.017). Transmission experiments conducted with T. tabaci adults indicated that 70% of the seedlings developed center rot symptoms 15 days after inoculation. Immunofluorescence microscopy with antibodies specific to P. ananatis revealed that the bacterium was localized only in the gut of T. tabaci adults. Mechanical inoculation of onion seedlings with fecal rinsates alone produced center rot but not with salivary secretions. Together these results suggested that T. tabaci could efficiently transmit P. ananatis and P. agglomerans.

Persistent, circulative transmission of begomoviruses by whitefly vectors.

PubMed

Rosen, Ran; Kanakala, Surapathrudu; Kliot, Adi; Cathrin Pakkianathan, Britto; Farich, Basheer Abu; Santana-Magal, Nadine; Elimelech, Meytar; Kontsedalov, Svetlana; Lebedev, Galina; Cilia, Michelle; Ghanim, Murad

2015-12-01

Begomoviruses comprise an emerging and economically important group of plant viruses exclusively transmitted by the sweetpotato whitefly Bemisia tabaci in many regions of the world. The past twenty years have witnessed significant progress in studying the molecular interactions between members of this virus group and B. tabaci. Mechanisms and proteins encoded by the insect vector and its bacterial symbionts, which have been shown to be important for virus transmission, have been identified and thoroughly studied. Despite the economic importance of this group of viruses and their impact on the global agriculture, progress in investigating the virus-vector interactions is moving slowly when compared with similar virus-vector systems in plants and animals. Major advances in this field and future perspectives will be discussed in this review. Copyright © 2015 Elsevier B.V. All rights reserved.

Onion thrips, Thrips tabaci, have gut bacteria that are closely related to the symbionts of the western flower thrips, Frankliniella occidentalis.

PubMed

de Vries, Egbert J; van der Wurff, André W G; Jacobs, Gerrit; Breeuwer, Johannes A J

2008-01-01

It has been shown that many insects have Enterobacteriaceae bacteria in their gut system. The western flower thrips, Frankliniella occidentalis Pergande [Thysanoptera: Thripidae], has a symbiotic relation with Erwinia species gut bacteria. To determine if other Thripidae species have similar bacterial symbionts, the onion thrips, Thrips tabaci, was studied because, like F. occidentalis, it is phytophagous. Contrary to F. occidentalis, T. tabaci is endemic in Europe and biotypes have been described. Bacteria were isolated from the majority of populations and biotypes of T. tabaci examined. Bacteria were present in high numbers in most individuals of the populations studied. Like F. occidentalis, T. tabaci contained one type of bacterium that clearly outnumbered all other types present in the gut. This bacterium was identified as an Erwinia species, as was also the case for F. occidentalis. However, its biochemical characteristics and 16S rDNA sequence differed from the bacteria present in F. occidentalis.

Onion Thrips, Thrips tabaci, Have Gut Bacteria That are Closely Related to the Symbionts of the Western Flower Thrips, Frankliniella occidentalis

PubMed Central

de Vries, Egbert J.; van der Wurff, André W. G.; Jacobs, Gerrit; Breeuwer, Johannes A. J.

2008-01-01

It has been shown that many insects have Enterobacteriaceae bacteria in their gut system. The western flower thrips, Frankliniella occidentalis Pergande [Thysanoptera: Thripidae], has a symbiotic relation with Erwinia species gut bacteria. To determine if other Thripidae species have similar bacterial symbionts, the onion thrips, Thrips tabaci, was studied because, like F. occidentalis, it is phytophagous. Contrary to F. occidentalis, T. tabaci is endemic in Europe and biotypes have been described. Bacteria were isolated from the majority of populations and biotypes of T. tabaci examined. Bacteria were present in high numbers in most individuals of the populations studied. Like F. occidentalis, T. tabaci contained one type of bacterium that clearly outnumbered all other types present in the gut. This bacterium was identified as an Erwinia species, as was also the case for F. occidentalis. However, its biochemical characteristics and 16S rDNA sequence differed from the bacteria present in F. occidentalis. PMID:20298113

Transcriptome changes occurred in the whitefly, B. tabaci MEAM1 in response to feeding on melon infected with the crinivirus, CYSDV

USDA-ARS?s Scientific Manuscript database

CYSDV, a crinivirus transmitted by the whitefly, B. tabaci, causes widespread losses in melon and other cucurbits. The virus emerged in the southwestern United States in 2006. It established in crops and weeds, and is transmitted to cucurbits by the resident population of B. tabaci MEAM1 each year. ...

Presence of Native Prey Does Not Divert Predation on Exotic Pests by Harmonia axyridis in Its Indigenous Range

PubMed Central

Zhang, Gui Fen; Lövei, Gábor L; Wu, Xia; Wan, Fang Hao

2016-01-01

In China, two invasive pests, Bemisia tabaci MEAM1 (Gennadius) and Frankliniella occidentalis (Pergande), often co-occur with the native pest, Aphis gossypii (Glover), on plants of Malvaceae and Cucurbitaceae. All three are preyed on by the native ladybird, Harmonia axyridis (Pallas); however, the native predator might be expected to prefer native prey to the exotic ones due to a shared evolutionary past. In order to clarify whether the presence of native prey affected the consumption of these two invasive species by the native predator, field-cage experiments were conducted. A duplex qPCR was used to simultaneously detect both non-native pests within the gut of the predator. H. axyridis readily accepted both invasive prey species, but preferred B. tabaci. With all three prey species available, H. axyridis consumption of B. tabaci was 39.3±2.2% greater than consumption of F. occidentalis. The presence of A. gossypii reduced (by 59.9% on B. tabaci, and by 60.6% on F. occidentalis), but did not stop predation on the two exotic prey when all three were present. The consumption of B. tabaci was similar whether it was alone or together with A. gossypii. However, the presence of aphids reduced predation on the invasive thrips. Thus, some invasive prey may be incorporated into the prey range of a native generalist predator even in the presence of preferred native prey. PMID:27391468

Colonization of onions by endophytic fungi and their impacts on the biology of Thrips tabaci.

PubMed

Muvea, Alexander M; Meyhöfer, Rainer; Subramanian, Sevgan; Poehling, Hans-Michael; Ekesi, Sunday; Maniania, Nguya K

2014-01-01

Endophytic fungi, which live within host plant tissues without causing any visible symptom of infection, are important mutualists that mediate plant-herbivore interactions. Thrips tabaci (Lindeman) is one of the key pests of onion, Allium cepa L., an economically important agricultural crop cultivated worldwide. However, information on endophyte colonization of onions, and their impacts on the biology of thrips feeding on them, is lacking. We tested the colonization of onion plants by selected fungal endophyte isolates using two inoculation methods. The effects of inoculated endophytes on T. tabaci infesting onion were also examined. Seven fungal endophytes used in our study were able to colonize onion plants either by the seed or seedling inoculation methods. Seed inoculation resulted in 1.47 times higher mean percentage post-inoculation recovery of all the endophytes tested as compared to seedling inoculation. Fewer thrips were observed on plants inoculated with Clonostachys rosea ICIPE 707, Trichoderma asperellum M2RT4, Trichoderma atroviride ICIPE 710, Trichoderma harzianum 709, Hypocrea lixii F3ST1 and Fusarium sp. ICIPE 712 isolates as compared to those inoculated with Fusarium sp. ICIPE 717 and the control treatments. Onion plants colonized by C. rosea ICIPE 707, T. asperellum M2RT4, T. atroviride ICIPE 710 and H. lixii F3ST1 had significantly lower feeding punctures as compared to the other treatments. Among the isolates tested, the lowest numbers of eggs were laid by T. tabaci on H. lixii F3ST1 and C. rosea ICIPE 707 inoculated plants. These results extend the knowledge on colonization of onions by fungal endophytes and their effects on Thrips tabaci.

Colonization of Onions by Endophytic Fungi and Their Impacts on the Biology of Thrips tabaci

PubMed Central

Muvea, Alexander M.; Meyhöfer, Rainer; Subramanian, Sevgan; Poehling, Hans-Michael; Ekesi, Sunday; Maniania, Nguya K.

2014-01-01

Endophytic fungi, which live within host plant tissues without causing any visible symptom of infection, are important mutualists that mediate plant–herbivore interactions. Thrips tabaci (Lindeman) is one of the key pests of onion, Allium cepa L., an economically important agricultural crop cultivated worldwide. However, information on endophyte colonization of onions, and their impacts on the biology of thrips feeding on them, is lacking. We tested the colonization of onion plants by selected fungal endophyte isolates using two inoculation methods. The effects of inoculated endophytes on T. tabaci infesting onion were also examined. Seven fungal endophytes used in our study were able to colonize onion plants either by the seed or seedling inoculation methods. Seed inoculation resulted in 1.47 times higher mean percentage post-inoculation recovery of all the endophytes tested as compared to seedling inoculation. Fewer thrips were observed on plants inoculated with Clonostachys rosea ICIPE 707, Trichoderma asperellum M2RT4, Trichoderma atroviride ICIPE 710, Trichoderma harzianum 709, Hypocrea lixii F3ST1 and Fusarium sp. ICIPE 712 isolates as compared to those inoculated with Fusarium sp. ICIPE 717 and the control treatments. Onion plants colonized by C. rosea ICIPE 707, T. asperellum M2RT4, T. atroviride ICIPE 710 and H. lixii F3ST1 had significantly lower feeding punctures as compared to the other treatments. Among the isolates tested, the lowest numbers of eggs were laid by T. tabaci on H. lixii F3ST1 and C. rosea ICIPE 707 inoculated plants. These results extend the knowledge on colonization of onions by fungal endophytes and their effects on Thrips tabaci. PMID:25254657

Improved Sweetpotato Whitefly and Potato Psyllid Control in Tomato by Combining the Mirid Dicyphus hesperus (Heteroptera: Miridae) With Specialist Parasitic Wasps.

PubMed

Calvo, F J; Torres-Ruiz, A; Velázquez-González, J; Rodríguez-Leyva, E; Lomeli-Flores, J R

2018-04-02

Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae) and Bactericera cockerelli Sulcer (Hemiptera: Psyllidae) are important pests in tomato, and the mirid Dicyphus hesperus Knight (Heteroptera: Miridae) has been shown as an effective predator of both pests. Although the predator was able to suppress populations of both pests, the remaining levels could still exceed tolerable levels. Thus, we here hypothesized whether the combination of D. hesperus with the specialist parasitoids Eretmocerus eremicus Rose y Zolnerowich (Hymenoptera: Aphelinidae) (whitefly) and Tamarixia triozae (Burks) (Hymenoptera: Eulophidae) (psyllid) would result in better pest control on a greenhouse scale. For that, we conducted a trial in which we compared the results against B. tabaci and B. cockerelli in greenhouses treated with D. hesperus alone or the predator in combination with the specialist parasitoids. The results showed that the predator was able to establish and suppress B. tabaci and B. cockerelli in tomato, but the addition of the specialist parasitoids resulted in better and more cost-effective pest control. Implementation of this method would therefore increase the robustness and reliability of biocontrol-based integrated pest management programmes for tomato crops, over methods based exclusively on D. hesperus release.

Knock down of Whitefly Gut Gene Expression and Mortality by Orally Delivered Gut Gene-Specific dsRNAs.

PubMed

Vyas, Meenal; Raza, Amir; Ali, Muhammad Yousaf; Ashraf, Muhammad Aleem; Mansoor, Shahid; Shahid, Ahmad Ali; Brown, Judith K

2017-01-01

Control of the whitefly Bemisia tabaci (Genn.) agricultural pest and plant virus vector relies on the use of chemical insecticides. RNA-interference (RNAi) is a homology-dependent innate immune response in eukaryotes, including insects, which results in degradation of the corresponding transcript following its recognition by a double-stranded RNA (dsRNA) that shares 100% sequence homology. In this study, six whitefly 'gut' genes were selected from an in silico-annotated transcriptome library constructed from the whitefly alimentary canal or 'gut' of the B biotype of B. tabaci, and tested for knock down efficacy, post-ingestion of dsRNAs that share 100% sequence homology to each respective gene target. Candidate genes were: Acetylcholine receptor subunit α, Alpha glucosidase 1, Aquaporin 1, Heat shock protein 70, Trehalase1, and Trehalose transporter1. The efficacy of RNAi knock down was further tested in a gene-specific functional bioassay, and mortality was recorded in 24 hr intervals, six days, post-treatment. Based on qPCR analysis, all six genes tested showed significantly reduced gene expression. Moderate-to-high whitefly mortality was associated with the down-regulation of osmoregulation, sugar metabolism and sugar transport-associated genes, demonstrating that whitefly survivability was linked with RNAi results. Silenced Acetylcholine receptor subunit α and Heat shock protein 70 genes showed an initial low whitefly mortality, however, following insecticide or high temperature treatments, respectively, significantly increased knockdown efficacy and death was observed, indicating enhanced post-knockdown sensitivity perhaps related to systemic silencing. The oral delivery of gut-specific dsRNAs, when combined with qPCR analysis of gene expression and a corresponding gene-specific bioassay that relates knockdown and mortality, offers a viable approach for functional genomics analysis and the discovery of prospective dsRNA biopesticide targets. The approach can

RNA Interference Based Approach to Down Regulate Osmoregulators of Whitefly (Bemisia tabaci): Potential Technology for the Control of Whitefly

USDA-ARS?s Scientific Manuscript database

Over the past decade RNA interference (RNAi) technology has emerged as a successful tool not only for functional genomics, but in planta expression of short interfering RNAs (siRNAs) could offer potential for insect pest management. Insects feeding exclusively on plant sap depend on osmotic pressure...

Spider Communities and Biological Control in Native Habitats Surrounding Greenhouses.

PubMed

Cotes, Belén; González, Mónica; Benítez, Emilio; De Mas, Eva; Clemente-Orta, Gemma; Campos, Mercedes; Rodríguez, Estefanía

2018-03-14

The promotion of native vegetation as a habitat for natural enemies, which could increase their abundance and fitness, is especially useful in highly simplified settings such as Mediterranean greenhouse landscapes. Spiders as generalist predators may also be involved in intra-guild predation. However, the niche complementarity provided by spiders as a group means that increased spider diversity may facilitate complementary control actions. In this study, the interactions between spiders, the two major horticultural pests, Bemisia tabaci and Frankliniella occidentalis , and their naturally occurring predators and parasitoids were evaluated in a mix of 21 newly planted shrubs selected for habitat management in a highly disturbed horticultural system. The effects of all factors were evaluated using redundancy analysis (RDA) and the generalized additive model (GAM) to assess the statistical significance of abundance of spiders and pests. The GAM showed that the abundance of both pests had a significant effect on hunter spider's abundance, whereas the abundance of B. tabaci , but not F. occidentalis , affected web-weavers' abundance. Ordination analysis showed that spider abundance closely correlated with that of B. tabaci but not with that of F. occidentalis , suggesting that complementarity occurs, and thereby probability of biocontrol, with respect to the targeted pest B. tabaci , although the temporal patterns of the spiders differed from those of F. occidentalis . Conservation strategies involving the establishment of these native plants around greenhouses could be an effective way to reduce pest populations outdoors.

Diversity and Phylogenetic Analyses of Bacterial Symbionts in Three Whitefly Species from Southeast Europe

PubMed Central

Skaljac, Marisa; Zanic, Katja; Puizina, Jasna; Lepen Pleic, Ivana; Ghanim, Murad

2017-01-01

Bemisia tabaci (Gennadius), Trialeurodes vaporariorum (Westwood), and Siphoninus phillyreae (Haliday) are whitefly species that harm agricultural crops in many regions of the world. These insects live in close association with bacterial symbionts that affect host fitness and adaptation to the environment. In the current study, we surveyed the infection of whitefly populations in Southeast Europe by various bacterial symbionts and performed phylogenetic analyses on the different symbionts detected. Arsenophonus and Hamiltonella were the most prevalent symbionts in all three whitefly species. Rickettsia was found to infect mainly B. tabaci, while Wolbachia mainly infected both B. tabaci and S. phillyreae. Furthermore, Cardinium was rarely found in the investigated whitefly populations, while Fritschea was never found in any of the whitefly species tested. Phylogenetic analyses revealed a diversity of several symbionts (e.g., Hamiltonella, Arsenophonus, Rickettsia), which appeared in several clades. Reproductively isolated B. tabaci and T. vaporariorum shared the same (or highly similar) Hamiltonella and Arsenophonus, while these symbionts were distinctive in S. phillyreae. Interestingly, Arsenophonus from S. phillyreae did not cluster with any of the reported sequences, which could indicate the presence of Arsenophonus, not previously associated with whiteflies. In this study, symbionts (Wolbachia, Rickettsia, and Cardinium) known to infect a wide range of insects each clustered in the same clades independently of the whitefly species. These results indicate horizontal transmission of bacterial symbionts between reproductively isolated whitefly species, a mechanism that can establish new infections that did not previously exist in whiteflies. PMID:29053633

Diversity and Phylogenetic Analyses of Bacterial Symbionts in Three Whitefly Species from Southeast Europe.

PubMed

Skaljac, Marisa; Kanakala, Surapathrudu; Zanic, Katja; Puizina, Jasna; Pleic, Ivana Lepen; Ghanim, Murad

2017-10-20

Bemisia tabaci (Gennadius), Trialeurodes vaporariorum (Westwood), and Siphoninus phillyreae (Haliday) are whitefly species that harm agricultural crops in many regions of the world. These insects live in close association with bacterial symbionts that affect host fitness and adaptation to the environment. In the current study, we surveyed the infection of whitefly populations in Southeast Europe by various bacterial symbionts and performed phylogenetic analyses on the different symbionts detected. Arsenophonus and Hamiltonella were the most prevalent symbionts in all three whitefly species. Rickettsia was found to infect mainly B. tabaci, while Wolbachia mainly infected both B. tabaci and S. phillyreae. Furthermore, Cardinium was rarely found in the investigated whitefly populations, while Fritschea was never found in any of the whitefly species tested. Phylogenetic analyses revealed a diversity of several symbionts (e.g., Hamiltonella, Arsenophonus, Rickettsia), which appeared in several clades. Reproductively isolated B. tabaci and T. vaporariorum shared the same (or highly similar) Hamiltonella and Arsenophonus, while these symbionts were distinctive in S. phillyreae. Interestingly, Arsenophonus from S. phillyreae did not cluster with any of the reported sequences, which could indicate the presence of Arsenophonus, not previously associated with whiteflies. In this study, symbionts (Wolbachia, Rickettsia, and Cardinium) known to infect a wide range of insects each clustered in the same clades independently of the whitefly species. These results indicate horizontal transmission of bacterial symbionts between reproductively isolated whitefly species, a mechanism that can establish new infections that did not previously exist in whiteflies.

Whiteflies interfere with indirect plant defense against spider mites in Lima bean

PubMed Central

Zhang, Peng-Jun; Zheng, Si-Jun; van Loon, Joop J. A.; Boland, Wilhelm; David, Anja; Mumm, Roland; Dicke, Marcel

2009-01-01

Plants under herbivore attack are able to initiate indirect defense by synthesizing and releasing complex blends of volatiles that attract natural enemies of the herbivore. However, little is known about how plants respond to infestation by multiple herbivores, particularly if these belong to different feeding guilds. Here, we report the interference by a phloem-feeding insect, the whitefly Bemisia tabaci, with indirect plant defenses induced by spider mites (Tetranychus urticae) in Lima bean (Phaseolus lunatus) plants. Additional whitefly infestation of spider-mite infested plants resulted in a reduced attraction of predatory mites (Phytoseiulus persimilis) compared to attraction to plants infested by spider mites only. This interference is shown to result from the reduction in (E)-β-ocimene emission from plants infested by both spider mites and whiteflies. When using exogenous salicylic acid (SA) application to mimic B. tabaci infestation, we observed similar results in behavioral and chemical analyses. Phytohormone and gene-expression analyses revealed that B. tabaci infestation, as well as SA application, inhibited spider mite-induced jasmonic acid (JA) production and reduced the expression of two JA-regulated genes, one of which encodes for the P. lunatus enzyme β-ocimene synthase that catalyzes the synthesis of (E)-β-ocimene. Remarkably, B. tabaci infestation concurrently inhibited SA production induced by spider mites. We therefore conclude that in dual-infested Lima bean plants the suppression of the JA signaling pathway by whitefly feeding is not due to enhanced SA levels. PMID:19965373

The autophagy pathway participates in resistance to tomato yellow leaf curl virus infection in whiteflies.

PubMed

Wang, Lan-Lan; Wang, Xin-Ru; Wei, Xue-Mei; Huang, Huang; Wu, Jian-Xiang; Chen, Xue-Xin; Liu, Shu-Sheng; Wang, Xiao-Wei

2016-09-01

Macroautophagy/autophagy plays an important role against pathogen infection in mammals and plants. However, little has been known about the role of autophagy in the interactions of insect vectors with the plant viruses, which they transmit. Begomoviruses are a group of single-stranded DNA viruses and are exclusively transmitted by the whitefly Bemisia tabaci in a circulative manner. In this study, we found that the infection of a begomovirus, tomato yellow leaf curl virus (TYLCV) could activate the autophagy pathway in the Middle East Asia Minor 1 (MEAM1) species of the B. tabaci complex as evidenced by the formation of autophagosomes and ATG8-II. Interestingly, the activation of autophagy led to the subsequent degradation of TYLCV coat protein (CP) and genomic DNA. While feeding the whitefly with 2 autophagy inhibitors (3-methyladenine and bafilomycin A1) and silencing the expression of Atg3 and Atg9 increased the viral load; autophagy activation via feeding of rapamycin notably decreased the amount of viral CP and DNA in the whitefly. Furthermore, we found that activation of whitefly autophagy could inhibit the efficiency of virus transmission; whereas inhibiting autophagy facilitated virus transmission. Taken together, these results indicate that TYLCV infection can activate the whitefly autophagy pathway, which leads to the subsequent degradation of virus. Furthermore, our report proves that an insect vector uses autophagy as an intrinsic antiviral program to repress the infection of a circulative-transmitted plant virus. Our data also demonstrate that TYLCV may replicate and trigger complex interactions with the insect vector.

Identification of an alternative knockdown resistance (kdr)-like mutation, M918L, and a novel mutation, V1010A, in the Thrips tabaci voltage-gated sodium channel gene.

PubMed

Wu, Meixiang; Gotoh, Hiroki; Waters, Timothy; Walsh, Douglas B; Lavine, Laura Corley

2014-06-01

Knockdown resistance (kdr) has been identified as a main mechanism against pyrethroid insecticides in many arthropod pests including in the onion thrips, Thrips tabaci. To characterize and identify pyrethroid-resistance in onion thrips in Washington state, we conducted insecticide bioassays and sequenced a region of the voltage gated sodium channel gene from several different T. tabaci populations. Field collected Thrips tabaci were found to have large variations in resistance to the pyrethroid insecticide lambda-cyhalothrin. We identified two single nucleotide substitutions in our analysis of a partial sequence of the T. tabaci voltage-gated sodium channel gene. One mutation resulted in the non-synonymous substitution of methionine with leucine (M918L), which is well known to be responsible for super knockdown resistance in some pest species. Another non-synonymous substitution, a valine (GTT) to alanine (GCT) replacement at amino acid 1010 (V1010A) was identified in our study and was associated with lambda-cyhalothrin resistance. We have characterized a known kdr mutation and identified a novel mutation in the voltage-gated sodium channel gene of Thrips tabaci associated with resistance to lambda-cyhalothrin. This gene region and these mutations are expected to be useful in the development of a diagnostic test to detect kdr resistance in many onion thrips populations. © 2013 Society of Chemical Industry.

Remote sensing for detecting and mapping whitefly (Bemisia tabaci) infestations

USDA-ARS?s Scientific Manuscript database

Remote sensing technology has long been used for detecting insect infestations on agricultural crops. With recent advances in remote sensing sensors and other spatial information technologies such as Global Position Systems (GPS) and Geographic Information Systems (GIS), remote sensing is finding mo...

Unusual occurrence of a DAG motif in the Ipomovirus Cassava brown streak virus and implications for its vector transmission.

PubMed

Ateka, Elijah; Alicai, Titus; Ndunguru, Joseph; Tairo, Fred; Sseruwagi, Peter; Kiarie, Samuel; Makori, Timothy; Kehoe, Monica A; Boykin, Laura M

2017-01-01

Cassava is the main staple food for over 800 million people globally. Its production in eastern Africa is being constrained by two devastating Ipomoviruses that cause cassava brown streak disease (CBSD); Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), with up to 100% yield loss for smallholder farmers in the region. To date, vector studies have not resulted in reproducible and highly efficient transmission of CBSV and UCBSV. Most virus transmission studies have used Bemisia tabaci (whitefly), but a maximum of 41% U/CBSV transmission efficiency has been documented for this vector. With the advent of next generation sequencing, researchers are generating whole genome sequences for both CBSV and UCBSV from throughout eastern Africa. Our initial goal for this study was to characterize U/CBSV whole genomes from CBSD symptomatic cassava plants sampled in Kenya. We have generated 8 new whole genomes (3 CBSV and 5 UCBSV) from Kenya, and in the process of analyzing these genomes together with 26 previously published sequences, we uncovered the aphid transmission associated DAG motif within coat protein genes of all CBSV whole genomes at amino acid positions 52-54, but not in UCBSV. Upon further investigation, the DAG motif was also found at the same positions in two other Ipomoviruses: Squash vein yellowing virus (SqVYV), Coccinia mottle virus (CocMoV). Until this study, the highly-conserved DAG motif, which is associated with aphid transmission was only noticed once, in SqVYV but discounted as being of minimal importance. This study represents the first comprehensive look at Ipomovirus genomes to determine the extent of DAG motif presence and significance for vector relations. The presence of this motif suggests that aphids could potentially be a vector of CBSV, SqVYV and CocMov. Further transmission and ipomoviral protein evolutionary studies are needed to confirm this hypothesis.

Transcriptomic Analysis of the Salivary Glands of an Invasive Whitefly

PubMed Central

Su, Yun-Lin; Li, Jun-Min; Li, Meng; Luan, Jun-Bo; Ye, Xiao-Dong; Wang, Xiao-Wei; Liu, Shu-Sheng

2012-01-01

Background Some species of the whitefly Bemisia tabaci complex cause tremendous losses to crops worldwide through feeding directly and virus transmission indirectly. The primary salivary glands of whiteflies are critical for their feeding and virus transmission. However, partly due to their tiny size, research on whitefly salivary glands is limited and our knowledge on these glands is scarce. Methodology/Principal Findings We sequenced the transcriptome of the primary salivary glands of the Mediterranean species of B. tabaci complex using an effective cDNA amplification method in combination with short read sequencing (Illumina). In a single run, we obtained 13,615 unigenes. The quantity of the unigenes obtained from the salivary glands of the whitefly is at least four folds of the salivary gland genes from other plant-sucking insects. To reveal the functions of the primary glands, sequence similarity search and comparisons with the whole transcriptome of the whitefly were performed. The results demonstrated that the genes related to metabolism and transport were significantly enriched in the primary salivary glands. Furthermore, we found that a number of highly expressed genes in the salivary glands might be involved in secretory protein processing, secretion and virus transmission. To identify potential proteins of whitefly saliva, the translated unigenes were put into secretory protein prediction. Finally, 295 genes were predicted to encode secretory proteins and some of them might play important roles in whitefly feeding. Conclusions/Significance: The combined method of cDNA amplification, Illumina sequencing and de novo assembly is suitable for transcriptomic analysis of tiny organs in insects. Through analysis of the transcriptome, genomic features of the primary salivary glands were dissected and biologically important proteins, especially secreted proteins, were predicted. Our findings provide substantial sequence information for the primary salivary glands

Analysis of Whitefly Transcriptional Responses to Beauveria bassiana Infection Reveals New Insights into Insect-Fungus Interactions

PubMed Central

Zhang, Shan; Li, Fang-Fang; Feng, Ming-Guang; Wang, Xiao-Wei; Liu, Shu-Sheng

2013-01-01

Background The fungal pathogen, Beauveria bassiana, is an efficient biocontrol agent against a variety of agricultural pests. A thorough understanding of the basic principles of insect-fungus interactions may enable the genetic modification of Beauveria bassiana to enhance its virulence. However, the molecular mechanism of insect response to Beauveria bassiana infection is poorly understood, let alone the identification of fungal virulent factors involved in pathogenesis. Methodology/Principal Findings Here, next generation sequencing technology was applied to examine the expression of whitefly (Bemisia tabaci) genes in response to the infection of Beauveria bassiana. Results showed that, compared to control, 654 and 1,681genes were differentially expressed at 48 hours and 72 hours post-infected whiteflies, respectively. Functional and enrichment analyses indicated that the DNA damage stimulus response and drug metabolism were important anti-fungi strategies of the whitefly. Mitogen-activated protein kinase (MAPK) pathway was also likely involved in the whitefly defense responses. Furthermore, the notable suppression of general metabolism and ion transport genes observed in 72 hours post-infected B. tabaci might be manipulated by fungal secreted effectors. By mapping the sequencing tags to B. bassiana genome, we also identified a number of differentially expressed fungal genes between the early and late infection stages. These genes are generally associated with fungal cell wall synthesis and energy metabolism. The expression of fungal cell wall protein genes might play an important role in fungal pathogenesis and the dramatically up-regulated enzymes of carbon metabolism indicate the increasing usage of energy during the fungal infection. Conclusions/Significance To our knowledge, this is the first report on the molecular mechanism of fungus-whitefly interactions. Our results provide a road map for future investigations on insect-pathogen interactions and

Analysis of whitefly transcriptional responses to Beauveria bassiana infection reveals new insights into insect-fungus interactions.

PubMed

Xia, Jun; Zhang, Chang-Rong; Zhang, Shan; Li, Fang-Fang; Feng, Ming-Guang; Wang, Xiao-Wei; Liu, Shu-Sheng

2013-01-01

The fungal pathogen, Beauveria bassiana, is an efficient biocontrol agent against a variety of agricultural pests. A thorough understanding of the basic principles of insect-fungus interactions may enable the genetic modification of Beauveria bassiana to enhance its virulence. However, the molecular mechanism of insect response to Beauveria bassiana infection is poorly understood, let alone the identification of fungal virulent factors involved in pathogenesis. Here, next generation sequencing technology was applied to examine the expression of whitefly (Bemisia tabaci) genes in response to the infection of Beauveria bassiana. Results showed that, compared to control, 654 and 1,681genes were differentially expressed at 48 hours and 72 hours post-infected whiteflies, respectively. Functional and enrichment analyses indicated that the DNA damage stimulus response and drug metabolism were important anti-fungi strategies of the whitefly. Mitogen-activated protein kinase (MAPK) pathway was also likely involved in the whitefly defense responses. Furthermore, the notable suppression of general metabolism and ion transport genes observed in 72 hours post-infected B. tabaci might be manipulated by fungal secreted effectors. By mapping the sequencing tags to B. bassiana genome, we also identified a number of differentially expressed fungal genes between the early and late infection stages. These genes are generally associated with fungal cell wall synthesis and energy metabolism. The expression of fungal cell wall protein genes might play an important role in fungal pathogenesis and the dramatically up-regulated enzymes of carbon metabolism indicate the increasing usage of energy during the fungal infection. To our knowledge, this is the first report on the molecular mechanism of fungus-whitefly interactions. Our results provide a road map for future investigations on insect-pathogen interactions and genetically modifying the fungus to enhance its efficiency in whitefly

Newer insecticides for plant virus disease management.

PubMed

Castle, Steven; Palumbo, John; Prabhaker, Nilima

2009-05-01

Effective management of insect and mite vectors of plant pathogens is of crucial importance to minimize vector-borne diseases in crops. Pesticides play an important role in managing vector populations by reducing the number of individuals that can acquire and transmit a virus, thereby potentially lowering disease incidence. Certain insecticides exhibit properties other than lethal toxicity that affect feeding behaviours or otherwise interfere with virus transmission. To evaluate the potential of various treatments against the Bemisia tabaci-transmitted Cucurbit yellow stunting disorder virus (CYSDV), insecticide field trials were conducted in Yuma, AZ, USA, during spring and autumn growing seasons. Differences in vector-intensity each season led to mixed results, but at least five insecticide treatments showed promise in limiting virus spread during spring 2008. Increasing concern among growers in this region regarding recent epidemics of CYSDV is leading to more intensive use of insecticides that threatens to erupt into unmanageable resistance. Sustainability of insecticides is an important goal of pest management and more specifically resistance management, especially for some of the most notorious vector species such as B. tabaci and Myzus persiscae that are likely to develop resistance.

Evaluating Weeds as Hosts of Tomato yellow leaf curl virus.

PubMed

Smith, Hugh A; Seijo, Teresa E; Vallad, Gary E; Peres, Natalia A; Druffel, Keri L

2015-08-01

Bemisia tabaci (Gennadius) biotype B transmits Tomato yellow leaf curl virus (TYLCV), which affects tomato production globally. Prompt destruction of virus reservoirs is a key component of virus management. Identification of weed hosts of TYLCV will be useful for reducing such reservoirs. The status of weeds as alternate hosts of TYLCV in Florida remains unclear. In greenhouse studies, B. tabaci adults from a colony reared on TYLCV-infected tomato were established in cages containing one of four weeds common to horticultural fields in central and south Florida. Cages containing tomato and cotton were also infested with viruliferous whiteflies as a positive control and negative control, respectively. Whitefly adults and plant tissue were tested periodically over 10 wk for the presence of TYLCV using PCR. After 10 wk, virus-susceptible tomato plants were placed in each cage to determine if whiteflies descended from the original adults were still infective. Results indicate that Bidens alba, Emilia fosbergii, and Raphanus raphanistrum are not hosts of TYLCV, and that Amaranthus retroflexus is a host. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The Contrasting Effects of Elevated CO2 on TYLCV Infection of Tomato Genotypes with and without the Resistance Gene, Mi-1.2.

PubMed

Guo, Huijuan; Huang, Lichao; Sun, Yucheng; Guo, Honggang; Ge, Feng

2016-01-01

Elevated atmospheric CO 2 typically enhances photosynthesis of C3 plants and alters primary and secondary metabolites in plant tissue. By modifying the defensive signaling pathways in host plants, elevated CO 2 could potentially affect the interactions between plants, viruses, and insects that vector viruses. R gene-mediated resistance in plants represents an efficient and highly specific defense against pathogens and herbivorous insects. The current study determined the effect of elevated CO 2 on tomato plants with and without the nematode resistance gene Mi-1.2 , which also confers resistance to some sap-sucking insects including whitefly, Bemisia tabaci . Furthermore, the subsequent effects of elevated CO 2 on the performance of the vector whiteflies and the severity of Tomato yellow leaf curl virus (TYLCV) were also determined. The results showed that elevated CO 2 increased the biomass, plant height, and photosynthetic rate of both the Moneymaker and the Mi-1.2 genotype. Elevated CO 2 decreased TYLCV disease incidence and severity for Moneymaker plants but had the opposite effect on Mi-1.2 plants whether the plants were agroinoculated or inoculated via B. tabaci feeding. Elevated CO 2 increased the salicylic acid (SA)-dependent signaling pathway on Moneymaker plants but decreased the SA-signaling pathway on Mi-1.2 plants when infected by TYLCV. Elevated CO 2 did not significantly affect B. tabaci fitness or the ability of viruliferous B. tabaci to transmit virus regardless of plant genotype. The results indicate that elevated CO 2 increases the resistance of Moneymaker plants but decreases the resistance of Mi-1.2 plants against TYLCV, whether the plants are agroinoculated or inoculated by the vector. Our results suggest that plant genotypes containing the R gene Mi-1.2 will be more vulnerable to TYLCV and perhaps to other plant viruses under elevated CO 2 conditions.

Thrips tabaci (Thysanoptera: Thripidae) and Iris yellow spot virus associated with onion transplants, onion volunteers, and weeds in Colorado

USDA-ARS?s Scientific Manuscript database

Thrips tabaci infestation was determined on onion transplants received in Colorado during March and April from out of state sources (Imperial Valley, near Phoenix Arizona, and southern Texas) during 2004 to 2008. In the five years of the study, 50% to 100% of the transplant lots sampled were found ...

Temporal dynamics of iris yellow spot virus and its vector, Thrips tabaci (Thysanoptera: Thripidae), in seeded and transplanted onion fields.

PubMed

Hsu, Cynthia L; Hoepting, Christine A; Fuchs, Marc; Shelton, Anthony M; Nault, Brian A

2010-04-01

Onion thrips, Thrips tabaci (Lindeman) (Thysanoptera: Thripidae), can reduce onion bulb yield and transmit iris yellow spot virus (IYSV) (Bunyaviridae: Tospovirus), which can cause additional yield losses. In New York, onions are planted using seeds and imported transplants. IYSV is not seed transmitted, but infected transplants have been found in other U.S. states. Transplants are also larger than seeded onions early in the season, and thrips, some of which may be viruliferous, may preferentially colonize larger plants. Limited information is available on the temporal dynamics of IYSV and its vector in onion fields. In 2007 and 2008, T. tabaci and IYSV levels were monitored in six seeded and six transplanted fields. We found significantly more thrips in transplanted fields early in the season, but by the end of the season seeded fields had higher levels of IYSV. The percentage of sample sites with IYSV-infected plants remained low (<12%) until August, when infection levels increased dramatically in some fields. The densities of adult and larval thrips in August and September were better predictors of final IYSV levels than early season thrips densities. For 2007 and 2008, the time onions were harvested may have been more important in determining IYSV levels than whether the onions were seeded or transplanted. Viruliferous thrips emigrating from harvested onion fields into nonharvested ones may be increasing the primary spread of IYSV in late-harvested onions. Managing T. tabaci populations before harvest, and manipulating the spatial arrangement of fields based on harvest date could mitigate the spread of IYSV.

Sweepoviruses cause disease in sweet potato and related Ipomoea spp.: fulfilling Koch's postulates for a divergent group in the genus begomovirus.

PubMed

Trenado, Helena P; Orílio, Anelise F; Márquez-Martín, Belén; Moriones, Enrique; Navas-Castillo, Jesús

2011-01-01

Sweet potato (Ipomoea batatas) and related Ipomoea species are frequently infected by monopartite begomoviruses (genus Begomovirus, family Geminiviridae), known as sweepoviruses. Unlike other geminiviruses, the genomes of sweepoviruses have been recalcitrant to rendering infectious clones to date. Thus, Koch's postulates have not been fullfilled for any of the viruses in this group. Three novel species of sweepoviruses have recently been described in Spain: Sweet potato leaf curl Lanzarote virus (SPLCLaV), Sweet potato leaf curl Spain virus (SPLCSV) and Sweet potato leaf curl Canary virus (SPLCCaV). Here we describe the generation of the first infectious clone of an isolate (ES:MAL:BG30:06) of SPLCLaV. The clone consisted of a complete tandem dimeric viral genome in a binary vector. Successful infection by agroinoculation of several species of Ipomoea (including sweet potato) and Nicotiana benthamiana was confirmed by PCR, dot blot and Southern blot hybridization. Symptoms observed in infected plants consisted of leaf curl, yellowing, growth reduction and vein yellowing. Two varieties of sweet potato, 'Beauregard' and 'Promesa', were infected by agroinoculation, and symptoms of leaf curl and interveinal loss of purple colouration were observed, respectively. The virus present in agroinfected plants was readily transmitted by the whitefly Bemisia tabaci to I. setosa plants. The progeny virus population present in agroinfected I. setosa and sweet potato plants was isolated and identity to the original isolate was confirmed by sequencing. Therefore, Koch's postulates were fulfilled for the first time for a sweepovirus.

Sweepoviruses Cause Disease in Sweet Potato and Related Ipomoea spp.: Fulfilling Koch's Postulates for a Divergent Group in the Genus Begomovirus

PubMed Central

Márquez-Martín, Belén; Moriones, Enrique; Navas-Castillo, Jesús

2011-01-01

Sweet potato (Ipomoea batatas) and related Ipomoea species are frequently infected by monopartite begomoviruses (genus Begomovirus, family Geminiviridae), known as sweepoviruses. Unlike other geminiviruses, the genomes of sweepoviruses have been recalcitrant to rendering infectious clones to date. Thus, Koch's postulates have not been fullfilled for any of the viruses in this group. Three novel species of sweepoviruses have recently been described in Spain: Sweet potato leaf curl Lanzarote virus (SPLCLaV), Sweet potato leaf curl Spain virus (SPLCSV) and Sweet potato leaf curl Canary virus (SPLCCaV). Here we describe the generation of the first infectious clone of an isolate (ES:MAL:BG30:06) of SPLCLaV. The clone consisted of a complete tandem dimeric viral genome in a binary vector. Successful infection by agroinoculation of several species of Ipomoea (including sweet potato) and Nicotiana benthamiana was confirmed by PCR, dot blot and Southern blot hybridization. Symptoms observed in infected plants consisted of leaf curl, yellowing, growth reduction and vein yellowing. Two varieties of sweet potato, ‘Beauregard’ and ‘Promesa’, were infected by agroinoculation, and symptoms of leaf curl and interveinal loss of purple colouration were observed, respectively. The virus present in agroinfected plants was readily transmitted by the whitefly Bemisia tabaci to I. setosa plants. The progeny virus population present in agroinfected I. setosa and sweet potato plants was isolated and identity to the original isolate was confirmed by sequencing. Therefore, Koch's postulates were fulfilled for the first time for a sweepovirus. PMID:22073314

Temperature stress effects in Bemisia tabaci (Hemiptera: Aleyrodidae) type B whiteflies

USDA-ARS?s Scientific Manuscript database

Oxidative stress occurs in response to changes in the redox equilibiurm, which may be caused by increases in reactive oxygen species (ROS), a decrease in antioxidant protection or failure of cells to repair oxidative damage. ROS are either free radicals, reactive molecules containing oxygen atoms or...

The Incredible Journey of Begomoviruses in Their Whitefly Vector

PubMed Central

Czosnek, Henryk; Hariton-Shalev, Aliza; Sobol, Iris; Gorovits, Rena; Ghanim, Murad

2017-01-01

Begomoviruses are vectored in a circulative persistent manner by the whitefly Bemisia tabaci. The insect ingests viral particles with its stylets. Virions pass along the food canal and reach the esophagus and the midgut. They cross the filter chamber and the midgut into the haemolymph, translocate into the primary salivary glands and are egested with the saliva into the plant phloem. Begomoviruses have to cross several barriers and checkpoints successfully, while interacting with would-be receptors and other whitefly proteins. The bulk of the virus remains associated with the midgut and the filter chamber. In these tissues, viral genomes, mainly from the tomato yellow leaf curl virus (TYLCV) family, may be transcribed and may replicate. However, at the same time, virus amounts peak, and the insect autophagic response is activated, which in turn inhibits replication and induces the destruction of the virus. Some begomoviruses invade tissues outside the circulative pathway, such as ovaries and fat cells. Autophagy limits the amounts of virus associated with these organs. In this review, we discuss the different sites begomoviruses need to cross to complete a successful circular infection, the role of the coat protein in this process and the sites that balance between virus accumulation and virus destruction. PMID:28946649

Transcriptome changes occurred in the whitefly, B. tabaci MEAM1 in response to feeding on melon infected with the crinivirus, CYSDV

USDA-ARS?s Scientific Manuscript database

Cucurbit yellow stunting disorder virus (CYSDV), a crinivirus transmitted by the whitefly, B. tabaci, causes widespread losses in melon in many parts of the world. The virus emerged in the southwestern United States (Arizona and California) and western Mexico in 2006 and rapidly became established ...

Stage-Related Defense Response Induction in Tomato Plants by Nesidiocoris tenuis

PubMed Central

Naselli, Mario; Urbaneja, Alberto; Siscaro, Gaetano; Jaques, Josep A.; Zappalà, Lucia; Flors, Víctor; Pérez-Hedo, Meritxell

2016-01-01

The beneficial effects of direct predation by zoophytophagous biological control agents (BCAs), such as the mirid bug Nesidiocoris tenuis, are well-known. However, the benefits of zoophytophagous BCAs’ relation with host plants, via induction of plant defensive responses, have not been investigated until recently. To date, only the females of certain zoophytophagous BCAs have been demonstrated to induce defensive plant responses in tomato plants. The aim of this work was to determine whether nymphs, adult females, and adult males of N. tenuis are able to induce defense responses in tomato plants. Compared to undamaged tomato plants (i.e., not exposed to the mirid), plants on which young or mature nymphs, or adult males or females of N. tenuis fed and developed were less attractive to the whitefly Bemisia tabaci, but were more attractive to the parasitoid Encarsia formosa. Female-exposed plants were more repellent to B. tabaci and more attractive to E. formosa than were male-exposed plants. When comparing young- and mature-nymph-exposed plants, the same level of repellence was obtained for B. tabaci, but mature-nymph-exposed plants were more attractive to E. formosa. The repellent effect is attributed to the signaling pathway of abscisic acid, which is upregulated in N. tenuis-exposed plants, whereas the parasitoid attraction was attributed to the activation of the jasmonic acid signaling pathway. Our results demonstrate that all motile stages of N. tenuis can trigger defensive responses in tomato plants, although these responses may be slightly different depending on the stage considered. PMID:27472328

Enterobacter tabaci sp. nov., a novel member of the genus Enterobacter isolated from a tobacco stem.

PubMed

Duan, Yan-Qing; Zhou, Xing-Kui; Di-Yan, Li; Li, Qing-Qing; Dang, Li-Zhi; Zhang, Yong-Guang; Qiu, Li-Hong; Nimaichand, Salam; Li, Wen-Jun

2015-11-01

A Gram-stain negative, motile, rod-shaped bacterium, designated strain YIM Hb-3(T), was isolated from the stem of a tobacco plant. The strain was observed to form convex, circular and yellow-colored colonies. The predominant respiratory quinone was identified as Q-8. The major fatty acids (>5%) detected were C(16:1)ω7c and/or C(16:1)ω6c (summed feature 3), C(16:0), C(17:0)cyclo, C(18:1)ω7c and/or C(18:1)ω6c (summed feature 8), C(14:0)3-OH and/or iso-C(16:1)I (summed feature 2), C(14:0) and C(12:0). The genomic DNA G+C content was determined to be 54.8 mol%. Phylogenetic trees based on 16S rRNA gene sequences and multilocus sequence analysis showed that strain YIM Hb-3(T) had the closest phylogenetic relationship with Enterobacter mori LMG 25706(T). DNA-DNA relatedness value between strain YIM Hb-3(T) and E. mori LMG 25706(T) was 46.9 ± 3.8%. On the basis of phenotypic and chemotaxonomic data, phylogenetic analysis, and DNA-DNA relatedness value, strain YIM Hb-3(T) is considered to represent a novel species of the genus Enterobacter, for which the name Enterobacter tabaci sp. nov. is proposed. The type strain is YIM Hb-3(T) (=KACC 17832(T) =KCTC 42694(T)).

Baseline Susceptibilities of B- and Q-biotype Bemisia tabaci to anthranilic diamides

USDA-ARS?s Scientific Manuscript database

Development of pyriproxyfen and neonicotinoid resistance in the B biotype whitefly and recent introduction of the Q biotype are threatening the current whitefly management programs in Arizona. Whether the novel anthranilic diamides chlorantraniliprole and cyantraniliprole can be integrated into the ...

Tomato Infection by Whitefly-Transmitted Circulative and Non-Circulative Viruses Induce Contrasting Changes in Plant Volatiles and Vector Behaviour

PubMed Central

Fereres, Alberto; Peñaflor, Maria Fernanda G. V.; Favaro, Carla F.; Azevedo, Kamila E. X.; Landi, Carolina H.; Maluta, Nathalie K. P.; Bento, José Mauricio S.; Lopes, Joao R.S.

2016-01-01

Virus infection frequently modifies plant phenotypes, leading to changes in behaviour and performance of their insect vectors in a way that transmission is enhanced, although this may not always be the case. Here, we investigated Bemisia tabaci response to tomato plants infected by Tomato chlorosis virus (ToCV), a non-circulative-transmitted crinivirus, and Tomato severe rugose virus (ToSRV), a circulative-transmitted begomovirus. Moreover, we examined the role of visual and olfactory cues in host plant selection by both viruliferous and non-viruliferous B. tabaci. Visual cues alone were assessed as targets for whitefly landing by placing leaves underneath a Plexiglas plate. A dual-choice arena was used to assess whitefly response to virus-infected and mock-inoculated tomato leaves under light and dark conditions. Thereafter, we tested the whitefly response to volatiles using an active air-flow Y-tube olfactometer, and chemically characterized the blends using gas chromatography coupled to mass spectrometry. Visual stimuli tests showed that whiteflies, irrespective of their infectious status, always preferred to land on virus-infected rather than on mock-inoculated leaves. Furthermore, whiteflies had no preference for either virus-infected or mock-inoculated leaves under dark conditions, but preferred virus-infected leaves in the presence of light. ToSRV-infection promoted a sharp decline in the concentration of some tomato volatiles, while an increase in the emission of some terpenes after ToCV infection was found. ToSRV-viruliferous whiteflies preferred volatiles emitted from mock-inoculated plants, a conducive behaviour to enhance virus spread, while volatiles from ToCV-infected plants were avoided by non-viruliferous whiteflies, a behaviour that is likely detrimental to the secondary spread of the virus. In conclusion, the circulative persistent begomovirus, ToSRV, seems to have evolved together with its vector B. tabaci to optimise its own spread. However

Tomato Infection by Whitefly-Transmitted Circulative and Non-Circulative Viruses Induce Contrasting Changes in Plant Volatiles and Vector Behaviour.

PubMed

Fereres, Alberto; Peñaflor, Maria Fernanda G V; Favaro, Carla F; Azevedo, Kamila E X; Landi, Carolina H; Maluta, Nathalie K P; Bento, José Mauricio S; Lopes, Joao R S

2016-08-11

Virus infection frequently modifies plant phenotypes, leading to changes in behaviour and performance of their insect vectors in a way that transmission is enhanced, although this may not always be the case. Here, we investigated Bemisia tabaci response to tomato plants infected by Tomato chlorosis virus (ToCV), a non-circulative-transmitted crinivirus, and Tomato severe rugose virus (ToSRV), a circulative-transmitted begomovirus. Moreover, we examined the role of visual and olfactory cues in host plant selection by both viruliferous and non-viruliferous B. tabaci. Visual cues alone were assessed as targets for whitefly landing by placing leaves underneath a Plexiglas plate. A dual-choice arena was used to assess whitefly response to virus-infected and mock-inoculated tomato leaves under light and dark conditions. Thereafter, we tested the whitefly response to volatiles using an active air-flow Y-tube olfactometer, and chemically characterized the blends using gas chromatography coupled to mass spectrometry. Visual stimuli tests showed that whiteflies, irrespective of their infectious status, always preferred to land on virus-infected rather than on mock-inoculated leaves. Furthermore, whiteflies had no preference for either virus-infected or mock-inoculated leaves under dark conditions, but preferred virus-infected leaves in the presence of light. ToSRV-infection promoted a sharp decline in the concentration of some tomato volatiles, while an increase in the emission of some terpenes after ToCV infection was found. ToSRV-viruliferous whiteflies preferred volatiles emitted from mock-inoculated plants, a conducive behaviour to enhance virus spread, while volatiles from ToCV-infected plants were avoided by non-viruliferous whiteflies, a behaviour that is likely detrimental to the secondary spread of the virus. In conclusion, the circulative persistent begomovirus, ToSRV, seems to have evolved together with its vector B. tabaci to optimise its own spread. However

Begomovirus diversity in tomato crops and weeds in Ecuador and the detection of a recombinant isolate of rhynchosia golden mosaic Yucatan virus infecting tomato.

PubMed

Paz-Carrasco, Lenin C; Castillo-Urquiza, Gloria P; Lima, Alison T M; Xavier, Cesar A D; Vivas-Vivas, Leticia M; Mizubuti, Eduardo S G; Zerbini, F Murilo

2014-08-01

Viral diseases caused by begomoviruses are of economic importance due to their adverse effects on the production of tropical and subtropical crops. In Ecuador, despite reports of significant infestations of Bemisia tabaci in the late 1990s, only very recently has a begomovirus, tomato leaf deformation virus (ToLDeV, also present in Peru), been reported in tomato. ToLDeV is the first monopartite begomovirus discovered that originated in the Americas, and its presence in Ecuador highlights the need for a wider survey of tomato-infecting begomoviruses in this country. Tomato and weed samples were collected in 2010 and 2011 in six provinces of Ecuador, and begomovirus genomes were cloned and sequenced using a rolling-circle-amplification-based approach. Most tomato samples from the provinces of Guayas, Loja, Manabi and Santa Elena were infected with tomato leaf deformation virus (ToLDeV). One sample from Manabi had a triple infection with ToLDeV, rhynchosia golden mosaic Yucatan virus (RhGMYuV) and an isolate that was a recombinant between the two. A new begomovirus was detected in another tomato sample from Manabi. Samples of Rhynchosia sp. from the provinces of Guayas and Manabi were infected by RhGMYuV. These results indicate not only the prevalence of ToLDeV in tomato in Ecuador but also the presence of other viruses, albeit at a much lower frequency.

Nucleotide sequence and phylogenetic analysis of Cucurbit yellow stunting disorder virus RNA 2.

PubMed

Livieratos, Ioannis C; Coutts, Robert H A

2002-06-01

The complete nucleotide sequence of Cucurbit yellow stunting disorder virus (CYSDV) RNA 2, a whitefly (Bemisia tabaci)-transmitted closterovirus with a bi-partite genome, is reported. CYSDV RNA 2 is 7,281 nucleotides long and contains the closterovirus hallmark gene array with a similar arrangement to the prototype member of the genus Crinivirus, Lettuce infectious yellows virus (LIYV). CYSDV RNA 2 contains open reading frames (ORFs) potentially encoding in a 5' to 3' direction for proteins of 5 kDa (ORF 1; hydrophobic protein), 62 kDa (ORF 2; heat shock protein 70 homolog, HSP70h), 59 kDa (ORF 3; protein of unknown function), 9 kDa (ORF 4; protein of unknown function), 28.5 kDa (ORF 5; coat protein, CP), 53 kDa (ORF 6; coat protein minor, CPm), and 26.5 kDa (ORF 7; protein of unknown function). Pairwise comparisons of CYSDV RNA 2-encoded proteins (HSP70h, p59 and CPm) among the closteroviruses showed that CYSDV is closely related to LIYV. Phylogenetic analysis based on the amino acid sequence of the HSP70h, indicated that CYSDV clusters with other members of the genus Crinivirus, and it is related to Little cherry virus-1 (LChV-1), but is distinct from the aphid- or mealybug-transmitted closteroviruses.

Within-Host Dynamics of the Emergence of Tomato Yellow Leaf Curl Virus Recombinants

PubMed Central

Urbino, Cica; Gutiérrez, Serafin; Antolik, Anna; Bouazza, Nabila; Doumayrou, Juliette; Granier, Martine; Martin, Darren P.; Peterschmitt, Michel

2013-01-01

Tomato yellow leaf curl virus (TYLCV) is a highly damaging begomovirus native to the Middle East. TYLCV has recently spread worldwide, recombining with other begomoviruses. Recent analysis of mixed infections between TYLCV and Tomato leaf curl Comoros begomovirus (ToLCKMV) has shown that, although natural selection preserves certain co-evolved intra-genomic interactions, numerous and diverse recombinants are produced at 120 days post-inoculation (dpi), and recombinant populations from different tomato plants are very divergent. Here, we investigate the population dynamics that lead to such patterns in tomato plants co-infected with TYLCV and ToLCKMV either by agro-inoculation or using the natural whitefly vector Bemisia tabaci. We monitored the frequency of parental and recombinant genotypes independently in 35 plants between 18 and 330 dpi and identified 177 recombinants isolated at different times. Recombinants were detected from 18 dpi and their frequency increased over time to reach about 50% at 150 dpi regardless of the inoculation method. The distribution of breakpoints detected on 96 fully sequenced recombinants was consistent with a continuous generation of new recombinants as well as random and deterministic effects in their maintenance. A severe population bottleneck of around 10 genomes was estimated during early systemic infection–a phenomenon that could account partially for the heterogeneity in recombinant patterns observed among plants. The detection of the same recombinant genome in six of the thirteen plants analysed beyond 30 dpi supported the influence of selection on observed recombination patterns. Moreover, a highly virulent recombinant genotype dominating virus populations within one plant has, apparently, the potential to be maintained in the natural population according to its infectivity, within-host accumulation, and transmission efficiency - all of which were similar or intermediate to those of the parent genotypes. Our results

The Role of Bacterial Chaperones in the Circulative Transmission of Plant Viruses by Insect Vectors

PubMed Central

Kliot, Adi; Ghanim, Murad

2013-01-01

Persistent circulative transmission of plant viruses involves complex interactions between the transmitted virus and its insect vector. Several studies have shown that insect vector proteins are involved in the passage and the transmission of the virus. Interestingly, proteins expressed by bacterial endosymbionts that reside in the insect vector, were also shown to influence the transmission of these viruses. Thus far, the transmission of two plant viruses that belong to different virus genera was shown to be facilitated by a bacterial chaperone protein called GroEL. This protein was shown to be implicated in the transmission of Potato leafroll virus (PLRV) by the green peach aphid Myzus persicae, and the transmission of Tomato yellow leaf curl virus (TYLCV) by the sweetpotato whitefly Bemisia tabaci. These tri-trophic levels of interactions and their possible evolutionary implications are reviewed. PMID:23783810

Plant-mediated horizontal transmission of Rickettsia endosymbiont between different whitefly species.

PubMed

Li, Yi-Han; Ahmed, Muhammad Z; Li, Shao-Jian; Lv, Ning; Shi, Pei-Qiong; Chen, Xiao-Sheng; Qiu, Bao-Li

2017-12-01

A growing number of studies have revealed the presence of closely related endosymbionts in phylogenetically distant arthropods, indicating horizontal transmission of these bacteria. Here we investigated the interspecific horizontal transmission of Rickettsia between two globally invasive whitefly species, Bemisia tabaci MEAM1 and B. tabaci MED, via cotton plants. We found both scattered and confined distribution patterns of Rickettsia in these whiteflies. After entering cotton leaves, Rickettsia was restricted to the leaf phloem vessels and could be taken up by both species of the Rickettsia-free whitefly adults, but only the scattered pattern was observed in the recipient whiteflies. Both the relative quantity of Rickettsia and the efficiency of transmitting Rickettsia into cotton leaves were significantly higher in MEAM1 females than in MED females. The retention time of Rickettsia transmitted from MEAM1 into cotton leaves was at least 5 days longer than that of MED. Phylogenetic analysis based on 16S rRNA and gltA genes confirmed that the Rickettsia extracted from the donor MEAM1, the cotton leaves, the recipient MEAM1 and the recipient MED were all identical. We conclude that cotton plants can mediate horizontal transmission of Rickettsia between different insect species, and that the transmission dynamics of Rickettsia vary with different host whitefly species. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A simple, rapid and inexpensive method for localization of Tomato yellow leaf curl virus and Potato leafroll virus in plant and insect vectors.

PubMed

Ghanim, Murad; Brumin, Marina; Popovski, Smadar

2009-08-01

A simple, rapid, inexpensive method for the localization of virus transcripts in plant and insect vector tissues is reported here. The method based on fluorescent in situ hybridization using short DNA oligonucleotides complementary to an RNA segment representing a virus transcript in the infected plant or insect vector. The DNA probe harbors a fluorescent molecule at its 5' or 3' ends. The protocol: simple fixation, hybridization, minimal washing and confocal microscopy, provides a highly specific signal. The reliability of the protocol was tested by localizing two phloem-limited plant virus transcripts in infected plants and insect tissues: Tomato yellow leaf curl virus (TYLCV) (Begomovirus: Geminiviridae), exclusively transmitted by the whitefly Bemisia tabaci (Gennadius) in a circulative non-propagative manner, and Potato leafroll virus (Polerovirus: Luteoviridae), similarly transmitted by the aphid Myzus persicae (Sulzer). Transcripts for both viruses were localized specifically to the phloem sieve elements of infected plants, while negative controls showed no signal. TYLCV transcripts were also localized to the digestive tract of B. tabaci, confirming TYLCV route of transmission. Compared to previous methods for localizing virus transcripts in plant and insect tissues that include complex steps for in-vitro probe preparation or antibody raising, tissue fixation, block preparation, sectioning and hybridization, the method described below provides very reliable, convincing, background-free results with much less time, effort and cost.

Zoophytophagous mirids provide pest control by inducing direct defences, antixenosis and attraction to parasitoids in sweet pepper plants.

PubMed

Bouagga, Sarra; Urbaneja, Alberto; Rambla, José L; Flors, Víctor; Granell, Antonio; Jaques, Josep A; Pérez-Hedo, Meritxell

2018-06-01

In addition to their services as predators, mirid predators are able to induce plant defences by phytophagy. However, whether this induction occurs in sweet pepper and whether it could be an additional benefit to their role as a biological control agent in this crop remain unknown. Here, these questions were investigated in two model insects, the mirids Nesidiocoris tenuis and Macrolophus pygmaeus. Plant feeding behaviour was observed in both N. tenuis and M. pygmaeus on sweet pepper and occupied 33% and 14% of total time spent on the plant, respectively. The punctures caused by mirid plant feeding induced the release of a blend of volatile organic compounds (VOCs) which repelled the herbivore pests Frankliniella occidentalis and Bemisia tabaci and attracted the whitefly parasitoid Encarsia formosa. The repellent effect on B. tabaci was observed for at least 7 days after initial exposure of the plant to N. tenuis, and attraction of E. formosa remained functional for 14 days. Plant defences induced by the feeding of mirid predators, their subsequent effects on the behaviour of both pests and natural enemies, and the persistence of these observed effects open the door to new control strategies in the sweet pepper crop. Further application of this research is discussed, such as the vaccination of plants by zoophytophagous mirids in the nursery before transplantation. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Plant virus differentially alters the plant's defense response to its closely related vectors.

PubMed

Shi, Xiaobin; Pan, Huipeng; Xie, Wen; Wu, Qingjun; Wang, Shaoli; Liu, Yang; Fang, Yong; Chen, Gong; Gao, Xiwu; Zhang, Youjun

2013-01-01

The whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), is one of the most widely distributed agricultural pests. In recent years, B. tabaci Q has invaded China, and Q has displaced B in many areas now. In a number of regions of the world, invasion by B and/or Q has been followed by outbreaks of tomato yellow leaf curl virus (TYLCV). Our previous study showed TYLCV directly and indirectly modified the feeding behavior of B. tabaci in favor of Q rather than B. In this study, we quantified the salicylic acid (SA) titers and relative gene expression of SA in tomato leaves that were infested with viruliferous or non-viruliferous B and Q. We also measured the impacts of exogenous SA on the performance of B and Q, including the effects on ovary development. SA titer was always higher in leaves that were infested with viruliferous B than with viruliferous Q, whereas the SA titer did not differ between leaves infested with non-viruliferous B and Q. The relative gene expression of SA signaling was increased by feeding of viruliferous B but was not increased by feeding of viruliferous Q. The life history traits of B and Q were adversely affected on SA-treated plants. On SA-treated plants, both B and Q had lower fecundity, shorter longevity, longer developmental time and lower survival rate than on untreated plants. Compared with whiteflies feeding on control plants, those feeding on SA-treated plants had fewer oocytes and slower ovary development. On SA-treated plants, viruliferous B had fewer oocytes than viruliferous Q. These results indicate that TYLCV tends to induce SA-regulated plant defense against B but SA-regulated plant defense against Q was reduced. In other words, Q may have a mutualistic relationship with TYLCV that results in the reduction of the plant's defense response.

ACE: an efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data.

PubMed

Guo, Dianhao; Luo, Jiapeng; Zhou, Yuenan; Xiao, Huamei; He, Kang; Yin, Chuanlin; Xu, Jianhua; Li, Fei

2017-07-10

Insecticide resistance is a substantial problem in controlling agricultural and medical pests. Detecting target site mutations is crucial to manage insecticide resistance. Though PCR-based methods have been widely used in this field, they are time-consuming and inefficient, and typically have a high false positive rate. Acetylcholinesterases (Ace) is the neural target of the widely used organophosphate (OP) and carbamate insecticides. However, there is not any software available to detect insecticide resistance associated mutations in RNA-Seq data at present. A computational pipeline ACE was developed to detect resistance mutations of ace in insect RNA-Seq data. Known ace resistance mutations were collected and used as a reference. We constructed a Web server for ACE, and the standalone software in both Linux and Windows versions is available for download. ACE was used to analyse 971 RNA-Seq data from 136 studies in 7 insect pests. The mutation frequency of each RNA-Seq dataset was calculated. The results indicated that the resistance frequency was 30%-44% in an eastern Ugandan Anopheles population, thus suggesting this resistance-conferring mutation has reached high frequency in these mosquitoes in Uganda. Analyses of RNA-Seq data from the diamondback moth Plutella xylostella indicated that the G227A mutation was positively related with resistance levels to organophosphate or carbamate insecticides. The wasp Nasonia vitripennis had a low frequency of resistant reads (<5%), but the agricultural pests Chilo suppressalis and Bemisia tabaci had a high resistance frequency. All ace reads in the 30 B. tabaci RNA-Seq data were resistant reads, suggesting that insecticide resistance has spread to very high frequency in B. tabaci. To the best of our knowledge, the ACE pipeline is the first tool to detect resistance mutations from RNA-Seq data, and it facilitates the full utilization of large-scale genetic data obtained by using next-generation sequencing.

Bensulfuron-Methyl Treatment of Soil Affects the Infestation of Whitefly, Aphid, and Tobacco Mosaic Virus on Nicotiana tabacum

PubMed Central

Li, Renyi; Islam, Saif Ul; Wu, Zujian; Ye, Xiujuan

2016-01-01

Bensulfuron-methyl (BSM) is widely used in paddy soil for weed control. BSM residue in the soil has been known to inhibit the growth of sensitive crop plants. However, it is unknown whether BSM residue can affect the agrosystem in general. In this study, we have found significant effects of BSM on the infestation of Bemisia tabaci, Myzus persicae, and Tobacco mosaic virus (TMV) in Nicotiana tabacum. The soil was treated with BSM before the pest inoculation. The herbicide-treated tobaccos showed resistance to B. tabaci, but this resistance could not be detected until 15-day post-infestation when smaller number of adults B. tabaci appeared. In M. persicae assay, the longevity of all development stages of insects, and the fecundity of insects were not significantly affected when feeding on BSM-treated plants. In TMV assay, the BSM treatment also reduced virus-induced lesions in early infection time. However, the titer of TMV in BSM treated plants increased greatly over time and was over 40-fold higher than the mock-infected control plants after 20 days. Further studies showed that BSM treatment increased both jasmonic acid (JA) and salicylic acid (SA) levels in tobacco, as well as the expression of target genes in the JA and SA signaling pathways, such as NtWIPK, NtPR1a, and NtPAL. NtPR1a and NtPAL were initially suppressed after virus-inoculation, while NtRDR1 and NtRDR6, which play a key role in fighting virus infection, only showed up- or were down-regulated 20 days post virus-inoculation. Taken together, our results suggested that BSM residue in the soil may affect the metabolism of important phytohormones such as JA and SA in sensitive plants and consequently affect the plant immune response against infections such as whitefly, aphids, and viruses. PMID:28083007

Evaluation of mustard plants and other products to control sweetpotato whitefly, Bemisia tabaci

USDA-ARS?s Scientific Manuscript database

A major insect pest of vegetables and horticultural crops in the southeast US is the sweetpotato whitefly.Scientists at the USDA-Agriculture Research Service, Center for Veterinary Entomology, Gainesaville, Florida, evaluated the effect of giant red mustard plants and commercial products to control ...

Investigating the Q invasion of Bemisia tabaci in Florida: Current status and update

USDA-ARS?s Scientific Manuscript database

Three separate Q haplotypes within Florida were discovered that could be used to associate populations known to be related by grower and plant type thereby tracking distribution routes. We determined that biotype Q entered Florida through at least two separate introductions. In-depth analysis of ins...

Quantifying conservation biological control for management of Bemisia tabaci (Hemiptera: Aleyrodidae) in cotton

USDA-ARS?s Scientific Manuscript database

Conservation biological control can be an effective tactic for minimizing insect-induced damage to agricultural production. The most effective manner of applying CBC is through an Integrated Pest Management (IPM) strategy, combining many tactics including cultural controls, pest sampling, the use of...

Gene-for-gene disease resistance: bridging insect pest and pathogen defense.

PubMed

Kaloshian, Isgouhi

2004-12-01

Active plant defense, also known as gene-for-gene resistance, is triggered when a plant resistance (R) gene recognizes the intrusion of a specific insect pest or pathogen. Activation of plant defense includes an array of physiological and transcriptional reprogramming. During the past decade, a large number of plant R genes that confer resistance to diverse group of pathogens have been cloned from a number of plant species. Based on predicted protein structures, these genes are classified into a small number of groups, indicating that structurally related R genes recognize phylogenetically distinct pathogens. An extreme example is the tomato Mi-1 gene, which confers resistance to potato aphid (Macrosiphum euphorbiae), whitefly (Bemisia tabaci), and root-knot nematodes (Meloidogyne spp.). While Mi-1 remains the only cloned insect R gene, there is evidence that gene-for-gene type of plant defense against piercing-sucking insects exists in a number of plant species.

Phytohormone ecology : Herbivory byThrips tabaci induces greater ethylene production in intact onions than mechanical damage alone.

PubMed

Kendall, D M; Bjostad, L B

1990-03-01

Herbivory byThrips tabaci affected production of the phytohormone ethylene from living onion foliage. Ethylene analysis was performed by gas chromatography on intact onion tissue. Thrips feeding damage and a crushed thrips extract stimulated significantly greater production of eihylene than could be explained by either one-time or semicontinuous mechanical damage alone, suggesting that ethylene-inducing cues may be transferred to the plant during feeding. This is the first demonstration of increased ethylene production from insect-infested intact plants. This study suggests that herbivores affect both the phytohormone physiology and secondary chemistry of living plants because ethylene has been shown to enhance production of defensive phytochemicals.

Diversity and localization of bacterial symbionts in three whitefly species (Hemiptera: Aleyrodidae) from the east coast of the Adriatic Sea.

PubMed

Skaljac, M; Zanić, K; Hrnčić, S; Radonjić, S; Perović, T; Ghanim, M

2013-02-01

Several whitefly species (Hemiptera: Aleyrodidae) are cosmopolitan phloem-feeders that cause serious damage in numerous agricultural crops. All whitefly species harbor a primary bacterial symbiont and a diverse array of secondary symbionts which may influence several aspects of the insect's biology. We surveyed infections by secondary symbionts in Bemisia tabaci (Gennadius), Trialeurodes vaporariorum (Westwood) and Siphoninus phillyreae (Haliday) from areas in the east cost of the Adriatic Sea. Both the Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED) B. tabaci genetic groups were detected in Montenegro, whereas only the MED was confirmed in Croatia. Trialeurodes vaporariorum and S. phillyreae were found in all areas surveyed. MEAM1 and MED exhibited similarity to previously reported infections, while populations of T. vaporariorum from Montenegro harbored Rickettsia, Wolbachia and Cardinium in addition to previously reported Hamiltonella and Arsenopnohus. Siphoninus phillyreae harbored Hamiltonella, Wolbachia, Cardinium and Arsenophonus, with the latter appearing in two alleles. Multiple infections of all symbionts were common in the three insect species tested, with some reaching near fixation. Florescent in situ hybridization showed new localization patterns for Hamiltonella in S. phillyreae, and the morphology of the bacteriosome differed from that observed in other whitefly species. Our results show new infections with bacterial symbionts in the whitefly species studied. Infections with the same symbionts in reproductively isolated whitefly species confirm complex relationships between whiteflies and bacterial symbionts, and suggest possible horizontal transfer of some of these bacteria.

Temperature stress, anti-oxidative enzyme activity and virus acquisition in Bemisia tabaci (Hemiptera: Aleyrodidae)

USDA-ARS?s Scientific Manuscript database

In most eukaryotic systems, antioxidants provide protection when cells are exposed to stressful environmental conditions. Antioxidants, such as superoxide dismutase (SOD), glutathione peroxidase (GPX) and catalase, function in a stepwise series with SOD initially preventing oxidative damage by conve...

Feeding by whiteflies suppresses downstream jasmonic acid signaling by eliciting salicylic acid signaling.

PubMed

Zhang, Peng-Jun; Li, Wei-Di; Huang, Fang; Zhang, Jin-Ming; Xu, Fang-Cheng; Lu, Yao-Bin

2013-05-01

Phloem-feeding whiteflies in the species complex Bemisia tabaci cause extensive crop damage worldwide. One of the reasons for their "success" is their ability to suppress the effectual jasmonic acid (JA) defenses of the host plant. However, little is understood about the mechanisms underlying whitefly suppression of JA-regulated defenses. Here, we showed that the expression of salicylic acid (SA)-responsive genes (EDS1 and PR1) in Arabidopsis thaliana was significantly enhanced during feeding by whitefly nymphs. Whereas upstream JA-responsive genes (LOX2 and OPR3) also were induced, the downstream JA-responsive gene (VSP1) was repressed, i.e., whiteflies only suppressed downstream JA signaling. Gene-expression analyses with various Arabidopsis mutants, including NahG, npr-1, ein2-1, and dde2-2, revealed that SA signaling plays a key role in the suppression of downstream JA defenses by whitefly feeding. Assays confirmed that SA activation enhanced whitefly performance by suppressing downstream JA defenses.

A multiplex PCR method discriminating between the TYLCV and TYLCV-Mld clades of tomato yellow leaf curl virus.

PubMed

Lefeuvre, P; Hoareau, M; Delatte, H; Reynaud, B; Lett, J-M

2007-09-01

Tomato yellow leaf curl virus (TYLCV) is one of the causal agents of tomato yellow leaf curl disease (TYLCD) and can cause up to 100% yield losses in tomato fields. As TYLCV continues to spread, many isolates have been described in different parts of the world. Recently two closely related but distinct TYLCV clades, called TYLCV and TYLCV-Mld, have been identified. Isolates from those two clades differ mainly in the nucleotide sequences of their replication associated protein genes but do not display significantly different symptomatology. In order to improve monitoring of the rapidly expanding worldwide TYLCD epidemic, a multiplex polymerase chain reaction assay (mPCR) was developed. A set of three primers were designed to detect and characterize the TYLCV and TYLCV-Mld clade isolates. The specificity and sensitivity of the mPCR were validated on TYLCV infected tomato plants and Bemisia tabaci whiteflies. Being cheap, fast and highly sensitive this new diagnostic tool should greatly simplify efforts to trace the global spread of TYLCV.

Species Delimitation and Global Biosecurity

PubMed Central

Boykin, Laura M.; Armstrong, Karen F.; Kubatko, Laura; De Barro, Paul

2012-01-01

Species delimitation directly impacts on global biosecurity. It is a critical element in the decisions made by national governments in regard to the flow of trade and to the biosecurity measures imposed to protect countries from the threat of invasive species. Here we outline a novel approach to species delimitation, “tip to root”, for two highly invasive insect pests, Bemisia tabaci (sweetpotato whitefly) and Lymantria dispar (Asian gypsy moth). Both species are of concern to biosecurity, but illustrate the extremes of phylogenetic resolution that present the most complex delimitation issues for biosecurity; B. tabaci having extremely high intra-specific genetic variability and L. dispar composed of relatively indistinct subspecies. This study tests a series of analytical options to determine their applicability as tools to provide more rigorous species delimitation measures and consequently more defensible species assignments and identification of unknowns for biosecurity. Data from established DNA barcode datasets (COI), which are becoming increasingly considered for adoption in biosecurity, were used here as an example. The analytical approaches included the commonly used Kimura two-parameter (K2P) inter-species distance plus four more stringent measures of taxon distinctiveness, (1) Rosenberg’s reciprocal monophyly, (P(AB)),1 (2) Rodrigo’s (P(randomly distinct)),2 (3) genealogical sorting index, (gsi),3 and (4) General mixed Yule-coalescent (GMYC).4,5 For both insect datasets, a comparative analysis of the methods revealed that the K2P distance method does not capture the same level of species distinctiveness revealed by the other three measures; in B. tabaci there are more distinct groups than previously identified using the K2P distances and for L. dipsar far less variation is apparent within the predefined subspecies. A consensus for the results from P(AB), P(randomly distinct) and gsi offers greater statistical confidence as to where genetic limits

Effect of foliar application of pyrifluquinazon on Bemisia tabaci (MED whitefly) and Amblyseius swirskii, 2016

USDA-ARS?s Scientific Manuscript database

With the overall goal to integrate the predatory mite Amblyseius swirskii in the management program of MED whitefly, the specific objective of this study was to evaluate pyrifluquinazon, a pyridine insecticide for whitefly control, and assess its compatibility with swirskii mite, and assess its comp...

Evolution and homoplasy at the bem6 microsatellite locus in three Bemisia tabaci cryptic species

USDA-ARS?s Scientific Manuscript database

The evolution of individual microsatellite loci is often complex and homoplasy is common but often goes undetected. Sequencing alleles at a microsatellite locus can provide a more complete picture of the common evolutionary mechanisms occurring at that locus and can reveal cases of homoplasy. Within...

Evaluation of potential new sources of melon host plant resistance to the whitefly, Bemisia tabaci

USDA-ARS?s Scientific Manuscript database

Melon (Cucumis melo L.) genotypes that support fewer numbers of whitefly could reduce the frequency or the amount of insecticide applications required to keep the insects in check, as was the case with cotton where measurable resistance to whitefly in some genotypes reduced the number of sprays, thu...

A transgenic approach to control hemipteran insects by expressing insecticidal genes under phloem-specific promoters.

PubMed

Javaid, Shaista; Amin, Imran; Jander, Georg; Mukhtar, Zahid; Saeed, Nasir A; Mansoor, Shahid

2016-10-06

The first generation transgenic crops used strong constitutive promoters for transgene expression. However, tissue-specific expression is desirable for more precise targeting of transgenes. Moreover, piercing/sucking insects, which are generally resistant to insecticidal Bacillus thuringiensis (Bt) proteins, have emerged as a major pests since the introduction of transgenic crops expressing these toxins. Phloem-specific promoters isolated from Banana bunchy top virus (BBTV) were used for the expression of two insecticidal proteins, Hadronyche versuta (Blue Mountains funnel-web spider) neurotoxin (Hvt) and onion leaf lectin, in tobacco (Nicotiana tabacum). Here we demonstrate that transgenic plants expressing Hvt alone or in combination with onion leaf lectin are resistant to Phenacoccus solenopsis (cotton mealybug), Myzus persicae (green peach aphids) and Bemisia tabaci (silver leaf whitefly). The expression of both proteins under different phloem-specific promoters resulted in close to 100% mortality and provided more rapid protection than Hvt alone. Our results suggest the employment of the Hvt and onion leaf lectin transgenic constructs at the commercial level will reduce the use of chemical pesticides for control of hemipteran insect pests.

New developments in insecticide resistance in the glasshouse whitefly (Trialeurodes vaporariorum) and the two-spotted spider mite (Tetranychus urticae) in the UK.

PubMed

Gorman, Kevin; Hewitt, Fiona; Denholm, Ian; Devine, Gregor J

2002-02-01

A recent survey of insecticide resistance in two of the most problematic pests in UK glasshouses revealed some new developments. At least some individuals in all UK samples of Trialeurodes vaporariorum that were tested resisted the insect growth regulator (IGR) buprofezin. The most strongly resistant strains were unaffected by the field application rate of this compound, and even samples from populations that had never been exposed to buprofezin contained individuals that survived the highest concentration applied (10,000 mg litre-1). The field rate of buprofezin was shown to select for resistance through vapour action alone. The benzophenylurea teflubenzuron, an unrelated IGR, was cross-resisted by buprofezin-resistant individuals. There was no evidence of resistance to imidacloprid, but all T vaporariorum strains tested, regardless of origin, exhibited a high innate tolerance to nicotine, when compared with another whitefly species, Bemisia tabaci. Marked resistance to fenbutatin oxide and tebufenpyrad was found in single glasshouse populations of Tetranychus urticae, but these compounds and abamectin appeared to remain highly effective against all other strains collected.

A Tomato necrotic dwarf virus isolate from Datura with poor transmissibility by the whitefly, Bemisia tabaci

USDA-ARS?s Scientific Manuscript database

Tomato necrotic dwarf virus (ToNDV); genus Torradovirus, is a whitefly-transmitted virus that caused significant losses for tomato production in the Imperial Valley of California during the 1980s. The virus causes severe stunting, dwarfing of leaves, foliar and fruit necrosis, and greatly reduced f...

Consequences of co-applying insecticides and fungicides for managing Thrips tabaci (Thysanoptera: Thripidae) on onion.

PubMed

Nault, Brian A; Hsu, Cynthia L; Hoepting, Christine A

2013-07-01

Insecticides and fungicides are commonly co-applied in a tank mix to protect onions from onion thrips, Thrips tabaci Lindeman, and foliar pathogens. Co-applications reduce production costs, but past research shows that an insecticide's performance can be reduced when co-applied with a fungicide. An evaluation was made of the effects of co-applying spinetoram, abamectin and spirotetramat with commonly used fungicides, with and without the addition of a penetrating surfactant, on onion thrips control in onion fields. Co-applications of insecticides with chlorothalonil fungicides reduced thrips control by 25-48% compared with control levels provided by the insecticides alone in three of five trials. Inclusion of a penetrating surfactant at recommended rates with the insecticide and chlorothalonil fungicide did not consistently overcome this problem. Co-applications of insecticides with other fungicides did not interfere with thrips control. Co-applications of pesticides targeting multiple organisms should be examined closely to ensure that control of each organism is not compromised. To manage onion thrips in onion most effectively, insecticides should be applied with a penetrating surfactant, and should be applied separately from chlorothalonil fungicides. © 2012 Society of Chemical Industry.

Herbivore Damage and Prior Egg Deposition on Host Plants Influence the Oviposition of the Generalist Moth Trichoplusia ni (Lepidoptera: Noctuidae).

PubMed

Coapio, Guadalupe G; Cruz-López, Leopoldo; Guerenstein, Pablo; Malo, Edi A; Rojas, Julio C

2016-12-01

Female insects have the difficult task of locating host plants that maximize the survival and success of their offspring. In this study, the oviposition preferences of the cabbage looper moth, Trichoplusia ni (Hübner), for soybean plants, Glycine max (L.), under various treatments-undamaged, mechanically damaged, damaged by T. ni or Spodoptera frugiperda (Smith) larvae or by Bemisia tabaci (Gennadius) adults, egg-free plants, and plants previously oviposited by conspecific or heterospecific females (S. frugiperda)-were investigated using two-choice tests. Additionally, the volatile compounds emitted by the plants under the different treatments were identified by gas chromatography-mass spectrometry. Our results showed that females showed no preferences for undamaged or mechanically damaged plants. However, they oviposited more often on undamaged plants than on those previously damaged by T. ni, S. frugiperda, or B. tabaci. In contrast, females preferred to oviposit on plants previously oviposited by conspecific and heterospecific females than on egg-free plants. Plants damaged by conspecific or heterospecific larvae emitted methyl salicylate, indole, and octyl butyrate, compounds not released by undamaged or mechanically damaged plants. Whitefly damage induced the release of higher quantities of Z(3)-hexenyl acetate, (R)-(+)-limonene, and (E)-β-ocimene compared to plants damaged by larvae and suppressed the emission of linalool. Egg deposition by conspecific and heterospecific moths induced the emission of (R)-(+)-limonene, octyl butyrate, and geranyl acetone but suppressed the release of linalool. This study showed that a generalist moth species can discriminate between plants of different quality, and suggests that females use volatile compounds as cues during this process. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Epidemiology and genetic diversity of criniviruses associated with tomato yellows disease in Greece.

PubMed

Orfanidou, C G; Dimitriou, C; Papayiannis, L C; Maliogka, V I; Katis, N I

2014-06-24

Tomato chlorosis virus (ToCV) and Tomato infectious chlorosis virus (TICV) are two whitefly transmitted viruses which are classified in the genus Crinivirus of the family Closteroviridae. Both induce similar yellowing symptoms in tomato and are responsible for severe economic losses. ToCV is transmitted by Bemisia tabaci Gennadious, Trialeurodes vaporariorum Westwood and Trialeurodes abutilonea Haldeman, whereas TICV is transmitted only by T. vaporariorum. An extensive study was conducted during 2009-2012 in order to identify the virus species involved in tomato yellowing disease in Greece. Samples from tomato, other crops and weeds belonging to 44 species from 26 families were collected and analyzed using molecular methods. In addition, adult whiteflies were collected and analyzed using morphological characters and DNA markers. Results showed that TICV prevailed in tomato crops (62.5%), while ToCV incidence was lower (20.5%) and confined in southern Greece. ToCV was also detected in lettuce plants showing mild yellowing symptoms for the first time in Greece. Approximately 13% of the tested weeds were found to be infected, with TICV being the predominant virus with an incidence of 10.8%, whereas ToCV was detected only in 2.2% of the analyzed samples. These results indicate that the host range of TICV and ToCV in Greece is far more extensive than previously believed. T. vaporariorum was the most widespread whitefly species in Greece (80%), followed by B. tabaci (biotypes B and Q) (20%). Sequence analysis of the CP and CPm genes from Greek tomato and weed isolates of ToCV and TICV showed that even though both viruses have very wide host ranges their populations show very low molecular divergence. Copyright © 2013 Elsevier B.V. All rights reserved.

The Facultative Symbiont Rickettsia Protects an Invasive Whitefly against Entomopathogenic Pseudomonas syringae Strains

PubMed Central

Hunter, Martha S.; Baltrus, David A.

2014-01-01

Facultative endosymbionts can benefit insect hosts in a variety of ways, including context-dependent roles, such as providing defense against pathogens. The role of some symbionts in defense may be overlooked, however, when pathogen infection is transient, sporadic, or asymptomatic. The facultative endosymbiont Rickettsia increases the fitness of the sweet potato whitefly (Bemisia tabaci) in some populations through mechanisms that are not yet understood. In this study, we investigated the role of Rickettsia in mediating the interaction between the sweet potato whitefly and Pseudomonas syringae, a common environmental bacterium, some strains of which are pathogenic to aphids. Our results show that P. syringae multiplies within whiteflies, leading to host death, and that whiteflies infected with Rickettsia show a decreased rate of death due to P. syringae. Experiments using plants coated with P. syringae confirmed that whiteflies can acquire the bacteria at a low rate while feeding, leading to increased mortality, particularly when the whiteflies are not infected with Rickettsia. These results suggest that P. syringae may affect whitefly populations in nature and that Rickettsia can ameliorate this effect. This study highlights the possible importance of interactions among opportunistic environmental pathogens and endosymbionts of insects. PMID:25217020

Recessive Resistance Derived from Tomato cv. Tyking-Limits Drastically the Spread of Tomato Yellow Leaf Curl Virus

PubMed Central

Pereira-Carvalho, Rita C.; Díaz-Pendón, Juan A.; Fonseca, Maria Esther N.; Boiteux, Leonardo S.; Fernández-Muñoz, Rafael; Moriones, Enrique; Resende, Renato O.

2015-01-01

The tomato yellow leaf curl disease (TYLCD) causes severe damage to tomato (Solanum lycopersicum L.) crops throughout tropical and subtropical regions of the world. TYLCD is associated with a complex of single-stranded circular DNA plant viruses of the genus Begomovirus (family Geminiviridae) transmitted by the whitefy Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae). The tomato inbred line TX 468-RG is a source of monogenic recessive resistance to begomoviruses derived from the hybrid cv. Tyking F1. A detailed analysis of this germplasm source against tomato yellow leaf curl virus-Israel (TYLCV-IL), a widespread TYLCD-associated virus, showed a significant restriction to systemic virus accumulation even under continuous virus supply. The resistance was effective in limiting the onset of TYLCV-IL in tomato, as significantly lower primary spread of the virus occurred in resistant plants. Also, even if a limited number of resistant plants could result infected, they were less efficient virus sources for secondary spread owing to the impaired TYLCV-IL accumulation. Therefore, the incorporation of this resistance into breeding programs might help TYLCD management by drastically limiting TYLCV-IL spread. PMID:26008699

Emamectin, a novel insecticide for controlling field crop pests.

PubMed

Ishaaya, Isaac; Kontsedalov, Svetlana; Horowitz, A Rami

2002-11-01

Emamectin is a macrocyclic lactone insecticide with low toxicity to non-target organisms and the environment, and is considered an important component in pest-management programmes for controlling field crop pests. It is a powerful compound for controlling the cotton bollworm Helicoverpa armigera (Hübner). A spray concentration of 25 mg AI litre-1 in a cotton field resulted in over 90% suppression of H armigera larvae up to day 28 after treatment, while similar mortality of the Egyptian cotton leafworm Spodoptera littoralis Boisduval, under the same conditions, was maintained for 3 days only. Emamectin is a potent compound for controlling the western flower thrips Frankliniella occidentalis (Pergande) under both laboratory and field conditions and its activity on adults was over 10-fold greater than that of abamectin. Spray concentrations of 10 and 50 mg AI litre-1 in Ageratum houstonianum Mill flowers resulted in total suppression of adults up to day 11 and of larvae up to day 20 after treatment. Under standard laboratory conditions, emamectin exhibits a considerable activity on the whitefly Bemisia tabaci (Gennadius) and the leafminer Liriomyza huidobrensis (Blanchard). Further studies are required to evaluate its potential activity on the latter pests under field conditions.

Virulence Factors of Geminivirus Interact with MYC2 to Subvert Plant Resistance and Promote Vector Performance[C][W

PubMed Central

Li, Ran; Weldegergis, Berhane T.; Li, Jie; Jung, Choonkyun; Qu, Jing; Sun, Yanwei; Qian, Hongmei; Tee, ChuanSia; van Loon, Joop J.A.; Dicke, Marcel; Chua, Nam-Hai; Liu, Shu-Sheng

2014-01-01

A pathogen may cause infected plants to promote the performance of its transmitting vector, which accelerates the spread of the pathogen. This positive effect of a pathogen on its vector via their shared host plant is termed indirect mutualism. For example, terpene biosynthesis is suppressed in begomovirus-infected plants, leading to reduced plant resistance and enhanced performance of the whiteflies (Bemisia tabaci) that transmit these viruses. Although begomovirus-whitefly mutualism has been known, the underlying mechanism is still elusive. Here, we identified βC1 of Tomato yellow leaf curl China virus, a monopartite begomovirus, as the viral genetic factor that suppresses plant terpene biosynthesis. βC1 directly interacts with the basic helix-loop-helix transcription factor MYC2 to compromise the activation of MYC2-regulated terpene synthase genes, thereby reducing whitefly resistance. MYC2 associates with the bipartite begomoviral protein BV1, suggesting that MYC2 is an evolutionarily conserved target of begomoviruses for the suppression of terpene-based resistance and the promotion of vector performance. Our findings describe how this viral pathogen regulates host plant metabolism to establish mutualism with its insect vector. PMID:25490915

Synthesis and biological activity of a new class of insecticides: the N-(5-aryl-1,3,4-thiadiazol-2-yl)amides.

PubMed

Eckelbarger, Joseph D; Parker, Marshall H; Yap, Maurice Ch; Buysse, Ann M; Babcock, Jonathan M; Hunter, Ricky; Adelfinskaya, Yelena; Samaritoni, Jack G; Garizi, Negar; Trullinger, Tony K

2017-04-01

Optimization studies on a high-throughput screening (HTS) hit led to the discovery of a series of N-(6-arylpyridazin-3-yl)amides with insecticidal activity. It was hypothesized that the isosteric replacement of the pyridazine ring with a 1,3,4-thiadiazole ring could lead to more potent biological activity and/or a broader sap-feeding pest spectrum. The resulting N-(5-aryl-1,3,4-thiadiazol-2-yl)amides were explored as a new class of insecticides. Several methods for 2-amino-1,3,4-thiadiazole synthesis were used for the preparation of key synthetic intermediates. Subsequent coupling to variously substituted carboxylic acid building blocks furnished the final targets, which were tested for insecticidal activity against susceptible strains of Aphis gossypii (Glover) (cotton aphid), Myzus persicae (Sulzer) (green peach aphid) and Bemisia tabaci (Gennadius) (sweetpotato whitefly). Structure-activity relationship (SAR) studies on both the amide tail and the aryl A-ring of novel N-(5-aryl-1,3,4-thiadiazol-2-yl)amides led to a new class of insecticidal molecules active against sap-feeding insect pests. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Insect stings to change gear for healthy plant: Improving maize drought tolerance by whitefly infestation.

PubMed

Park, Yong-Soon; Ryu, Choong-Min

2016-05-03

Since plants first appeared about 1.1 billion years ago, they have been faced with biotic and abiotic stresses in their environment. To overcome these stresses, plants developed defense strategies. Accumulating evidence suggests that the whitefly [Bemisia tabaci (Genn.)] affects the regulation of plant defenses and physiology. A recent study demonstrates that aboveground whitefly infestation positively modulates root biomass and anthocyanin pigmentation on brace roots of maize plants (Zea mays L.). In agreement with these observations, indole-3-acetic acid (IAA) and jasmonic acid (JA) contents and the expression of IAA- and JA-related genes are higher in whitefly-infested maize plants than in non-infected control plants. Interestingly, the fresh weight of whitefly-infested maize plants is approximately 20% higher than in non-infected control plants under water stress conditions. Further investigation has revealed that hydrogen peroxide (H2O2) accumulates in whitefly-infested maize plants after water stoppage. Taken together, these results suggest that activation of phytohormones- (i.e., IAA and JA) and H2O2-mediated maize signaling pathways triggered by aboveground whitefly infestation promotes drought resistance. They also provide an insight into how inter-kingdom interactions can improve drought tolerance in plants.

Transgenic plants expressing the AaIT/GNA fusion protein show increased resistance and toxicity to both chewing and sucking pests.

PubMed

Liu, Shu-Min; Li, Jie; Zhu, Jin-Qi; Wang, Xiao-Wei; Wang, Cheng-Shu; Liu, Shu-Sheng; Chen, Xue-Xin; Li, Sheng

2016-04-01

The adoption of pest-resistant transgenic plants to reduce yield losses and decrease pesticide use has been successful. To achieve the goal of controlling both chewing and sucking pests in a given transgenic plant, we generated transgenic tobacco, Arabidopsis, and rice plants expressing the fusion protein, AaIT/GNA, in which an insecticidal scorpion venom neurotoxin (Androctonus australis toxin, AaIT) is fused to snowdrop lectin (Galanthus nivalis agglutinin, GNA). Compared with transgenic tobacco and Arabidopsis plants expressing AaIT or GNA, transgenic plants expressing AaIT/GNA exhibited increased resistance and toxicity to one chewing pest, the cotton bollworm, Helicoverpa armigera. Transgenic tobacco and rice plants expressing AaIT/GNA showed increased resistance and toxicity to two sucking pests, the whitefly, Bemisia tabaci, and the rice brown planthopper, Nilaparvata lugens, respectively. Moreover, in the field, transgenic rice plants expressing AaIT/GNA exhibited a significant improvement in grain yield when infested with N. lugens. This study shows that expressing the AaIT/GNA fusion protein in transgenic plants can be a useful approach for controlling pests, particularly sucking pests which are not susceptible to the toxin in Bt crops. © 2015 Institute of Zoology, Chinese Academy of Sciences.

Climate Change: Life history adaptation by a global whitefly, Bemisia tabaci, with rising temperature and carbon dioxide

USDA-ARS?s Scientific Manuscript database

Introduction: Climate change can have direct and indirect impacts on living organisms. A rise in ambient temperature and elevated carbon dioxide (CO2) concentrations due to global warming may have assorted impacts on arthropods such as altered life cycles, altered reproductive patterns, and change...

Evolution and homoplasy at the Bem6 microsatellite locus in three sweetpotato whitefly (Bemisia tabaci) cryptic species

USDA-ARS?s Scientific Manuscript database

The evolution of individual microsatellite loci is often complex and homoplasy is common but often goes undetected. Sequencing alleles at a microsatellite locus can provide a more complete picture of the common evolutionary mechanisms occurring at that locus and can reveal cases of homoplasy. Within...

First report of Bemisia tabaci biotype Q in Costa Rica and detection of viruliferous whiteflies in greenhouses

USDA-ARS?s Scientific Manuscript database

Whiteflies are a complex that comprises multiple species and biotypes or races which are capable of affecting crops by phloem feeding, virus transmission and promotion of fungal colonization. The distribution of these pests is worldwide. In Costa Rica, a country located in the tropics, the most prob...

Tissue-specific changes of glutamine synthetase activity in oats after rhizosphere infestation by Pseudomonas syringae pv. tabaci. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knight, T.J.; Temple, S.; Sengupta-Gopalan, C.

1996-05-15

Oats (Avena sativa L. lodi) tolerant of rhizosphere infestation by Pseudomonas syringae pv. tabaci when challenged by the pathogen experience tissue-specific alterations of ammonia assimilatory capabilities. Altered ammonia assimilatory potentials between root and leaf tissue result from selective inactivation of glutamine synthetase (GS) by the toxin Tabtoxinine-B-lactam (TBL). Root GS is sensitive and leaf GSs are resistant to TBL inactivation. With prolonged challenge by the pathogen root GS activity decreases but leaf GS specific activity increase. Higher leaf GS activity is due to decreased rates of degradation rather than increased GS synthesis. Higher leaf GS activity and elevated levels ofmore » GS polypeptide appear to result from a limited interaction between GS and TBL leading to the accumulation of a less active but more stable GS holoenzyme. Tolerant challenged oats besides surviving rhizosphere infestation, experience enhanced growth. A strong correlation exists between leaf GS activity and whole plant fresh weight, suggesting that tissue-specific changes in ammonia assimilatory capability provides the plant a more efficient mechanism for uptake and utilization of nitrogen.« less

Suppression of cotton leaf curl disease symptoms in Gossypium hirsutum through over expression of host-encoded miRNAs.

PubMed

Akmal, Mohd; Baig, Mirza S; Khan, Jawaid A

2017-12-10

Cotton leaf curl disease (CLCuD), a major factor resulting in the enormous yield losses in cotton crop, is caused by a distinct monopartite begomovirus in association with Cotton leaf curl Multan betasatellite (CLCuMB). Micro(mi)RNAs are known to regulate gene expression in eukaryotes, including antiviral defense in plants. In a previous study, we had computationally identified a set of cotton miRNAs, which were shown to have potential targets in the genomes of Cotton leaf curl Multan virus (CLCuMuV) and CLCuMB at multiple loci. In the current study, effect of Gossypium arboreum-encoded miRNAs on the genome of CLCuMuV and CLCuMB was investigated in planta. Two computationally predicted cotton-encoded miRNAs (miR398 and miR2950) that showed potential to bind multiple Open Reading Frames (ORFs; C1, C4, V1, and non- coding intergenic region) of CLCuMuV, and (βC1) of CLCuMB were selected. Functional validation of miR398 and miR2950 was done by overexpression approach in G. hirsutum var. HS6. A total of ten in vitro cotton plants were generated from independent events and subjected to biological and molecular analyses. Presence of the respective Precursor (pre)-miRNA was confirmed through PCR and Southern blotting, and their expression level was assessed by semi quantitative RT-PCR, Real Time quantitative PCR and northern hybridization in the PCR-positive lines. Southern hybridization revealed 2-4 copy integration of T-DNA in the genome of the transformed lines. Remarkably, expression of pre-miRNAs was shown up to 5.8-fold higher in the transgenic (T 0 ) lines as revealed by Real Time PCR. The virus resistance was monitored following inoculation of the transgenic cotton lines with viruliferous whitefly (Bemisia tabaci) insect vector. After inoculation, four of the transgenic lines remained apparently symptom free. While a very low titre of viral DNA could be detected by Rolling circle amplification, betasatellite responsible for symptom induction could not be detected

Horizontal transmission of the insect symbiont Rickettsia is plant-mediated

PubMed Central

Caspi-Fluger, Ayelet; Inbar, Moshe; Mozes-Daube, Netta; Katzir, Nurit; Portnoy, Vitaly; Belausov, Eduard; Hunter, Martha S.; Zchori-Fein, Einat

2012-01-01

Bacteria in the genus Rickettsia, best known as vertebrate pathogens vectored by blood-feeding arthropods, can also be found in phytophagous insects. The presence of closely related bacterial symbionts in evolutionarily distant arthropod hosts presupposes a means of horizontal transmission, but no mechanism for this transmission has been described. Using a combination of experiments with live insects, molecular analyses and microscopy, we found that Rickettsia were transferred from an insect host (the whitefly Bemisia tabaci) to a plant, moved inside the phloem, and could be acquired by other whiteflies. In one experiment, Rickettsia was transferred from the whitefly host to leaves of cotton, basil and black nightshade, where the bacteria were restricted to the phloem cells of the plant. In another experiment, Rickettsia-free adult whiteflies, physically segregated but sharing a cotton leaf with Rickettsia-plus individuals, acquired the Rickettsia at a high rate. Plants can serve as a reservoir for horizontal transmission of Rickettsia, a mechanism which may explain the occurrence of phylogenetically similar symbionts among unrelated phytophagous insect species. This plant-mediated transmission route may also exist in other insect–symbiont systems and, since symbionts may play a critical role in the ecology and evolution of their hosts, serve as an immediate and powerful tool for accelerated evolution. PMID:22113034

Transient Expression and Cellular Localization of Recombinant Proteins in Cultured Insect Cells.

PubMed

Fabrick, Jeffrey A; Hull, J Joe

2017-04-20

Heterologous protein expression systems are used for the production of recombinant proteins, the interpretation of cellular trafficking/localization, and the determination of the biochemical function of proteins at the sub-organismal level. Although baculovirus expression systems are increasingly used for protein production in numerous biotechnological, pharmaceutical, and industrial applications, nonlytic systems that do not involve viral infection have clear benefits but are often overlooked and underutilized. Here, we describe a method for generating nonlytic expression vectors and transient recombinant protein expression. This protocol allows for the efficient cellular localization of recombinant proteins and can be used to rapidly discern protein trafficking within the cell. We show the expression of four recombinant proteins in a commercially available insect cell line, including two aquaporin proteins from the insect Bemisia tabaci, as well as subcellular marker proteins specific for the cell plasma membrane and for intracellular lysosomes. All recombinant proteins were produced as chimeras with fluorescent protein markers at their carboxyl termini, which allows for the direct detection of the recombinant proteins. The double transfection of cells with plasmids harboring constructs for the genes of interest and a known subcellular marker allows for live cell imaging and improved validation of cellular protein localization.

Differential profiles of direct and indirect modification of vector feeding behaviour by a plant virus.

PubMed

He, Wen-Bo; Li, Jie; Liu, Shu-Sheng

2015-01-08

Plant viruses interact with their insect vectors directly and indirectly via host plants, and this tripartite interaction may produce fitness benefits to both the vectors and the viruses. Our previous studies show that the Middle East-Asia Minor 1 (MEAM1) species of the whitefly Bemisia tabaci complex improved its performance on tobacco plants infected by the Tomato yellow leaf curl China virus (TYLCCNV), which it transmits, although virus infection of the whitefly per se reduced its performance. Here, we use electrical penetration graph recording to investigate the direct and indirect effects of TYLCCNV on the feeding behaviour of MEAM1. When feeding on either cotton, a non-host of TYLCCNV, or uninfected tobacco, a host of TYLCCNV, virus-infection of the whiteflies impeded their feeding. Interestingly, when viruliferous whiteflies fed on virus-infected tobacco, their feeding activities were no longer negatively affected; instead, the virus promoted whitefly behaviour related to rapid and effective sap ingestion. Our findings show differential profiles of direct and indirect modification of vector feeding behaviour by a plant virus, and help to unravel the behavioural mechanisms underlying a mutualistic relationship between an insect vector and a plant virus that also has features reminiscent of an insect pathogen.

Natal Host Plants Can Alter Herbivore Competition.

PubMed

Pan, Huipeng; Preisser, Evan L; Su, Qi; Jiao, Xiaoguo; Xie, Wen; Wang, Shaoli; Wu, Qingjun; Zhang, Youjun

2016-01-01

Interspecific competition between herbivores is widely recognized as an important determinant of community structure. Although researchers have identified a number of factors capable of altering competitive interactions, few studies have addressed the influence of neighboring plant species. If adaptation to/ epigenetic effects of an herbivore's natal host plant alter its performance on other host plants, then interspecific herbivore interactions may play out differently in heterogeneous and homogenous plant communities. We tested wether the natal host plant of a whitefly population affected interactions between the Middle-east Asia Minor 1 (MEAM1) and Mediterranean (MED) cryptic species of the whitefly Bemisia tabaci by rearing the offspring of a cabbage-derived MEAM1 population and a poinsettia-derived MED population together on three different host plants: cotton, poinsettia, and cabbage. We found that MED dominated on poinsettia and that MEAM1 dominated on cabbage, results consistent with previous research. MED also dominated when reared with MEAM1 on cotton, however, a result at odds with multiple otherwise-similar studies that reared both species on the same natal plant. Our work provides evidence that natal plants affect competitive interactions on another plant species, and highlights the potential importance of neighboring plant species on herbivore community composition in agricultral systems.

Natal Host Plants Can Alter Herbivore Competition

PubMed Central

Pan, Huipeng; Preisser, Evan L.; Su, Qi; Jiao, Xiaoguo; Xie, Wen; Wang, Shaoli; Wu, Qingjun

2016-01-01

Interspecific competition between herbivores is widely recognized as an important determinant of community structure. Although researchers have identified a number of factors capable of altering competitive interactions, few studies have addressed the influence of neighboring plant species. If adaptation to/ epigenetic effects of an herbivore’s natal host plant alter its performance on other host plants, then interspecific herbivore interactions may play out differently in heterogeneous and homogenous plant communities. We tested wether the natal host plant of a whitefly population affected interactions between the Middle-east Asia Minor 1 (MEAM1) and Mediterranean (MED) cryptic species of the whitefly Bemisia tabaci by rearing the offspring of a cabbage-derived MEAM1 population and a poinsettia-derived MED population together on three different host plants: cotton, poinsettia, and cabbage. We found that MED dominated on poinsettia and that MEAM1 dominated on cabbage, results consistent with previous research. MED also dominated when reared with MEAM1 on cotton, however, a result at odds with multiple otherwise-similar studies that reared both species on the same natal plant. Our work provides evidence that natal plants affect competitive interactions on another plant species, and highlights the potential importance of neighboring plant species on herbivore community composition in agricultral systems. PMID:28030636

The Facultative Symbiont Rickettsia Protects an Invasive Whitefly against Entomopathogenic Pseudomonas syringae Strains.

PubMed

Hendry, Tory A; Hunter, Martha S; Baltrus, David A

2014-12-01

Facultative endosymbionts can benefit insect hosts in a variety of ways, including context-dependent roles, such as providing defense against pathogens. The role of some symbionts in defense may be overlooked, however, when pathogen infection is transient, sporadic, or asymptomatic. The facultative endosymbiont Rickettsia increases the fitness of the sweet potato whitefly (Bemisia tabaci) in some populations through mechanisms that are not yet understood. In this study, we investigated the role of Rickettsia in mediating the interaction between the sweet potato whitefly and Pseudomonas syringae, a common environmental bacterium, some strains of which are pathogenic to aphids. Our results show that P. syringae multiplies within whiteflies, leading to host death, and that whiteflies infected with Rickettsia show a decreased rate of death due to P. syringae. Experiments using plants coated with P. syringae confirmed that whiteflies can acquire the bacteria at a low rate while feeding, leading to increased mortality, particularly when the whiteflies are not infected with Rickettsia. These results suggest that P. syringae may affect whitefly populations in nature and that Rickettsia can ameliorate this effect. This study highlights the possible importance of interactions among opportunistic environmental pathogens and endosymbionts of insects. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Differential profiles of direct and indirect modification of vector feeding behaviour by a plant virus

PubMed Central

He, Wen-Bo; Li, Jie; Liu, Shu-Sheng

2015-01-01

Plant viruses interact with their insect vectors directly and indirectly via host plants, and this tripartite interaction may produce fitness benefits to both the vectors and the viruses. Our previous studies show that the Middle East-Asia Minor 1 (MEAM1) species of the whitefly Bemisia tabaci complex improved its performance on tobacco plants infected by the Tomato yellow leaf curl China virus (TYLCCNV), which it transmits, although virus infection of the whitefly per se reduced its performance. Here, we use electrical penetration graph recording to investigate the direct and indirect effects of TYLCCNV on the feeding behaviour of MEAM1. When feeding on either cotton, a non-host of TYLCCNV, or uninfected tobacco, a host of TYLCCNV, virus-infection of the whiteflies impeded their feeding. Interestingly, when viruliferous whiteflies fed on virus-infected tobacco, their feeding activities were no longer negatively affected; instead, the virus promoted whitefly behaviour related to rapid and effective sap ingestion. Our findings show differential profiles of direct and indirect modification of vector feeding behaviour by a plant virus, and help to unravel the behavioural mechanisms underlying a mutualistic relationship between an insect vector and a plant virus that also has features reminiscent of an insect pathogen. PMID:25567524

Plantmediated horizontal transmission of Wolbachia between whiteflies

PubMed Central

Li, Shao-Jian; Ahmed, Muhammad Z; Lv, Ning; Shi, Pei-Qiong; Wang, Xing-Min; Huang, Ji-Lei; Qiu, Bao-Li

2017-01-01

Maternal transmission is the main transmission pathway of facultative bacterial endosymbionts, but phylogenetically distant insect hosts harbor closely related endosymbionts, suggesting that horizontal transmission occurs in nature. Here we report the first case of plant-mediated horizontal transmission of Wolbachia between infected and uninfected Bemisia tabaci AsiaII7 whiteflies. After infected whiteflies fed on cotton leaves, Wolbachia was visualized, both in the phloem vessels and in some novel ‘reservoir' spherules along the phloem by fluorescence in situ hybridization using Wolbachia-specific 16S rRNA probes and transmission electron microscopy. Wolbachia persisted in the plant leaves for at least 50 days. When the Wolbachia-free whiteflies fed on the infected plant leaves, the majority of them became infected with the symbiont and vertically transmitted it to their progeny. Multilocus sequence typing and sequencing of the wsp (Wolbachia surface protein) gene confirmed that the sequence type of Wolbachia in the donor whiteflies, cotton phloem and the recipient whiteflies are all identical (sequence type 388). These results were replicated using cowpea and cucumber plants, suggesting that horizontal transmission is also possible through other plant species. Our findings may help explain why Wolbachia bacteria are so abundant in arthropods, and suggest that in some species, Wolbachia may be maintained in populations by horizontal transmission. PMID:27935594

Onion thrips (Thrips tabaci (Thysanoptera: Thripidae)) in cabbage on Prince Edward Island: observations on planting date and variety choice.

PubMed

Blatt, Suzanne; Ryan, Andrew; Adams, Shelley; Driscoll, Joanne

2015-01-01

Onion thrips (Thrips tabaci Lindeman (Thysanoptera: Thripidae)) can be a pest in organic onion production on Prince Edward Island. This study was to examine the effect of planting time and variety on infestation levels and damage by onion thrips on cabbage (Brassicae oleracea capitala (L.)). A field site was planted with 2 main and 8 lesser varieties of cabbage over 4 planting dates. Some varieties were short season and harvested on July 31 with longer season varieties harvested on September 2. Blue sticky traps were used to capture thrips migrating into the field site from July 22-September 2. Traps were counted weekly and cabbage heads within the field site were visually surveyed for thrips. At harvest, heads were weighed and measured, thrips damage was assessed then the head was dissected and thrips counted on the first four layers of the head. Thrips exhibited a preference for Lennox over Bronco throughout the season although thrips populations were not high enough to effect economic damage in 2014. Planting date influenced cabbage head weight and size with later plantings yielding the largest heads. Use of planting date and variety to avoid thrips populations is discussed.

Comparing the regional epidemiology of the cassava mosaic and cassava brown streak virus pandemics in Africa.

PubMed

Legg, J P; Jeremiah, S C; Obiero, H M; Maruthi, M N; Ndyetabula, I; Okao-Okuja, G; Bouwmeester, H; Bigirimana, S; Tata-Hangy, W; Gashaka, G; Mkamilo, G; Alicai, T; Lava Kumar, P

2011-08-01

The rapid geographical expansion of the cassava mosaic disease (CMD) pandemic, caused by cassava mosaic geminiviruses, has devastated cassava crops in 12 countries of East and Central Africa since the late 1980s. Region-level surveys have revealed a continuing pattern of annual spread westward and southward along a contiguous 'front'. More recently, outbreaks of cassava brown streak disease (CBSD) were reported from Uganda and other parts of East Africa that had been hitherto unaffected by the disease. Recent survey data reveal several significant contrasts between the regional epidemiology of these two pandemics: (i) severe CMD radiates out from an initial centre of origin, whilst CBSD seems to be spreading from independent 'hot-spots'; (ii) the severe CMD pandemic has arisen from recombination and synergy between virus species, whilst the CBSD pandemic seems to be a 'new encounter' situation between host and pathogen; (iii) CMD pandemic spread has been tightly linked with the appearance of super-abundant Bemisia tabaci whitefly vector populations, in contrast to CBSD, where outbreaks have occurred 3-12 years after whitefly population increases; (iv) the CMGs causing CMD are transmitted in a persistent manner, whilst the two cassava brown streak viruses appear to be semi-persistently transmitted; and (v) different patterns of symptom expression mean that phytosanitary measures could be implemented easily for CMD but have limited effectiveness, whereas similar measures are difficult to apply for CBSD but are potentially very effective. An important similarity between the pandemics is that the viruses occurring in pandemic-affected areas are also found elsewhere, indicating that contrary to earlier published conclusions, the viruses per se are unlikely to be the key factors driving the two pandemics. A diagrammatic representation illustrates the temporal relationship between B. tabaci abundance and changing incidences of both CMD and CBSD in the Great Lakes region

Effects of heat stress on survival of Frankliniella occidentalis (Thysanoptera: Thripidae) and Thrips tabaci (Thysanoptera: Thripidae).

PubMed

Wang, J C; Zhang, B; Wang, J P; Li, H G; Wang, S F; Sun, L J; Zheng, C Y

2014-08-01

Temperature is known to play a crucial role in the population dynamics of insects. Insects have evolved different mechanisms to resist unfavorable extreme temperatures. In recent years, western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), and onion thrips, Thrips tabaci (Lindeman) (Thysanoptera: Thripidae), have caused significant damage to vegetable crops. Because of global warming and expanding areas of vegetable cultivation, a study of the effects of heat stress on these thrips species is warranted. We exposed the various developmental stages of western flower thrips and onion thrips to temperatures of 41, 43, or 45 degrees C for 2, 6, 12, 24, or 36 h to determine the effects of heat stress on survival. Our results showed that the heat resistance of nonadult western flower thrips was greater than that of the nonadult onion thrips, and that the natural heat resistant ability was the primary factor in heat resistance in western flower thrips. In contrast, the heat resistance of adult onion thrips was greater than that of the adult western flower thrips, which was primarily the result of the ability of searching suitable microenvironment that enabled the onion thrips to mitigate the effects of high temperatures more efficiently than the western flower thrips. Our analysis of the differences in heat resistance between western flower thrips and onion thrips provides important information for the development of thermal treatments for controlling western flower thrips and onion thrips.

Action threshold for applying insect growth regulators to tomato for management of irregular ripening caused by Bemisia argentifolii (Homoptera: Aleyrodidae).

PubMed

Schuster, D J

2002-04-01

The whitefly Bemisia argentifolii Bellows & Perring is a major pest of tomatoes, causing an irregular ripening disorder characterized externally by incomplete or inhibited reddening of fruit, especially in longitudinal sections, and internally by an increase in the amount of white tissue. Experiments were undertaken during the spring and fall of 1997 and 1998 and the spring of 1999 to develop an action threshold for applying the insect growth regulators (IGRs) buprofezin and pyriproxyfen to manage B. argentifolii and irregular ripening. The IGRs were applied when predetermined thresholds were reached and were compared with a high rate of the systemic insecticide imidacloprid, which was applied at transplanting and provided season-long whitefly control. Only plots treated when the numbers of sessile nymphs (second through fourth instars) reached five per 10 leaflets consistently had both external and internal irregular ripening severity ratings similar to the imidacloprid standard. Results were similar for buprofezin and pyriproxyfen even though the modes of action differ. The five nymphs per 10 leaflets threshold lends itself to field scouting because nymphal counts completed in the field using the unaided eye supplemented with a 10x hand lens were linearly and significantly related to counts completed in the laboratory with a dissecting microscope.

Long-Distance Dispersal Potential for Onion Thrips (Thysanoptera: Thripidae) and Iris yellow spot virus (Bunyaviridae: Tospovirus) in an Onion Ecosystem.

PubMed

Smith, Erik A; Fuchs, M; Shields, E J; Nault, B A

2015-08-01

Onion thrips, Thrips tabaci Lindeman, is a worldwide pest of onion whose feeding damage and transmission of Iris yellow spot virus (IYSV) may reduce onion yields. Little is known about the seasonal dynamics of T. tabaci dispersal, the distance of dispersal, or the movement of thrips infected with IYSV during the onion-growing season. To address these questions, T. tabaci adults were collected using transparent sticky card traps in commercial onion fields three times during the onion-growing season (June, July, and late August) at varying heights above the canopy (0.5-6 m above soil surface) and with trap-equipped unmanned aircraft (UAVs) flying 50-60 m above onion fields during August sampling periods in 2012 and 2013. Randomly selected subsamples of captured T. tabaci were tested for IYSV using RT-PCR. Most T. tabaci adults were captured in late August and near the onion canopy (<2 m) throughout the season. However, 4% of T. tabaci adults captured on sticky cards were at altitudes ≥2 m, and T. tabaci were also captured on UAV-mounted traps. These data strongly suggest that long-distance dispersal occurs. More T. tabaci captured on sticky cards tested positive for IYSV in August (53.6%) than earlier in the season (2.3 to 21.5% in June and July, respectively), and 20 and 15% of T. tabaci captured on UAV-mounted traps tested positive for IYSV in 2012 and 2013, respectively. Our results indicate that T. tabaci adults, including viruliferous individuals, engage in long-distance dispersal late in the season and likely contribute to the spread of IYSV. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

GenomeFingerprinter: the genome fingerprint and the universal genome fingerprint analysis for systematic comparative genomics.

PubMed

Ai, Yuncan; Ai, Hannan; Meng, Fanmei; Zhao, Lei

2013-01-01

No attention has been paid on comparing a set of genome sequences crossing genetic components and biological categories with far divergence over large size range. We define it as the systematic comparative genomics and aim to develop the methodology. First, we create a method, GenomeFingerprinter, to unambiguously produce a set of three-dimensional coordinates from a sequence, followed by one three-dimensional plot and six two-dimensional trajectory projections, to illustrate the genome fingerprint of a given genome sequence. Second, we develop a set of concepts and tools, and thereby establish a method called the universal genome fingerprint analysis (UGFA). Particularly, we define the total genetic component configuration (TGCC) (including chromosome, plasmid, and phage) for describing a strain as a systematic unit, the universal genome fingerprint map (UGFM) of TGCC for differentiating strains as a universal system, and the systematic comparative genomics (SCG) for comparing a set of genomes crossing genetic components and biological categories. Third, we construct a method of quantitative analysis to compare two genomes by using the outcome dataset of genome fingerprint analysis. Specifically, we define the geometric center and its geometric mean for a given genome fingerprint map, followed by the Euclidean distance, the differentiate rate, and the weighted differentiate rate to quantitatively describe the difference between two genomes of comparison. Moreover, we demonstrate the applications through case studies on various genome sequences, giving tremendous insights into the critical issues in microbial genomics and taxonomy. We have created a method, GenomeFingerprinter, for rapidly computing, geometrically visualizing, intuitively comparing a set of genomes at genome fingerprint level, and hence established a method called the universal genome fingerprint analysis, as well as developed a method of quantitative analysis of the outcome dataset. These have set

Glucose concentration alters dissolved oxygen levels in liquid cultures of Beauveria bassiana and affects formation and bioefficacy of blastospores.

PubMed

Mascarin, Gabriel Moura; Jackson, Mark A; Kobori, Nilce Naomi; Behle, Robert W; Dunlap, Christopher A; Delalibera Júnior, Ítalo

2015-08-01

The filamentous fungus Beauveria bassiana is an economically important pathogen of numerous arthropod pests and is able to grow in submerged culture as filaments (mycelia) or as budding yeast-like blastospores. In this study, we evaluated the effect of dissolved oxygen and high glucose concentrations on blastospore production by submerged cultures of two isolates of B. bassiana, ESALQ1432 and GHA. Results showed that maintaining adequate dissolved oxygen levels coupled with high glucose concentrations enhanced blastospore yields by both isolates. High glucose concentrations increased the osmotic pressure of the media and coincided with higher dissolved oxygen levels and increased production of significantly smaller blastospores compared with blastospores produced in media with lower concentrations of glucose. The desiccation tolerance of blastospores dried to less than 2.6 % moisture was not affected by the glucose concentration of the medium but was isolate dependent. Blastospores of isolate ESALQ1432 produced in media containing 140 g glucose L(-1) showed greater virulence toward whitefly nymphs (Bemisia tabaci) as compared with blastospores produced in media containing 40 g glucose L(-1). These results suggest a synergistic effect between glucose concentration and oxygen availability on changing morphology and enhancing the yield and efficacy of blastospores of B. bassiana, thereby facilitating the development of a cost-effective production method for this blastospore-based bioinsecticide.

Electrostatic Insect Sweeper for Eliminating Whiteflies Colonizing Host Plants: A Complementary Pest Control Device in An Electric Field Screen-Guarded Greenhouse.

PubMed

Takikawa, Yoshihiro; Matsuda, Yoshinori; Kakutani, Koji; Nonomura, Teruo; Kusakari, Shin-Ichi; Okada, Kiyotsugu; Kimbara, Junji; Osamura, Kazumi; Toyoda, Hideyoshi

2015-05-12

Our greenhouse tomatoes have suffered from attacks by viruliferous whiteflies Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) over the last 10 years. The fundamental countermeasure was the application of an electric field screen to the greenhouse windows to prevent their entry. However, while the protection was effective, it was incomplete, because of the lack of a guard at the greenhouse entrance area; in fact, the pests entered from the entrance door when workers entered and exited. To address this, we developed a portable electrostatic insect sweeper as a supplementary technique to the screen. In this sweeper, eight insulated conductor wires (ICWs) were arranged at constant intervals along a polyvinylchloride (PVC) pipe and covered with a cylindrical stainless net. The ICWs and metal net were linked to a DC voltage generator (operated by 3-V alkaline batteries) inside the grip and oppositely electrified to generate an electric field between them. Whiteflies on the plants were attracted to the sweeper that was gently slid along the leaves. This apparatus was easy to operate on-site in a greenhouse and enabled capture of the whiteflies detected during the routine care of the tomato plants. Using this apparatus, we caught all whiteflies that invaded the non-guarded entrance door and minimized the appearance and spread of the viral disease in tomato plants in the greenhouse.

Assessing transmission of crop diseases by insect vectors in a landscape context.

PubMed

Carrière, Y; Degain, B; Hartfield, K A; Nolte, K D; Marsh, S E; Ellers-Kirk, C; Van Leeuwen, W J D; Liesner, L; Dutilleul, P; Palumbo, J C

2014-02-01

Theory indicates that landscape composition affects transmission of vector-borne crop diseases, but few empirical studies have investigated how landscape composition affects plant disease epidemiology. Since 2006, Bemisia tabaci (Gennadius) has vectored the cucurbit yellow stunting disorder virus (CYSDV) to cantaloupe and honeydew melons (Cucumis melo L.) in the southwestern United States and northern Mexico, causing significant reductions in yield of fall melons and increased use of insecticides. Here, we show that a landscape-based approach allowing simultaneous assessment of impacts of local (i.e., planting date) and regional (i.e., landscape composition) factors provides valuable insights on how to reduce crop disease risks. Specifically, we found that planting fall melon fields early in the growing season, eliminating plants germinating from seeds produced by spring melons after harvest, and planting fall melon fields away from cotton and spring melon fields may significantly reduce the incidence of CYSDV infection in fall melons. Because the largest scale of significance of the positive association between abundance of cotton and spring melon fields and CYSDV incidence was 1,750 and 3,000 m, respectively, reducing areas of cotton and spring melon fields within these distances from fall melon fields may decrease CYSDV incidence. Our results indicate that landscape-based studies will be fruitful to alleviate limitations imposed on crop production by vector-borne diseases.

Insecticidal Effects on the Spatial Progression of Tomato Yellow Leaf Curl Virus and Movement of Its Whitefly Vector in Tomato.

PubMed

Dempsey, M; Riley, D G; Srinivasan, R

2017-06-01

Commercial management of whitefly-transmitted Tomato yellow leaf curl virus (TYLCV) typically relies on insecticide control of whitefly vectors as a first line of defense. We quantified this effect in crop tunnel studies, with validation in a tomato field setting. Tomato yellow leaf curl virus-infected and Bemisia tabaci (Gennadius)-infested source plants were planted at the beginning of tunneled rows to serve as inoculum source, so that movement of whiteflies and TYLCV symptoms could be tracked down the length of the tunnel over time. Tunnel study results showed that proximity to the source plant was a more important factor than insecticide treatments. Insecticide-treated tomato transplants did tend to suppress whitefly incidence and slowed TYLCV movement in comparison with the untreated check; however, tomato plants planted closer to the source plant had higher incidence of whiteflies and TYLCV infection, regardless of treatment. In a large tomato plot study with a controlled inoculum source, insecticide treatments significantly reduced the spread of TYLCV. When uninhibited by insecticide treatment, 80% of the TYLCV spread was restricted to <15 m from the source plant (<11 m in the validation study), with insecticide treatment generally reducing the distance and magnitude of this spread. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Transcriptional Response of Virus-Infected Cassava and Identification of Putative Sources of Resistance for Cassava Brown Streak Disease

PubMed Central

Maruthi, M. N.; Bouvaine, Sophie; Tufan, Hale A.; Mohammed, Ibrahim U.; Hillocks, Rory J.

2014-01-01

Cassava (Manihot esculenta) is a major food staple in sub-Saharan Africa, which is severely affected by cassava brown streak disease (CBSD). The aim of this study was to identify resistance for CBSD as well as to understand the mechanism of putative resistance for providing effective control for the disease. Three cassava varieties; Kaleso, Kiroba and Albert were inoculated with cassava brown streak viruses by grafting and also using the natural insect vector the whitefly, Bemisia tabaci. Kaleso expressed mild or no disease symptoms and supported low concentrations of viruses, which is a characteristic of resistant plants. In comparison, Kiroba expressed severe leaf but milder root symptoms, while Albert was susceptible with severe symptoms both on leaves and roots. Real-time PCR was used to estimate virus concentrations in cassava varieties. Virus quantities were higher in Kiroba and Albert compared to Kaleso. The Illumina RNA-sequencing was used to further understand the genetic basis of resistance. More than 700 genes were uniquely overexpressed in Kaleso in response to virus infection compared to Albert. Surprisingly, none of them were similar to known resistant gene orthologs. Some of the overexpressed genes, however, belonged to the hormone signalling pathways and secondary metabolites, both of which are linked to plant resistance. These genes should be further characterised before confirming their role in resistance to CBSD. PMID:24846209

Silverleaf Whitefly Induces Salicylic Acid Defenses and Suppresses Effectual Jasmonic Acid Defenses1[W][OA

PubMed Central

Zarate, Sonia I.; Kempema, Louisa A.; Walling, Linda L.

2007-01-01

The basal defenses important in curtailing the development of the phloem-feeding silverleaf whitefly (Bemisia tabaci type B; SLWF) on Arabidopsis (Arabidopsis thaliana) were investigated. Sentinel defense gene RNAs were monitored in SLWF-infested and control plants. Salicylic acid (SA)-responsive gene transcripts accumulated locally (PR1, BGL2, PR5, SID2, EDS5, PAD4) and systemically (PR1, BGL2, PR5) during SLWF nymph feeding. In contrast, jasmonic acid (JA)- and ethylene-dependent RNAs (PDF1.2, VSP1, HEL, THI2.1, FAD3, ERS1, ERF1) were repressed or not modulated in SLWF-infested leaves. To test for a role of SA and JA pathways in basal defense, SLWF development on mutant and transgenic lines that constitutively activate or impair defense pathways was determined. By monitoring the percentage of SLWF nymphs in each instar, we show that mutants that activate SA defenses (cim10) or impair JA defenses (coi1) accelerated SLWF nymphal development. Reciprocally, mutants that activate JA defenses (cev1) or impair SA defenses (npr1, NahG) slowed SLWF nymphal development. Furthermore, when npr1 plants, which do not activate downstream SA defenses, were treated with methyl jasmonate, a dramatic delay in nymph development was observed. Collectively, these results showed that SLWF-repressed, JA-regulated defenses were associated with basal defense to the SLWF. PMID:17189328

Silverleaf whitefly induces salicylic acid defenses and suppresses effectual jasmonic acid defenses.

PubMed

Zarate, Sonia I; Kempema, Louisa A; Walling, Linda L

2007-02-01

The basal defenses important in curtailing the development of the phloem-feeding silverleaf whitefly (Bemisia tabaci type B; SLWF) on Arabidopsis (Arabidopsis thaliana) were investigated. Sentinel defense gene RNAs were monitored in SLWF-infested and control plants. Salicylic acid (SA)-responsive gene transcripts accumulated locally (PR1, BGL2, PR5, SID2, EDS5, PAD4) and systemically (PR1, BGL2, PR5) during SLWF nymph feeding. In contrast, jasmonic acid (JA)- and ethylene-dependent RNAs (PDF1.2, VSP1, HEL, THI2.1, FAD3, ERS1, ERF1) were repressed or not modulated in SLWF-infested leaves. To test for a role of SA and JA pathways in basal defense, SLWF development on mutant and transgenic lines that constitutively activate or impair defense pathways was determined. By monitoring the percentage of SLWF nymphs in each instar, we show that mutants that activate SA defenses (cim10) or impair JA defenses (coi1) accelerated SLWF nymphal development. Reciprocally, mutants that activate JA defenses (cev1) or impair SA defenses (npr1, NahG) slowed SLWF nymphal development. Furthermore, when npr1 plants, which do not activate downstream SA defenses, were treated with methyl jasmonate, a dramatic delay in nymph development was observed. Collectively, these results showed that SLWF-repressed, JA-regulated defenses were associated with basal defense to the SLWF.

High-level of resistance to spinosad, emamectin benzoate and carbosulfan in populations of Thrips tabaci collected in Israel.

PubMed

Lebedev, Galina; Abo-Moch, Fauzi; Gafni, Guy; Ben-Yakir, David; Ghanim, Murad

2013-02-01

The onion thrips, Thrips tabaci Lindeman, is a major pest of several crop plants in the genus Allium, such as onions, garlic and chives. In Israel, these crops are grown in open fields and in protected housing. This thrips is usually controlled by the application of chemical insecticides. In recent years, spinosad, emamectin benzoate and carbosulfan have been the major insecticides used for the control of the onion thrips. In the last 4 years, growers of chives and green onion from several regions of Israel have reported a significant decrease in the efficacy of insecticides used to control the onion thrips. The susceptibility of 14 populations of the onion thrips, collected mainly from chives between the years 2007 and 2011, to spinosad, emamectin benzoate and carbosulfan was tested using a laboratory bioassay. The majority of the populations showed significant levels of resistance to at least one of the insecticides. LC(50) values calculated for two of the studied populations showed that the resistance factor for spinosad compared with the susceptible population is 21 393, for carbosulfan 54 and for emamectin benzoate 36. Only two populations, collected from organic farms, were susceptible to the insecticides tested. This is the first report of a high resistance level to spinosad, the major insecticide used to control the onion thrips. Resistance cases to spinosad were associated with failures to control the pest. Populations resistant to spinosad also had partial or complete resistance to other insecticides used for controlling the onion thrips. Copyright © 2012 Society of Chemical Industry.

Whole-genome sequencing for comparative genomics and de novo genome assembly.

PubMed

Benjak, Andrej; Sala, Claudia; Hartkoorn, Ruben C

2015-01-01

Next-generation sequencing technologies for whole-genome sequencing of mycobacteria are rapidly becoming an attractive alternative to more traditional sequencing methods. In particular this technology is proving useful for genome-wide identification of mutations in mycobacteria (comparative genomics) as well as for de novo assembly of whole genomes. Next-generation sequencing however generates a vast quantity of data that can only be transformed into a usable and comprehensible form using bioinformatics. Here we describe the methodology one would use to prepare libraries for whole-genome sequencing, and the basic bioinformatics to identify mutations in a genome following Illumina HiSeq or MiSeq sequencing, as well as de novo genome assembly following sequencing using Pacific Biosciences (PacBio).

Ensembl Genomes 2016: more genomes, more complexity

PubMed Central

Kersey, Paul Julian; Allen, James E.; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J.; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J.; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K.; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D.; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello–Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M.; Howe, Kevin L.; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M.

2016-01-01

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. PMID:26578574

Ensembl Genomes 2016: more genomes, more complexity.

PubMed

Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

2016-01-04

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Enabling functional genomics with genome engineering

PubMed Central

Hilton, Isaac B.; Gersbach, Charles A.

2015-01-01

Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances. PMID:26430154

phiGENOME: an integrative navigation throughout bacteriophage genomes.

PubMed

Stano, Matej; Klucar, Lubos

2011-11-01

phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

No cross-resistance between imidacloprid and pymetrozine in the brown planthopper: status and mechanisms.

PubMed

Yang, Yuanxue; Huang, Lixin; Wang, Yunchao; Zhang, Yixi; Fang, Siqi; Liu, Zewen

2016-06-01

Cross-resistance between insecticides, especially from different groups, can be extremely unpredictable, and it has been a serious concern in pest control. Pymetrozine has been widely used to control Nilaparvata lugens with the suspension of imidacloprid for the resistance, and N. lugens has showed obvious pymetrozine resistance in recent years. To investigate the possible cross-resistance between imidacloprid and pymetrozine is very important to avoid the adverse effects on resistance development and pest control. Bioassays of two field populations in five consecutive years showed that imidacloprid resistance decreased greatly, while pymetrozine resistance increased significantly. The synergist piperonyl butoxide (PBO) could synergize both imidacloprid and pymetrozine in all field populations, which indicated the importance of P450s in the resistance to two insecticides. Imidacloprid resistance was reported to be associated with two P450s, CYP6AY1 and CYP6ER1, which could metabolize imidacloprid efficiently. However, the recombinant proteins of these two P450s did not show any enzymatic activity to metabolize pymetrozine. The pymetrozine susceptibility did not change when CYP6AY1 and CYP6ER1 mRNA levels were reduced by RNA interference (RNAi), although which could obviously decrease imidacloprid resistance. In vivo and in vitro studies provided evidences to demonstrate that there was no cross-resistance between imidacloprid and pymetrozine in N. lugens, which was different from the findings in Bemisia tabaci. Copyright © 2015. Published by Elsevier Inc.

Control of the Tomato Leafminer, Tuta absoluta (Lepidoptera: Gelechiidae), in Open-Field Tomatoes by Indigenous Natural Enemies Occurring in Israel.

PubMed

Shaltiel-Harpaz, Liora; Gerling, Dan; Graph, Shaul; Kedoshim, Hendrika; Azolay, Lotem; Rozenberg, Tamir; Nachache, Yaakov; Steinberg, Shimon; Allouche, Arnon; Alon, Tamar

2016-02-01

The tomato leafminer, Tuta absoluta (Meyrick), had established in Israel by 2010, attacking both open-field tomatoes and greenhouse crops.We searched for its natural enemies in open-field tomatoes, and tried to determine their potential for controlling this pest. We surveyed the local natural enemies in open tomato fields and measured their impact on pest populations in an unsprayed field. We assessed the suppressive ability of the dominant hemipteran predator, Nesidiocoris tenuis Reuter, against T. absoluta under controlled laboratory conditions and evaluated the impact of its augmentation on T. absoluta control in open-field tomatoes. We found five natural enemy species:the predator, N. tenuis, two braconids, and two eulophids. Predation accounted for 64.5±9.2% (mean ± SE) of T. absoluta larval mortality, whereas parasitism accounted for 20.96±7.5%. Together, they eliminated the pest population at tomato harvest time. Under controlled conditions, predation by N. tenuis rose from 58 to 72% with increased density of T. absoluta, suggesting positive density dependence. The reduction of T. absoluta (83%) by N. tenuis was higher than that of Bemisia tabaci (32%), suggesting a preference of N. tenuis for T. absoluta. Augmentation of N.tenuis was as effective as conventional treatment insecticide treatment, and plant damage was low and did not seem to affect yield. Results indicate that reduced pesticide use enables indigenous natural enemies, particularly N.tenuis, to successfully control T. absoluta and prevent crop damage in open-field tomatoes.

Comparative Toxicities of Newer and Conventional Insecticides: Against Four Generalist Predator Species.

PubMed

Prabhaker, Nilima; Naranjo, Steven; Perring, Thomas; Castle, Steven

2017-12-05

Generalist insect predators play an essential role in regulating the populations of Bemisia tabaci and other pests in agricultural systems, but may be affected negatively by insecticides applied for pest management. Evaluation of insecticide compatibility with specific predator species can provide a basis for making treatment decisions with the aim of conserving natural enemies. Eleven insecticides representing six modes of action groups were evaluated for toxicity against four predator species and at different developmental stages. Full-concentration series bioassays were conducted on laboratory-reared or insectary-supplied predators using Petri dish and systemic uptake bioassay techniques. Highest toxicities were observed with imidacloprid and clothianidin against first and second instar nymphs of Geocoris punctipes (Say) (Hemiptera: Geocoridae). Later instar nymphs were less susceptible to neonicotinoid treatments based on higher LC50s observed with imidacloprid, thiamethoxam, and dinotefuran against third or fourth instar nymphs. The pyrethroid insecticide bifenthrin was highly toxic against adults of G. punctipes and Orius insidiosus (Say) (Hemiptera: Anthocoridae). Standard concentration/mortality evaluation of nonacute toxicity insecticides, including buprofezin, pyriproxyfen, spirotetramat, and spiromesifen, was inconclusive in terms of generating probit statistics. However, low mortality levels of insects exposed for up to 120 h suggested minimal lethality with the exception of pyriproxyfen that was mildly toxic to Chrysoperla rufilabris (Burmeister) (Neuroptera: Chrysopidae). Published by Oxford University Press on behalf of Entomological Society of America 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Aboveground Whitefly Infestation Modulates Transcriptional Levels of Anthocyanin Biosynthesis and Jasmonic Acid Signaling-Related Genes and Augments the Cope with Drought Stress of Maize

PubMed Central

Park, Yong-Soon; Bae, Dong-Won; Ryu, Choong-Min

2015-01-01

Up to now, the potential underlying molecular mechanisms by which maize (Zea mays L.) plants elicit defense responses by infestation with a phloem feeding insect whitefly [Bemisia tabaci (Genn.)] have been barely elucidated against (a)biotic stresses. To fill this gap of current knowledge maize plants were infested with whitefly and these plants were subsequently assessed the levels of water loss. To understand the mode of action, plant hormone contents and the stress-related mRNA expression were evaluated. Whitefly-infested maize plants did not display any significant phenotypic differences in above-ground tissues (infested site) compared with controls. By contrast, root (systemic tissue) biomass was increased by 2-fold by whitefly infestation. The levels of endogenous indole-3-acetic acid (IAA), jasmonic acid (JA), and hydrogen peroxide (H2O2) were significantly higher in whitefly-infested plants. The biosynthetic or signaling-related genes for JA and anthocyanins were highly up-regulated. Additionally, we found that healthier plants were obtained in whitefly-infested plants under drought conditions. The weight of whitefly-infested plants was approximately 20% higher than that of control plants at 14 d of drought treatment. The drought tolerance-related genes, ZmbZIP72, ZmSNAC1, and ZmABA1, were highly expressed in the whitefly-infected plants. Collectively, our results suggest that IAA/JA-derived maize physiological changes and correlation of H2O2 production and water loss are modulated by above-ground whitefly infestation in maize plants. PMID:26630288

Navigating yeast genome maintenance with functional genomics.

PubMed

Measday, Vivien; Stirling, Peter C

2016-03-01

Maintenance of genome integrity is a fundamental requirement of all organisms. To address this, organisms have evolved extremely faithful modes of replication, DNA repair and chromosome segregation to combat the deleterious effects of an unstable genome. Nonetheless, a small amount of genome instability is the driver of evolutionary change and adaptation, and thus a low level of instability is permitted in populations. While defects in genome maintenance almost invariably reduce fitness in the short term, they can create an environment where beneficial mutations are more likely to occur. The importance of this fact is clearest in the development of human cancer, where genome instability is a well-established enabling characteristic of carcinogenesis. This raises the crucial question: what are the cellular pathways that promote genome maintenance and what are their mechanisms? Work in model organisms, in particular the yeast Saccharomyces cerevisiae, has provided the global foundations of genome maintenance mechanisms in eukaryotes. The development of pioneering genomic tools inS. cerevisiae, such as the systematic creation of mutants in all nonessential and essential genes, has enabled whole-genome approaches to identifying genes with roles in genome maintenance. Here, we review the extensive whole-genome approaches taken in yeast, with an emphasis on functional genomic screens, to understand the genetic basis of genome instability, highlighting a range of genetic and cytological screening modalities. By revealing the biological pathways and processes regulating genome integrity, these analyses contribute to the systems-level map of the yeast cell and inform studies of human disease, especially cancer. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Enabling functional genomics with genome engineering.

PubMed

Hilton, Isaac B; Gersbach, Charles A

2015-10-01

Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances. © 2015 Hilton and Gersbach; Published by Cold Spring Harbor Laboratory Press.

Genome Maps, a new generation genome browser.

PubMed

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-07-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

Genome Maps, a new generation genome browser

PubMed Central

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-01-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications.

PubMed

Laird, Matthew R; Langille, Morgan G I; Brinkman, Fiona S L

2015-10-15

A simple static image of genomes and associated metadata is very limiting, as researchers expect rich, interactive tools similar to the web applications found in the post-Web 2.0 world. GenomeD3Plot is a light weight visualization library written in javascript using the D3 library. GenomeD3Plot provides a rich API to allow the rapid visualization of complex genomic data using a convenient standards based JSON configuration file. When integrated into existing web services GenomeD3Plot allows researchers to interact with data, dynamically alter the view, or even resize or reposition the visualization in their browser window. In addition GenomeD3Plot has built in functionality to export any resulting genome visualization in PNG or SVG format for easy inclusion in manuscripts or presentations. GenomeD3Plot is being utilized in the recently released Islandviewer 3 (www.pathogenomics.sfu.ca/islandviewer/) to visualize predicted genomic islands with other genome annotation data. However, its features enable it to be more widely applicable for dynamic visualization of genomic data in general. GenomeD3Plot is licensed under the GNU-GPL v3 at https://github.com/brinkmanlab/GenomeD3Plot/. brinkman@sfu.ca. © The Author 2015. Published by Oxford University Press.

Pesticide-mediated interspecific competition between local and invasive thrips pests.

PubMed

Zhao, Xueyin; Reitz, Stuart R; Yuan, Huiguo; Lei, Zhongren; Paini, Dean Ronald; Gao, Yulin

2017-01-13

Competitive interactions between species can be mitigated or even reversed in the presence of anthropogenic influences. The thrips species Frankliniella occidentalis and Thrips tabaci are highly invasive and damaging agricultural pests throughout the world. Where the species co-occur, one species tends to eventually predominate over the other. Avermectin and beta-cypermethrin are commonly used insecticides to manage thrips in China, and laboratory bioassays demonstrated that F. occidentalis is significantly less susceptible than T. tabaci to these insecticides. In laboratory cage trials in which both species were exposed to insecticide treated cabbage plants, F. occidentalis became the predominant species. In contrast, T. tabaci completely displaced F. occidentalis on plants that were not treated with insecticides. In field trials, the species co-existed on cabbage before insecticide treatments began, but with T. tabaci being the predominant species. Following application of avermectin or beta-cypermethrin, F. occidentalis became the predominant species, while in plots not treated with insecticides, T. tabaci remained the predominant species. These results indicate that T. tabaci is an intrinsically superior competitor to F. occidentalis, but its competitive advantage can be counteracted through differential susceptibilities of the species to insecticides. These results further demonstrate the importance of external factors, such as insecticide applications, in mediating the outcome of interspecific interactions and produce rapid unanticipated shifts in the demographics of pest complexes.

Pesticide-mediated interspecific competition between local and invasive thrips pests

PubMed Central

Zhao, Xueyin; Reitz, Stuart R.; Yuan, Huiguo; Lei, Zhongren; Paini, Dean Ronald; Gao, Yulin

2017-01-01

Competitive interactions between species can be mitigated or even reversed in the presence of anthropogenic influences. The thrips species Frankliniella occidentalis and Thrips tabaci are highly invasive and damaging agricultural pests throughout the world. Where the species co-occur, one species tends to eventually predominate over the other. Avermectin and beta-cypermethrin are commonly used insecticides to manage thrips in China, and laboratory bioassays demonstrated that F. occidentalis is significantly less susceptible than T. tabaci to these insecticides. In laboratory cage trials in which both species were exposed to insecticide treated cabbage plants, F. occidentalis became the predominant species. In contrast, T. tabaci completely displaced F. occidentalis on plants that were not treated with insecticides. In field trials, the species co-existed on cabbage before insecticide treatments began, but with T. tabaci being the predominant species. Following application of avermectin or beta-cypermethrin, F. occidentalis became the predominant species, while in plots not treated with insecticides, T. tabaci remained the predominant species. These results indicate that T. tabaci is an intrinsically superior competitor to F. occidentalis, but its competitive advantage can be counteracted through differential susceptibilities of the species to insecticides. These results further demonstrate the importance of external factors, such as insecticide applications, in mediating the outcome of interspecific interactions and produce rapid unanticipated shifts in the demographics of pest complexes. PMID:28084404

Reduction of viral load in whitefly (Bemisia tabaci Gen.) feeding on RNAi-mediated bean golden mosaic virus resistant transgenic bean plants.

PubMed

de Paula, Nayhanne T; de Faria, Josias C; Aragão, Francisco J L

2015-12-02

The RNAi concept was explored to silence the rep gene from the bean golden mosaic virus (BGMV) and a genetically modified (GM) bean immune to the virus was previously generated. We investigated if BGMV-viruliferous whiteflies would reduce viral amount after feeding on GM plants. BGMV DNA amount was significantly reduced in whiteflies feeding in GM-plants (compared with insects feeding on non-GM plants) for a period of 4 and 8 days in 52% and 84% respectively. Copyright © 2015 Elsevier B.V. All rights reserved.

Analysis of a native whitefly transcriptome and its sequence divergence with two invasive whitefly species.

PubMed

Wang, Xiao-Wei; Zhao, Qiong-Yi; Luan, Jun-Bo; Wang, Yu-Jun; Yan, Gen-Hong; Liu, Shu-Sheng

2012-10-04

Genomic divergence between invasive and native species may provide insight into the molecular basis underlying specific characteristics that drive the invasion and displacement of closely related species. In this study, we sequenced the transcriptome of an indigenous species, Asia II 3, of the Bemisia tabaci complex and compared its genetic divergence with the transcriptomes of two invasive whiteflies species, Middle East Asia Minor 1 (MEAM1) and Mediterranean (MED), respectively. More than 16 million reads of 74 base pairs in length were obtained for the Asia II 3 species using the Illumina sequencing platform. These reads were assembled into 52,535 distinct sequences (mean size: 466 bp) and 16,596 sequences were annotated with an E-value above 10-5. Protein family comparisons revealed obvious diversification among the transcriptomes of these species suggesting species-specific adaptations during whitefly evolution. On the contrary, substantial conservation of the whitefly transcriptomes was also evident, despite their differences. The overall divergence of coding sequences between the orthologous gene pairs of Asia II 3 and MEAM1 is 1.73%, which is comparable to the average divergence of Asia II 3 and MED transcriptomes (1.84%) and much higher than that of MEAM1 and MED (0.83%). This is consistent with the previous phylogenetic analyses and crossing experiments suggesting these are distinct species. We also identified hundreds of highly diverged genes and compiled sequence identify data into gene functional groups and found the most divergent gene classes are Cytochrome P450, Glutathione metabolism and Oxidative phosphorylation. These results strongly suggest that the divergence of genes related to metabolism might be the driving force of the MEAM1 and Asia II 3 differentiation. We also analyzed single nucleotide polymorphisms within the orthologous gene pairs of indigenous and invasive whiteflies which are helpful for the investigation of association between

Analysis of a native whitefly transcriptome and its sequence divergence with two invasive whitefly species

PubMed Central

2012-01-01

Background Genomic divergence between invasive and native species may provide insight into the molecular basis underlying specific characteristics that drive the invasion and displacement of closely related species. In this study, we sequenced the transcriptome of an indigenous species, Asia II 3, of the Bemisia tabaci complex and compared its genetic divergence with the transcriptomes of two invasive whiteflies species, Middle East Asia Minor 1 (MEAM1) and Mediterranean (MED), respectively. Results More than 16 million reads of 74 base pairs in length were obtained for the Asia II 3 species using the Illumina sequencing platform. These reads were assembled into 52,535 distinct sequences (mean size: 466 bp) and 16,596 sequences were annotated with an E-value above 10-5. Protein family comparisons revealed obvious diversification among the transcriptomes of these species suggesting species-specific adaptations during whitefly evolution. On the contrary, substantial conservation of the whitefly transcriptomes was also evident, despite their differences. The overall divergence of coding sequences between the orthologous gene pairs of Asia II 3 and MEAM1 is 1.73%, which is comparable to the average divergence of Asia II 3 and MED transcriptomes (1.84%) and much higher than that of MEAM1 and MED (0.83%). This is consistent with the previous phylogenetic analyses and crossing experiments suggesting these are distinct species. We also identified hundreds of highly diverged genes and compiled sequence identify data into gene functional groups and found the most divergent gene classes are Cytochrome P450, Glutathione metabolism and Oxidative phosphorylation. These results strongly suggest that the divergence of genes related to metabolism might be the driving force of the MEAM1 and Asia II 3 differentiation. We also analyzed single nucleotide polymorphisms within the orthologous gene pairs of indigenous and invasive whiteflies which are helpful for the investigation of

GenomeGraphs: integrated genomic data visualization with R.

PubMed

Durinck, Steffen; Bullard, James; Spellman, Paul T; Dudoit, Sandrine

2009-01-06

Biological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different genomic datasets in a versatile manner. In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses. We developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets. GenomeGraphs uses the biomaRt package to perform on-line annotation queries to Ensembl and translates these to gene/transcript structures in viewports of the grid graphics package. This allows genomic annotation to be plotted together with experimental data. GenomeGraphs can also be used to plot custom annotation tracks in combination with different experimental data types together in one plot using the same genomic coordinate system. GenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R.

Ultrafast Comparison of Personal Genomes via Precomputed Genome Fingerprints.

PubMed

Glusman, Gustavo; Mauldin, Denise E; Hood, Leroy E; Robinson, Max

2017-01-01

We present an ultrafast method for comparing personal genomes. We transform the standard genome representation (lists of variants relative to a reference) into "genome fingerprints" via locality sensitive hashing. The resulting genome fingerprints can be meaningfully compared even when the input data were obtained using different sequencing technologies, processed using different pipelines, represented in different data formats and relative to different reference versions. Furthermore, genome fingerprints are robust to up to 30% missing data. Because of their reduced size, computation on the genome fingerprints is fast and requires little memory. For example, we could compute all-against-all pairwise comparisons among the 2504 genomes in the 1000 Genomes data set in 67 s at high quality (21 μs per comparison, on a single processor), and achieved a lower quality approximation in just 11 s. Efficient computation enables scaling up a variety of important genome analyses, including quantifying relatedness, recognizing duplicative sequenced genomes in a set, population reconstruction, and many others. The original genome representation cannot be reconstructed from its fingerprint, effectively decoupling genome comparison from genome interpretation; the method thus has significant implications for privacy-preserving genome analytics.

Ultrafast Comparison of Personal Genomes via Precomputed Genome Fingerprints

PubMed Central

Glusman, Gustavo; Mauldin, Denise E.; Hood, Leroy E.; Robinson, Max

2017-01-01

We present an ultrafast method for comparing personal genomes. We transform the standard genome representation (lists of variants relative to a reference) into “genome fingerprints” via locality sensitive hashing. The resulting genome fingerprints can be meaningfully compared even when the input data were obtained using different sequencing technologies, processed using different pipelines, represented in different data formats and relative to different reference versions. Furthermore, genome fingerprints are robust to up to 30% missing data. Because of their reduced size, computation on the genome fingerprints is fast and requires little memory. For example, we could compute all-against-all pairwise comparisons among the 2504 genomes in the 1000 Genomes data set in 67 s at high quality (21 μs per comparison, on a single processor), and achieved a lower quality approximation in just 11 s. Efficient computation enables scaling up a variety of important genome analyses, including quantifying relatedness, recognizing duplicative sequenced genomes in a set, population reconstruction, and many others. The original genome representation cannot be reconstructed from its fingerprint, effectively decoupling genome comparison from genome interpretation; the method thus has significant implications for privacy-preserving genome analytics. PMID:29018478

The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.

PubMed

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-02-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

Family genome browser: visualizing genomes with pedigree information.

PubMed

Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong

2015-07-15

Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Genomics and functional genomics in Chlamydomonas reinhardtii

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blaby, Ian K.; Blaby-Haas, Crysten E.

The availability of the Chlamydomonas reinhardtii nuclear genome sequence continues to enable researchers to address biological questions relevant to algae, land plants and animals in unprecedented ways. As we continue to characterize and understand biological processes in C. reinhardtii and translate that knowledge to other systems, we are faced with the realization that many genes encode proteins without a defined function. The field of functional genomics aims to close this gap between genome sequence and protein function. Transcriptomes, proteomes and phenomes can each provide layers of gene-specific functional data while supplying a global snapshot of cellular behavior under different conditions.more » Herein we present a brief history of functional genomics, the present status of the C. reinhardtii genome, how genome-wide experiments can aid in supplying protein function inferences, and provide an outlook for functional genomics in C. reinhardtii.« less

Genomics and functional genomics in Chlamydomonas reinhardtii

DOE PAGES

Blaby, Ian K.; Blaby-Haas, Crysten E.

2017-03-21

The availability of the Chlamydomonas reinhardtii nuclear genome sequence continues to enable researchers to address biological questions relevant to algae, land plants and animals in unprecedented ways. As we continue to characterize and understand biological processes in C. reinhardtii and translate that knowledge to other systems, we are faced with the realization that many genes encode proteins without a defined function. The field of functional genomics aims to close this gap between genome sequence and protein function. Transcriptomes, proteomes and phenomes can each provide layers of gene-specific functional data while supplying a global snapshot of cellular behavior under different conditions.more » Herein we present a brief history of functional genomics, the present status of the C. reinhardtii genome, how genome-wide experiments can aid in supplying protein function inferences, and provide an outlook for functional genomics in C. reinhardtii.« less

Inter-regional differences in baseline toxicity of Bemisia argentifolii (Homoptera: Aleyrodidae) to the two insect growth regulators, buprofezin and pyriproxyfen.

PubMed

Toscano, N C; Prabhaker, N; Castle, S J; Henneberry, T J

2001-12-01

A survey of 53 Bemisia argentifolii Bellows & Perring populations from different agricultural regions in California and Arizona was conducted from 1997 to 1999 to establish baseline toxicological responses to buprofezin and pyriproxyfen. Although both compounds proved to be highly toxic even in minute quantities to specific stages, geographical and temporal differences in responses were detected using a leaf spray bioassay technique. Monitoring for three years revealed that six to seven populations had higher LC50 values but not greater survival when exposed to these two insecticides. A significant difference in relative susceptibility to buprofezin was first observed in late season 1997 in San Joaquin Valley populations with LC50s ranging from 16 to 22 microg (AI)/liter(-1) compared with IC50s of 1 to 3 mg (AI)/liter(-1) in Imperial, Palo Verde Valley and Yuma populations. Whiteflies collected in subsequent years from these and other locations showed an increase in susceptibility to buprofezin. Regional differences in susceptibilities to pyriproxyfen were minimal within the same years. Three years of sampling revealed consistently higher LC50s to pyriproxyfen in populations from Palo Verde Valley, CA, compared with whiteflies from Imperial, San Joaquin Valley or Yuma. As was the case with buprofezin, a decline in LC50s to pyriproxyfen was observed in whiteflies from all locations sampled in 1999. However, no correlation was observed between buprofezin and pyriproxyfen toxicity in any of the strains. The variable toxicities observed to both compounds over a period of 3 yr may be due principally to inherent differences among geographical populations or due to past chemical use which may confer positive or negative cross-resistance to buprofezin or pyriproxyfen.

Photoinhibition and photoinhibition-like damage to the photosynthetic apparatus in tobacco leaves induced by pseudomonas syringae pv. Tabaci under light and dark conditions.

PubMed

Cheng, Dan-Dan; Zhang, Zi-Shan; Sun, Xing-Bin; Zhao, Min; Sun, Guang-Yu; Chow, Wah Soon

2016-01-25

Pseudomonas syringae pv. tabaci (Pst), which is the pathogen responsible for tobacco wildfire disease, has received considerable attention in recent years. The objective of this study was to clarify the responses of photosystem I (PSI) and photosystem II (PSII) to Pst infection in tobacco leaves. The net photosynthetic rate (Pn) and carboxylation efficiency (CE) were inhibited by Pst infection. The normalized relative variable fluorescence at the K step (W k) and the relative variable fluorescence at the J step (V J) increased while the maximal quantum yield of PSII (F v/F m) and the density of Q A-reducing PSII reaction centers per cross section (RC/CSm) decreased, indicating that the reaction centers, and the donor and acceptor sides of PSII were all severely damaged after Pst infection. The PSI activity decreased as the infection progressed. Furthermore, we observed a considerable overall degradation of PsbO, D1, PsaA proteins and an over-accumulation of reactive oxygen species (ROS). Photoinhibition and photoinhibition-like damage were observed under light and dark conditions, respectively, after Pst infection of tobacco leaves. The damage was greater in the dark. ROS over-accumulation was not the primary cause of the photoinhibition and photoinhibition-like damage. The PsbO, D1 and PsaA proteins appear to be the targets during Pst infection under light and dark conditions.

WheatGenome.info: A Resource for Wheat Genomics Resource.

PubMed

Lai, Kaitao

2016-01-01

An integrated database with a variety of Web-based systems named WheatGenome.info hosting wheat genome and genomic data has been developed to support wheat research and crop improvement. The resource includes multiple Web-based applications, which are implemented as a variety of Web-based systems. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This portal provides links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/ .

Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine

PubMed Central

Elsik, Christine G.; Tayal, Aditi; Diesh, Colin M.; Unni, Deepak R.; Emery, Marianne L.; Nguyen, Hung N.; Hagen, Darren E.

2016-01-01

We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. PMID:26578564

Haemonchus contortus: Genome Structure, Organization and Comparative Genomics.

PubMed

Laing, R; Martinelli, A; Tracey, A; Holroyd, N; Gilleard, J S; Cotton, J A

2016-01-01

One of the first genome sequencing projects for a parasitic nematode was that for Haemonchus contortus. The open access data from the Wellcome Trust Sanger Institute provided a valuable early resource for the research community, particularly for the identification of specific genes and genetic markers. Later, a second sequencing project was initiated by the University of Melbourne, and the two draft genome sequences for H. contortus were published back-to-back in 2013. There is a pressing need for long-range genomic information for genetic mapping, population genetics and functional genomic studies, so we are continuing to improve the Wellcome Trust Sanger Institute assembly to provide a finished reference genome for H. contortus. This review describes this process, compares the H. contortus genome assemblies with draft genomes from other members of the strongylid group and discusses future directions for parasite genomics using the H. contortus model. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genome U-Plot: a whole genome visualization.

PubMed

Gaitatzes, Athanasios; Johnson, Sarah H; Smadbeck, James B; Vasmatzis, George

2018-05-15

The ability to produce and analyze whole genome sequencing (WGS) data from samples with structural variations (SV) generated the need to visualize such abnormalities in simplified plots. Conventional two-dimensional representations of WGS data frequently use either circular or linear layouts. There are several diverse advantages regarding both these representations, but their major disadvantage is that they do not use the two-dimensional space very efficiently. We propose a layout, termed the Genome U-Plot, which spreads the chromosomes on a two-dimensional surface and essentially quadruples the spatial resolution. We present the Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities. We compare conventional visualization schemas with the Genome U-Plot using visualization metrics such as number of line crossings and crossing angle resolution measures. Based on our metrics, we improve the readability of the resulting graph by at least 2-fold, making apparent important features and making it easy to identify important genomic changes. A whole genome visualization tool with high spatial resolution and improved aesthetic qualities. An implementation and documentation of the Genome U-Plot is publicly available at https://github.com/gaitat/GenomeUPlot. vasmatzis.george@mayo.edu. Supplementary data are available at Bioinformatics online.

Whole-exome/genome sequencing and genomics.

PubMed

Grody, Wayne W; Thompson, Barry H; Hudgins, Louanne

2013-12-01

As medical genetics has progressed from a descriptive entity to one focused on the functional relationship between genes and clinical disorders, emphasis has been placed on genomics. Genomics, a subelement of genetics, is the study of the genome, the sum total of all the genes of an organism. The human genome, which is contained in the 23 pairs of nuclear chromosomes and in the mitochondrial DNA of each cell, comprises >6 billion nucleotides of genetic code. There are some 23,000 protein-coding genes, a surprisingly small fraction of the total genetic material, with the remainder composed of noncoding DNA, regulatory sequences, and introns. The Human Genome Project, launched in 1990, produced a draft of the genome in 2001 and then a finished sequence in 2003, on the 50th anniversary of the initial publication of Watson and Crick's paper on the double-helical structure of DNA. Since then, this mass of genetic information has been translated at an ever-increasing pace into useable knowledge applicable to clinical medicine. The recent advent of massively parallel DNA sequencing (also known as shotgun, high-throughput, and next-generation sequencing) has brought whole-genome analysis into the clinic for the first time, and most of the current applications are directed at children with congenital conditions that are undiagnosable by using standard genetic tests for single-gene disorders. Thus, pediatricians must become familiar with this technology, what it can and cannot offer, and its technical and ethical challenges. Here, we address the concepts of human genomic analysis and its clinical applicability for primary care providers.

A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus.

PubMed

Lack, Justin B; Lange, Jeremy D; Tang, Alison D; Corbett-Detig, Russell B; Pool, John E

2016-12-01

The Drosophila Genome Nexus is a population genomic resource that provides D. melanogaster genomes from multiple sources. To facilitate comparisons across data sets, genomes are aligned using a common reference alignment pipeline which involves two rounds of mapping. Regions of residual heterozygosity, identity-by-descent, and recent population admixture are annotated to enable data filtering based on the user's needs. Here, we present a significant expansion of the Drosophila Genome Nexus, which brings the current data object to a total of 1,121 wild-derived genomes. New additions include 305 previously unpublished genomes from inbred lines representing six population samples in Egypt, Ethiopia, France, and South Africa, along with another 193 genomes added from recently-published data sets. We also provide an aligned D. simulans genome to facilitate divergence comparisons. This improved resource will broaden the range of population genomic questions that can addressed from multi-population allele frequencies and haplotypes in this model species. The larger set of genomes will also enhance the discovery of functionally relevant natural variation that exists within and between populations. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Visualization for genomics: the Microbial Genome Viewer.

PubMed

Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

2004-07-22

A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine.

PubMed

Elsik, Christine G; Tayal, Aditi; Diesh, Colin M; Unni, Deepak R; Emery, Marianne L; Nguyen, Hung N; Hagen, Darren E

2016-01-04

We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Tapping the promise of genomics in species with complex, nonmodel genomes.

PubMed

Hirsch, Candice N; Buell, C Robin

2013-01-01

Genomics is enabling a renaissance in all disciplines of plant biology. However, many plant genomes are complex and remain recalcitrant to current genomic technologies. The complexities of these nonmodel plant genomes are attributable to gene and genome duplication, heterozygosity, ploidy, and/or repetitive sequences. Methods are available to simplify the genome and reduce these barriers, including inbreeding and genome reduction, making these species amenable to current sequencing and assembly methods. Some, but not all, of the complexities in nonmodel genomes can be bypassed by sequencing the transcriptome rather than the genome. Additionally, comparative genomics approaches, which leverage phylogenetic relatedness, can aid in the interpretation of complex genomes. Although there are limitations in accessing complex nonmodel plant genomes using current sequencing technologies, genome manipulation and resourceful analyses can allow access to even the most recalcitrant plant genomes.

Ensembl genomes 2016: more genomes, more complexity

USDA-ARS?s Scientific Manuscript database

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent...

The Sequenced Angiosperm Genomes and Genome Databases.

PubMed

Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

2018-01-01

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

The Sequenced Angiosperm Genomes and Genome Databases

PubMed Central

Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

2018-01-01

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology. PMID:29706973

GenColors-based comparative genome databases for small eukaryotic genomes.

PubMed

Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

2013-01-01

Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.

Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio.

PubMed

Manolio, Teri A

2016-10-01

Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. Published by Elsevier Ireland Ltd.

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

PubMed

Machado, Henrique; Gram, Lone

2017-01-01

Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

The coffee genome hub: a resource for coffee genomes

PubMed Central

Dereeper, Alexis; Bocs, Stéphanie; Rouard, Mathieu; Guignon, Valentin; Ravel, Sébastien; Tranchant-Dubreuil, Christine; Poncet, Valérie; Garsmeur, Olivier; Lashermes, Philippe; Droc, Gaëtan

2015-01-01

The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released. In the context of the C. canephora genome sequencing project and to support post-genomics efforts, we developed the Coffee Genome Hub (http://coffee-genome.org/), an integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee. We provide the complete genome sequence of C. canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics, syntenic blocks, genetic markers and genetic maps. The hub relies on generic software (e.g. GMOD tools) for easy querying, visualizing and downloading research data. It includes a Genome Browser enhanced by a Community Annotation System, enabling the improvement of automatic gene annotation through an annotation editor. In addition, the hub aims at developing interoperability among other existing South Green tools managing coffee data (phylogenomics resources, SNPs) and/or supporting data analyses with the Galaxy workflow manager. PMID:25392413

Methodology for developing life tables for sessile insects in the field using the Whitefly, Bemisia tabaci, in cotton as a model system

USDA-ARS?s Scientific Manuscript database

Life tables provide a means of measuring the schedules of birth and death from populations over time. They also can be used to quantify the sources and rates of mortality in populations, which has a variety of applications in ecology, including agricultural ecosystems. Horizontal, or cohort-based, l...

Genome size analyses of Pucciniales reveal the largest fungal genomes.

PubMed

Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

2014-01-01

Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

Genome size analyses of Pucciniales reveal the largest fungal genomes

PubMed Central

Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G.; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T.; Loureiro, João; Talhinhas, Pedro

2014-01-01

Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research. PMID:25206357

Light Suppresses Bacterial Population through the Accumulation of Hydrogen Peroxide in Tobacco Leaves Infected with Pseudomonas syringae pv. tabaci

PubMed Central

Cheng, Dan-Dan; Liu, Mei-Jun; Sun, Xing-Bin; Zhao, Min; Chow, Wah S.; Sun, Guang-Yu; Zhang, Zi-Shan; Hu, Yan-Bo

2016-01-01

Pseudomonas syringae pv. tabaci (Pst) is a hemibiotrophic bacterial pathogen responsible for tobacco wildfire disease. Although considerable research has been conducted on the tobacco plant’s tolerance to Pst, the role of light in the responses of the photosystems to Pst infection is poorly understood. This study aimed to elucidate the underlying mechanisms of the reduced photosystem damage in tobacco leaves due to Pst infection under light conditions. Compared to dark conditions, Pst infection under light conditions resulted in less chlorophyll degradation and a smaller decline in photosynthetic function. Although the maximal quantum yield of photosystem II (PSII) and the activity of the photosystem I (PSI) complex decreased as Pst infection progressed, damage to PSI and PSII after infection was reduced under light conditions compared to dark conditions. Pst was 17-fold more abundant in tobacco leaves under dark compared to light conditions at 3 days post inoculation (dpi). Additionally, H2O2 accumulated to a high level in tobacco leaves after Pst infection under light conditions; although to a lesser extent, H2O2 accumulation was also significant under dark conditions. Pretreatment with H2O2 alleviated chlorotic lesions and decreased Pst abundance in tobacco leaves at 3 dpi under dark conditions. MV pretreatment had the same effects under light conditions, whereas 3-(3,4-dichlorophenyl)-1,1-dimethylurea pretreatment aggravated chlorotic lesions and increased the Pst population. These results indicate that chlorotic symptoms and the size of the bacterial population are each negatively correlated with H2O2 accumulation. In other words, light appears to suppress the Pst population in tobacco leaves through the accumulation of H2O2 during infection. PMID:27148334

Home - The Cancer Genome Atlas - Cancer Genome - TCGA

Cancer.gov

The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing.

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

PubMed Central

Machado, Henrique; Gram, Lone

2017-01-01

Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms. PMID:28706512

Center for Cancer Genomics | Office of Cancer Genomics

Cancer.gov

The Center for Cancer Genomics (CCG) was established to unify the National Cancer Institute's activities in cancer genomics, with the goal of advancing genomics research and translating findings into the clinic to improve the precise diagnosis and treatment of cancers. In addition to promoting genomic sequencing approaches, CCG aims to accelerate structural, functional and computational research to explore cancer mechanisms, discover new cancer targets, and develop new therapeutics.

Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes.

PubMed

Janicki, Mateusz; Rooke, Rebecca; Yang, Guojun

2011-08-01

A major portion of most eukaryotic genomes are transposable elements (TEs). During evolution, TEs have introduced profound changes to genome size, structure, and function. As integral parts of genomes, the dynamic presence of TEs will continue to be a major force in reshaping genomes. Early computational analyses of TEs in genome sequences focused on filtering out "junk" sequences to facilitate gene annotation. When the high abundance and diversity of TEs in eukaryotic genomes were recognized, these early efforts transformed into the systematic genome-wide categorization and classification of TEs. The availability of genomic sequence data reversed the classical genetic approaches to discovering new TE families and superfamilies. Curated TE databases and their accurate annotation of genome sequences in turn facilitated the studies on TEs in a number of frontiers including: (1) TE-mediated changes of genome size and structure, (2) the influence of TEs on genome and gene functions, (3) TE regulation by host, (4) the evolution of TEs and their population dynamics, and (5) genomic scale studies of TE activity. Bioinformatics and genomic approaches have become an integral part of large-scale studies on TEs to extract information with pure in silico analyses or to assist wet lab experimental studies. The current revolution in genome sequencing technology facilitates further progress in the existing frontiers of research and emergence of new initiatives. The rapid generation of large-sequence datasets at record low costs on a routine basis is challenging the computing industry on storage capacity and manipulation speed and the bioinformatics community for improvement in algorithms and their implementations.

Biological control strategies for the South American tomato moth (Lepidoptera: Gelechiidae) in greenhouse tomatoes.

PubMed

Cabello, Tomas; Gallego, Juan R; Fernandez, Francisco J; Gamez, Manuel; Vila, Enric; Del Pino, Modesto; Hernandez-Suarez, Estrella

2012-12-01

The South American tomato pinworm, Tuta absoluta (Meyrick) has been introduced into new geographic areas, including the Mediterranean region, where it has become a serious threat to tomato production. Three greenhouse trials conducted in tomato crops during 2009 and 2010 explored control strategies using the egg-parasitoid Trichogramma achaeae Nagaraja and Nagarkatti compared with chemical control. The effectiveness of the predator Nesidiocoris tenuis (Reuter) was also tested. In greenhouses with early pest infestations (discrete generations), periodic inundative releases (eight releases at a rate of 50 adults/m2, twice a week) were necessary to achieve an adequate parasitism level (85.63 +/- 5.70%) early in the growing season. However, only one inoculative release (100 adults/m2) was sufficient to achieve a comparatively high parasitism level (91.03 +/- 12.58%) under conditions of high pest incidence and overlapping generations. Some intraguild competition was observed between T. achaeae and the predator, N. tenuis. This mirid species is commonly used in Mediterranean greenhouse tomato crops for the control of the sweetpotato whitefly, Bemisia tabaci (Gennadius). Tomato cultivars were also observed to influence the activity of natural enemies, mainly N. tenuis (whose average numbers ranged between 0.17 +/- 0.03 and 0.41 +/- 0.05 nymphs per leaf depending on the cultivar). This may be because of differences in plant nutrients in different cultivars, which may affect the feeding of omnivorous insects. In contrast, cultivar effects on T. achaeae were less apparent or possibly nonexistent. Nevertheless, there was an indirect effect in as much as T. achaeae was favored in cultivars not liked by N. tenuis.

Enhanced Methanol Production in Plants Provides Broad Spectrum Insect Resistance

PubMed Central

Dixit, Sameer; Upadhyay, Santosh Kumar; Singh, Harpal; Sidhu, Om Prakash; Verma, Praveen Chandra; K, Chandrashekar

2013-01-01

Plants naturally emit methanol as volatile organic compound. Methanol is toxic to insect pests; but the quantity produced by most of the plants is not enough to protect them against invading insect pests. In the present study, we demonstrated that the over-expression of pectin methylesterase, derived from Arabidopsis thaliana and Aspergillus niger, in transgenic tobacco plants enhances methanol production and resistance to polyphagous insect pests. Methanol content in the leaves of transgenic plants was measured using proton nuclear spectroscopy (1H NMR) and spectra showed up to 16 fold higher methanol as compared to control wild type (WT) plants. A maximum of 100 and 85% mortality in chewing insects Helicoverpa armigera and Spodoptera litura larvae was observed, respectively when fed on transgenic plants leaves. The surviving larvae showed less feeding, severe growth retardation and could not develop into pupae. In-planta bioassay on transgenic lines showed up to 99 and 75% reduction in the population multiplication of plant sap sucking pests Myzus persicae (aphid) and Bemisia tabaci (whitefly), respectively. Most of the phenotypic characters of transgenic plants were similar to WT plants. Confocal microscopy showed no deformities in cellular integrity, structure and density of stomata and trichomes of transgenic plants compared to WT. Pollen germination and tube formation was also not affected in transgenic plants. Cell wall enzyme transcript levels were comparable with WT. This study demonstrated for the first time that methanol emission can be utilized for imparting broad range insect resistance in plants. PMID:24223989

Vector development and vitellogenin determine the transovarial transmission of begomoviruses.

PubMed

Wei, Jing; He, Ya-Zhou; Guo, Qi; Guo, Tao; Liu, Yin-Quan; Zhou, Xue-Ping; Liu, Shu-Sheng; Wang, Xiao-Wei

2017-06-27

The majority of plant viruses are transmitted by insect vectors between hosts, and transovarial transmission of viruses from vector parents to offspring has great significance to their epidemiology. Begomoviruses are transmitted by the whitefly Bemisia tabaci in a circulative manner and are maintained through a plant-insect-plant cycle. Other routes of begomovirus transmission are not clearly known. Here, we report that transovarial transmission from female whiteflies to offspring often happens for one begomovirus, Tomato yellow leaf curl virus (TYLCV), and may have contributed significantly to its global spread. We found that TYLCV entry of the reproductive organ of its vector mainly depended on the developmental stage of the whitefly ovary, and the transovarial transmission of TYLCV to offspring increased with whitefly adult age. The specific interaction between virus coat protein (CP) and whitefly vitellogenin (Vg) was vital for virus entry into whitefly ovary. When knocking down the expression of Vg, the entry of TYLCV into ovary was inhibited and the transovarial transmission efficiency decreased. In contrast, another begomovirus, Papaya leaf curl China virus (PaLCuCNV), CP did not interact with whitefly Vg, and PaLCuCNV could not be transovarially transmitted by whiteflies. We further showed that TYLCV could be maintained for at least two generations in the absence of virus-infected plants, and the adult progenies were able to infect healthy plants in both the laboratory and field. This study reports the transovarial transmission mechanism of begomoviruses, and it may help to explain the evolution and global spread of some begomoviruses.

Comparative primate genomics: emerging patterns of genome content and dynamics

PubMed Central

Rogers, Jeffrey; Gibbs, Richard A.

2014-01-01

Preface Advances in genome sequencing technologies have created new opportunities for comparative primate genomics. Genome assemblies have been published for several primates, with analyses of several others underway. Whole genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved. Genomic data for macaques and other nonhuman primates provide valuable insight into genetic similarities and differences among species used as models for disease-related research. This review summarizes current knowledge regarding primate genome content and dynamics and offers a series of goals for the near future. PMID:24709753

Comparative primate genomics: emerging patterns of genome content and dynamics.

PubMed

Rogers, Jeffrey; Gibbs, Richard A

2014-05-01

Advances in genome sequencing technologies have created new opportunities for comparative primate genomics. Genome assemblies have been published for various primate species, and analyses of several others are underway. Whole-genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved. Genomic data for macaques and other non-human primates offer valuable insights into genetic similarities and differences among species that are used as models for disease-related research. This Review summarizes current knowledge regarding primate genome content and dynamics, and proposes a series of goals for the near future.

RPAN: rice pan-genome browser for ∼3000 rice genomes.

PubMed

Sun, Chen; Hu, Zhiqiang; Zheng, Tianqing; Lu, Kuangchen; Zhao, Yue; Wang, Wensheng; Shi, Jianxin; Wang, Chunchao; Lu, Jinyuan; Zhang, Dabing; Li, Zhikang; Wei, Chaochun

2017-01-25

A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome

USDA-ARS?s Scientific Manuscript database

CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of human, animals, microorganisms, and plants. Success of such genome editing is highly dependent on the availability of suitable target sites in the genomes to be edited. Many specific t...

Genomics Portals: integrative web-platform for mining genomics data.

PubMed

Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

2010-01-13

A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

Genomics Portals: integrative web-platform for mining genomics data

PubMed Central

2010-01-01

Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org. PMID:20070909

The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics1[C][W

PubMed Central

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F.X.; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-01-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species. PMID:23184232

Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute’s genomic medicine portfolio

PubMed Central

Manolio, Teri A.

2016-01-01

Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual’s genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of “Genomic Medicine Meetings,” under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and diffficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI’s genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. PMID:27612677

Comparative genome analysis in the integrated microbial genomes (IMG) system.

PubMed

Markowitz, Victor M; Kyrpides, Nikos C

2007-01-01

Comparative genome analysis is critical for the effective exploration of a rapidly growing number of complete and draft sequences for microbial genomes. The Integrated Microbial Genomes (IMG) system (img.jgi.doe.gov) has been developed as a community resource that provides support for comparative analysis of microbial genomes in an integrated context. IMG allows users to navigate the multidimensional microbial genome data space and focus their analysis on a subset of genes, genomes, and functions of interest. IMG provides graphical viewers, summaries, and occurrence profile tools for comparing genes, pathways, and functions (terms) across specific genomes. Genes can be further examined using gene neighborhoods and compared with sequence alignment tools.

Comparing Mycobacterium tuberculosis genomes using genome topology networks.

PubMed

Jiang, Jianping; Gu, Jianlei; Zhang, Liang; Zhang, Chenyi; Deng, Xiao; Dou, Tonghai; Zhao, Guoping; Zhou, Yan

2015-02-14

Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene duplication and genome rearrangement, can lead to different phenotypes among strains, and an investigation of genes affected by SVs may extend our knowledge of the relationships between SVs and phenotypes in microbes, especially in pathogenic bacteria. In this work, we introduce a 'Genome Topology Network' (GTN) method based on gene homology and gene locations to analyze genomic SVs and perform phylogenetic analysis. Furthermore, the concept of 'unfixed ortholog' has been proposed, whose members are affected by SVs in genome topology among close species. To improve the precision of 'unfixed ortholog' recognition, a strategy to detect annotation differences and complete gene annotation was applied. To assess the GTN method, a set of thirteen complete M. tuberculosis genomes was analyzed as a case study. GTNs with two different gene homology-assigning methods were built, the Clusters of Orthologous Groups (COG) method and the orthoMCL clustering method, and two phylogenetic trees were constructed accordingly, which may provide additional insights into whole genome-based phylogenetic analysis. We obtained 24 unfixable COG groups, of which most members were related to immunogenicity and drug resistance, such as PPE-repeat proteins (COG5651) and transcriptional regulator TetR gene family members (COG1309). The GTN method has been implemented in PERL and released on our website. The tool can be downloaded from http://homepage.fudan.edu.cn/zhouyan/gtn/ , and allows re-annotating the 'lost' genes among closely related genomes, analyzing genes affected by SVs, and performing phylogenetic analysis. With this tool, many immunogenic-related and drug resistance-related genes

A universal genomic coordinate translator for comparative genomics

PubMed Central

2014-01-01

Background Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N. Results Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of

A universal genomic coordinate translator for comparative genomics.

PubMed

Zamani, Neda; Sundström, Görel; Meadows, Jennifer R S; Höppner, Marc P; Dainat, Jacques; Lantz, Henrik; Haas, Brian J; Grabherr, Manfred G

2014-06-30

Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N. Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across

Microbial genomic taxonomy

PubMed Central

2013-01-01

A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, <10 in Karlin genomic signature, and > 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups. PMID:24365132

Integrated genome browser: visual analytics platform for genomics.

PubMed

Freese, Nowlan H; Norris, David C; Loraine, Ann E

2016-07-15

Genome browsers that support fast navigation through vast datasets and provide interactive visual analytics functions can help scientists achieve deeper insight into biological systems. Toward this end, we developed Integrated Genome Browser (IGB), a highly configurable, interactive and fast open source desktop genome browser. Here we describe multiple updates to IGB, including all-new capabilities to display and interact with data from high-throughput sequencing experiments. To demonstrate, we describe example visualizations and analyses of datasets from RNA-Seq, ChIP-Seq and bisulfite sequencing experiments. Understanding results from genome-scale experiments requires viewing the data in the context of reference genome annotations and other related datasets. To facilitate this, we enhanced IGB's ability to consume data from diverse sources, including Galaxy, Distributed Annotation and IGB-specific Quickload servers. To support future visualization needs as new genome-scale assays enter wide use, we transformed the IGB codebase into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data. IGB is open source and is freely available from http://bioviz.org/igb aloraine@uncc.edu. © The Author 2016. Published by Oxford University Press.

Genome build information is an essential part of genomic track files.

PubMed

Kanduri, Chakravarthi; Domanska, Diana; Hovig, Eivind; Sandve, Geir Kjetil

2017-09-14

Genomic locations are represented as coordinates on a specific genome build version, but the build information is frequently missing when coordinates are provided. We show that this information is essential to correctly interpret and analyse the genomic intervals contained in genomic track files. Although not a substitute for best practices, we also provide a tool to predict the genome build version of genomic track files.

Using Partial Genomic Fosmid Libraries for Sequencing CompleteOrganellar Genomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

McNeal, Joel R.; Leebens-Mack, James H.; Arumuganathan, K.

2005-08-26

Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However, for some organisms it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. Amore » minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.« less

Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science.

PubMed

Smith, David Roy

2017-05-01

Next-generation sequencing technologies have revolutionized genomics and altered the scientific publication landscape. Life-science journals abound with genome papers-peer-reviewed descriptions of newly sequenced chromosomes. Although they once filled the pages of Nature and Science, genome papers are now mostly relegated to journals with low-impact factors. Some have forecast the death of the genome paper and argued that they are using up valuable resources and not advancing science. However, the publication rate of genome papers is on the rise. This increase is largely because some journals have created a new category of manuscript called genome reports, which are short, fast-tracked papers describing a chromosome sequence(s), its GenBank accession number and little else. In 2015, for example, more than 2000 genome reports were published, and 2016 is poised to bring even more. Here, I highlight the growing popularity of genome reports and discuss their merits, drawbacks and impact on science and the academic publication infrastructure. Genome reports can be excellent assets for the research community, but they are also being used as quick and easy routes to a publication, and in some instances they are not peer reviewed. One of the best arguments for genome reports is that they are a citable, user-generated genomic resource providing essential methodological and biological information, which may not be present in the sequence database. But they are expensive and time-consuming avenues for achieving such a goal. © The Author 2016. Published by Oxford University Press.

Genome-wide comparisons of phylogenetic similarities between partial genomic regions and the full-length genome in Hepatitis E virus genotyping.

PubMed

Wang, Shuai; Wei, Wei; Luo, Xuenong; Cai, Xuepeng

2014-01-01

Besides the complete genome, different partial genomic sequences of Hepatitis E virus (HEV) have been used in genotyping studies, making it difficult to compare the results based on them. No commonly agreed partial region for HEV genotyping has been determined. In this study, we used a statistical method to evaluate the phylogenetic performance of each partial genomic sequence from a genome wide, by comparisons of evolutionary distances between genomic regions and the full-length genomes of 101 HEV isolates to identify short genomic regions that can reproduce HEV genotype assignments based on full-length genomes. Several genomic regions, especially one genomic region at the 3'-terminal of the papain-like cysteine protease domain, were detected to have relatively high phylogenetic correlations with the full-length genome. Phylogenetic analyses confirmed the identical performances between these regions and the full-length genome in genotyping, in which the HEV isolates involved could be divided into reasonable genotypes. This analysis may be of value in developing a partial sequence-based consensus classification of HEV species.

Application of resequencing to rice genomics, functional genomics and evolutionary analysis

PubMed Central

2014-01-01

Rice is a model system used for crop genomics studies. The completion of the rice genome draft sequences in 2002 not only accelerated functional genome studies, but also initiated a new era of resequencing rice genomes. Based on the reference genome in rice, next-generation sequencing (NGS) using the high-throughput sequencing system can efficiently accomplish whole genome resequencing of various genetic populations and diverse germplasm resources. Resequencing technology has been effectively utilized in evolutionary analysis, rice genomics and functional genomics studies. This technique is beneficial for both bridging the knowledge gap between genotype and phenotype and facilitating molecular breeding via gene design in rice. Here, we also discuss the limitation, application and future prospects of rice resequencing. PMID:25006357

OryzaGenome: Genome Diversity Database of Wild Oryza Species.

PubMed

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

2016-01-01

The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a text-based browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tab-delimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

GenomeVIP: a cloud platform for genomic variant discovery and interpretation

PubMed Central

Mashl, R. Jay; Scott, Adam D.; Huang, Kuan-lin; Wyczalkowski, Matthew A.; Yoon, Christopher J.; Niu, Beifang; DeNardo, Erin; Yellapantula, Venkata D.; Handsaker, Robert E.; Chen, Ken; Koboldt, Daniel C.; Ye, Kai; Fenyö, David; Raphael, Benjamin J.; Wendl, Michael C.; Ding, Li

2017-01-01

Identifying genomic variants is a fundamental first step toward the understanding of the role of inherited and acquired variation in disease. The accelerating growth in the corpus of sequencing data that underpins such analysis is making the data-download bottleneck more evident, placing substantial burdens on the research community to keep pace. As a result, the search for alternative approaches to the traditional “download and analyze” paradigm on local computing resources has led to a rapidly growing demand for cloud-computing solutions for genomics analysis. Here, we introduce the Genome Variant Investigation Platform (GenomeVIP), an open-source framework for performing genomics variant discovery and annotation using cloud- or local high-performance computing infrastructure. GenomeVIP orchestrates the analysis of whole-genome and exome sequence data using a set of robust and popular task-specific tools, including VarScan, GATK, Pindel, BreakDancer, Strelka, and Genome STRiP, through a web interface. GenomeVIP has been used for genomic analysis in large-data projects such as the TCGA PanCanAtlas and in other projects, such as the ICGC Pilots, CPTAC, ICGC-TCGA DREAM Challenges, and the 1000 Genomes SV Project. Here, we demonstrate GenomeVIP's ability to provide high-confidence annotated somatic, germline, and de novo variants of potential biological significance using publicly available data sets. PMID:28522612

Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy.

PubMed

Rittmann, Bruce E; Krajmalnik-Brown, Rosa; Halden, Rolf U

2008-08-01

Microorganisms can produce renewable energy in large quantities and without damaging the environment or disrupting food supply. The microbial communities must be robust and self-stabilizing, and their essential syntrophies must be managed. Pre-genomic, genomic and post-genomic tools can provide crucial information about the structure and function of these microbial communities. Applying these tools will help accelerate the rate at which microbial bioenergy processes move from intriguing science to real-world practice.

Decoding the genome beyond sequencing: the new phase of genomic research.

PubMed

Heng, Henry H Q; Liu, Guo; Stevens, Joshua B; Bremer, Steven W; Ye, Karen J; Abdallah, Batoul Y; Horne, Steven D; Ye, Christine J

2011-10-01

While our understanding of gene-based biology has greatly improved, it is clear that the function of the genome and most diseases cannot be fully explained by genes and other regulatory elements. Genes and the genome represent distinct levels of genetic organization with their own coding systems; Genes code parts like protein and RNA, but the genome codes the structure of genetic networks, which are defined by the whole set of genes, chromosomes and their topological interactions within a cell. Accordingly, the genetic code of DNA offers limited understanding of genome functions. In this perspective, we introduce the genome theory which calls for the departure of gene-centric genomic research. To make this transition for the next phase of genomic research, it is essential to acknowledge the importance of new genome-based biological concepts and to establish new technology platforms to decode the genome beyond sequencing. Copyright © 2011 Elsevier Inc. All rights reserved.

Genome Surfing As Driver of Microbial Genomic Diversity.

PubMed

Choudoir, Mallory J; Panke-Buisse, Kevin; Andam, Cheryl P; Buckley, Daniel H

2017-08-01

Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Genomic HyperBrowser: an analysis web server for genome-scale data

PubMed Central

Sandve, Geir K.; Gundersen, Sveinung; Johansen, Morten; Glad, Ingrid K.; Gunathasan, Krishanthi; Holden, Lars; Holden, Marit; Liestøl, Knut; Nygård, Ståle; Nygaard, Vegard; Paulsen, Jonas; Rydbeck, Halfdan; Trengereid, Kai; Clancy, Trevor; Drabløs, Finn; Ferkingstad, Egil; Kalaš, Matúš; Lien, Tonje; Rye, Morten B.; Frigessi, Arnoldo; Hovig, Eivind

2013-01-01

The immense increase in availability of genomic scale datasets, such as those provided by the ENCODE and Roadmap Epigenomics projects, presents unprecedented opportunities for individual researchers to pose novel falsifiable biological questions. With this opportunity, however, researchers are faced with the challenge of how to best analyze and interpret their genome-scale datasets. A powerful way of representing genome-scale data is as feature-specific coordinates relative to reference genome assemblies, i.e. as genomic tracks. The Genomic HyperBrowser (http://hyperbrowser.uio.no) is an open-ended web server for the analysis of genomic track data. Through the provision of several highly customizable components for processing and statistical analysis of genomic tracks, the HyperBrowser opens for a range of genomic investigations, related to, e.g., gene regulation, disease association or epigenetic modifications of the genome. PMID:23632163

The Genomic HyperBrowser: an analysis web server for genome-scale data.

PubMed

Sandve, Geir K; Gundersen, Sveinung; Johansen, Morten; Glad, Ingrid K; Gunathasan, Krishanthi; Holden, Lars; Holden, Marit; Liestøl, Knut; Nygård, Ståle; Nygaard, Vegard; Paulsen, Jonas; Rydbeck, Halfdan; Trengereid, Kai; Clancy, Trevor; Drabløs, Finn; Ferkingstad, Egil; Kalas, Matús; Lien, Tonje; Rye, Morten B; Frigessi, Arnoldo; Hovig, Eivind

2013-07-01

The immense increase in availability of genomic scale datasets, such as those provided by the ENCODE and Roadmap Epigenomics projects, presents unprecedented opportunities for individual researchers to pose novel falsifiable biological questions. With this opportunity, however, researchers are faced with the challenge of how to best analyze and interpret their genome-scale datasets. A powerful way of representing genome-scale data is as feature-specific coordinates relative to reference genome assemblies, i.e. as genomic tracks. The Genomic HyperBrowser (http://hyperbrowser.uio.no) is an open-ended web server for the analysis of genomic track data. Through the provision of several highly customizable components for processing and statistical analysis of genomic tracks, the HyperBrowser opens for a range of genomic investigations, related to, e.g., gene regulation, disease association or epigenetic modifications of the genome.

Fungal Genomics Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grigoriev, Igor

The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scalemore » genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.« less

Genome resequencing in Populus: Revealing large-scale genome variation and implications on specialized-trait genomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muchero, Wellington; Labbe, Jessy L; Priya, Ranjan

2014-01-01

To date, Populus ranks among a few plant species with a complete genome sequence and other highly developed genomic resources. With the first genome sequence among all tree species, Populus has been adopted as a suitable model organism for genomic studies in trees. However, far from being just a model species, Populus is a key renewable economic resource that plays a significant role in providing raw materials for the biofuel and pulp and paper industries. Therefore, aside from leading frontiers of basic tree molecular biology and ecological research, Populus leads frontiers in addressing global economic challenges related to fuel andmore » fiber production. The latter fact suggests that research aimed at improving quality and quantity of Populus as a raw material will likely drive the pursuit of more targeted and deeper research in order to unlock the economic potential tied in molecular biology processes that drive this tree species. Advances in genome sequence-driven technologies, such as resequencing individual genotypes, which in turn facilitates large scale SNP discovery and identification of large scale polymorphisms are key determinants of future success in these initiatives. In this treatise we discuss implications of genome sequence-enable technologies on Populus genomic and genetic studies of complex and specialized-traits.« less

Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome.

PubMed

Wang, Yi; Liu, Xianju; Ren, Chong; Zhong, Gan-Yuan; Yang, Long; Li, Shaohua; Liang, Zhenchang

2016-04-21

CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of humans, animals, microorganisms, and plants. Success of such genome editing is highly dependent on the availability of suitable target sites in the genomes to be edited. Many specific target sites for CRISPR/Cas9 have been computationally identified for several annual model and crop species, but such sites have not been reported for perennial, woody fruit species. In this study, we identified and characterized five types of CRISPR/Cas9 target sites in the widely cultivated grape species Vitis vinifera and developed a user-friendly database for editing grape genomes in the future. A total of 35,767,960 potential CRISPR/Cas9 target sites were identified from grape genomes in this study. Among them, 22,597,817 target sites were mapped to specific genomic locations and 7,269,788 were found to be highly specific. Protospacers and PAMs were found to distribute uniformly and abundantly in the grape genomes. They were present in all the structural elements of genes with the coding region having the highest abundance. Five PAM types, TGG, AGG, GGG, CGG and NGG, were observed. With the exception of the NGG type, they were abundantly present in the grape genomes. Synteny analysis of similar genes revealed that the synteny of protospacers matched the synteny of homologous genes. A user-friendly database containing protospacers and detailed information of the sites was developed and is available for public use at the Grape-CRISPR website ( http://biodb.sdau.edu.cn/gc/index.html ). Grape genomes harbour millions of potential CRISPR/Cas9 target sites. These sites are widely distributed among and within chromosomes with predominant abundance in the coding regions of genes. We developed a publicly-accessible Grape-CRISPR database for facilitating the use of the CRISPR/Cas9 system as a genome editing tool for functional studies and molecular breeding of grapes. Among

Genome projects and the functional-genomic era.

PubMed

Sauer, Sascha; Konthur, Zoltán; Lehrach, Hans

2005-12-01

The problems we face today in public health as a result of the -- fortunately -- increasing age of people and the requirements of developing countries create an urgent need for new and innovative approaches in medicine and in agronomics. Genomic and functional genomic approaches have a great potential to at least partially solve these problems in the future. Important progress has been made by procedures to decode genomic information of humans, but also of other key organisms. The basic comprehension of genomic information (and its transfer) should now give us the possibility to pursue the next important step in life science eventually leading to a basic understanding of biological information flow; the elucidation of the function of all genes and correlative products encoded in the genome, as well as the discovery of their interactions in a molecular context and the response to environmental factors. As a result of the sequencing projects, we are now able to ask important questions about sequence variation and can start to comprehensively study the function of expressed genes on different levels such as RNA, protein or the cell in a systematic context including underlying networks. In this article we review and comment on current trends in large-scale systematic biological research. A particular emphasis is put on technology developments that can provide means to accomplish the tasks of future lines of functional genomics.

GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.

PubMed

Yuan, Lina; Yu, Yang; Zhu, Yanmin; Li, Yulai; Li, Changqing; Li, Rujiao; Ma, Qin; Siu, Gilman Kit-Hang; Yu, Jun; Jiang, Taijiao; Xiao, Jingfa; Kang, Yu

2017-01-25

Next-generation sequencing (NGS) technologies have greatly promoted the genomic study of prokaryotes. However, highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining insights into the genome biology. Reference-assisted tools are promising in genome assembly, but tend to result in false assembly when the assigned reference has extensive rearrangements. Herein, we present GAAP, a genome assembly pipeline for scaffolding based on core-gene-defined Genome Organizational Framework (cGOF) described in our previous study. Instead of assigning references, we use the multiple-reference-derived cGOFs as indexes to assist in order and orientation of the scaffolds and build a skeleton structure, and then use read pairs to extend scaffolds, called local scaffolding, and distinguish between true and chimeric adjacencies in the scaffolds. In our performance tests using both empirical and simulated data of 15 genomes in six species with diverse genome size, complexity, and all three categories of cGOFs, GAAP outcompetes or achieves comparable results when compared to three other reference-assisted programs, AlignGraph, Ragout and MeDuSa. GAAP uses both cGOF and pair-end reads to create assemblies in genomic scale, and performs better than the currently available reference-assisted assembly tools as it recovers more assemblies and makes fewer false locations, especially for species with extensive rearranged genomes. Our method is a promising solution for reconstruction of genome sequence from short reads of NGS.

Genomes as geography: using GIS technology to build interactive genome feature maps

PubMed Central

Dolan, Mary E; Holden, Constance C; Beard, M Kate; Bult, Carol J

2006-01-01

Background Many commonly used genome browsers display sequence annotations and related attributes as horizontal data tracks that can be toggled on and off according to user preferences. Most genome browsers use only simple keyword searches and limit the display of detailed annotations to one chromosomal region of the genome at a time. We have employed concepts, methodologies, and tools that were developed for the display of geographic data to develop a Genome Spatial Information System (GenoSIS) for displaying genomes spatially, and interacting with genome annotations and related attribute data. In contrast to the paradigm of horizontally stacked data tracks used by most genome browsers, GenoSIS uses the concept of registered spatial layers composed of spatial objects for integrated display of diverse data. In addition to basic keyword searches, GenoSIS supports complex queries, including spatial queries, and dynamically generates genome maps. Our adaptation of the geographic information system (GIS) model in a genome context supports spatial representation of genome features at multiple scales with a versatile and expressive query capability beyond that supported by existing genome browsers. Results We implemented an interactive genome sequence feature map for the mouse genome in GenoSIS, an application that uses ArcGIS, a commercially available GIS software system. The genome features and their attributes are represented as spatial objects and data layers that can be toggled on and off according to user preferences or displayed selectively in response to user queries. GenoSIS supports the generation of custom genome maps in response to complex queries about genome features based on both their attributes and locations. Our example application of GenoSIS to the mouse genome demonstrates the powerful visualization and query capability of mature GIS technology applied in a novel domain. Conclusion Mapping tools developed specifically for geographic data can be

Population Genomics of Infectious and Integrated Wolbachia pipientis Genomes in Drosophila ananassae

PubMed Central

Choi, Jae Young; Bubnell, Jaclyn E.; Aquadro, Charles F.

2015-01-01

Coevolution between Drosophila and its endosymbiont Wolbachia pipientis has many intriguing aspects. For example, Drosophila ananassae hosts two forms of W. pipientis genomes: One being the infectious bacterial genome and the other integrated into the host nuclear genome. Here, we characterize the infectious and integrated genomes of W. pipientis infecting D. ananassae (wAna), by genome sequencing 15 strains of D. ananassae that have either the infectious or integrated wAna genomes. Results indicate evolutionarily stable maternal transmission for the infectious wAna genome suggesting a relatively long-term coevolution with its host. In contrast, the integrated wAna genome showed pseudogene-like characteristics accumulating many variants that are predicted to have deleterious effects if present in an infectious bacterial genome. Phylogenomic analysis of sequence variation together with genotyping by polymerase chain reaction of large structural variations indicated several wAna variants among the eight infectious wAna genomes. In contrast, only a single wAna variant was found among the seven integrated wAna genomes examined in lines from Africa, south Asia, and south Pacific islands suggesting that the integration occurred once from a single infectious wAna genome and then spread geographically. Further analysis revealed that for all D. ananassae we examined with the integrated wAna genomes, the majority of the integrated wAna genomic regions is represented in at least two copies suggesting a double integration or single integration followed by an integrated genome duplication. The possible evolutionary mechanism underlying the widespread geographical presence of the duplicate integration of the wAna genome is an intriguing question remaining to be answered. PMID:26254486

Dramatic improvement in genome assembly achieved using doubled-haploid genomes.

PubMed

Zhang, Hong; Tan, Engkong; Suzuki, Yutaka; Hirose, Yusuke; Kinoshita, Shigeharu; Okano, Hideyuki; Kudoh, Jun; Shimizu, Atsushi; Saito, Kazuyoshi; Watabe, Shugo; Asakawa, Shuichi

2014-10-27

Improvement in de novo assembly of large genomes is still to be desired. Here, we improved draft genome sequence quality by employing doubled-haploid individuals. We sequenced wildtype and doubled-haploid Takifugu rubripes genomes, under the same conditions, using the Illumina platform and assembled contigs with SOAPdenovo2. We observed 5.4-fold and 2.6-fold improvement in the sizes of the N50 contig and scaffold of doubled-haploid individuals, respectively, compared to the wildtype, indicating that the use of a doubled-haploid genome aids in accurate genome analysis.

WheatGenome.info: an integrated database and portal for wheat genome information.

PubMed

Lai, Kaitao; Berkman, Paul J; Lorenc, Michal Tadeusz; Duran, Chris; Smits, Lars; Manoli, Sahana; Stiller, Jiri; Edwards, David

2012-02-01

Bread wheat (Triticum aestivum) is one of the most important crop plants, globally providing staple food for a large proportion of the human population. However, improvement of this crop has been limited due to its large and complex genome. Advances in genomics are supporting wheat crop improvement. We provide a variety of web-based systems hosting wheat genome and genomic data to support wheat research and crop improvement. WheatGenome.info is an integrated database resource which includes multiple web-based applications. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second-generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This system includes links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/.

Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species.

PubMed

Hirao, Tomonori; Watanabe, Atsushi; Kurita, Manabu; Kondo, Teiji; Takata, Katsuhiko

2008-06-23

The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, Cycas taitungensis, Pinus thunbergii, and Pinus koraiensis have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of Cryptomeria japonica, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms. The C. japonica cp genome is 131,810 bp in length, with 112 single copy genes and two duplicated (trnI-CAU, trnQ-UUG) genes that give a total of 116 genes. Compared to other land plant cp genomes, the C. japonica cp has lost one of the relevant large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperms, such as Cycas and Gingko, and additionally has completely lost its trnR-CCG, partially lost its trnT-GGU, and shows diversification of accD. The genomic structure of the C. japonica cp genome also differs significantly from those of other plant species. For example, we estimate that a minimum of 15 inversions would be required to transform the gene organization of the Pinus thunbergii cp genome into that of C. japonica. In the C. japonica cp genome, direct repeat and inverted repeat sequences are observed at the inversion and translocation endpoints, and these sequences may be associated with the genomic rearrangements. The observed differences in genomic structure between C. japonica and other land plants, including pines, strongly support the

Personal genomics services: whose genomes?

PubMed

Gurwitz, David; Bregman-Eschet, Yael

2009-07-01

New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

Insights into structural variations and genome rearrangements in prokaryotic genomes.

PubMed

Periwal, Vinita; Scaria, Vinod

2015-01-01

Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Schistosoma comparative genomics: integrating genome structure, parasite biology and anthelmintic discovery

PubMed Central

Swain, Martin T.; Larkin, Denis M.; Caffrey, Conor R.; Davies, Stephen J.; Loukas, Alex; Skelly, Patrick J.; Hoffmann, Karl F.

2011-01-01

Schistosoma genomes provide a comprehensive resource for identifying the molecular processes that shape parasite evolution and for discovering novel chemotherapeutic or immunoprophylactic targets. Here, we demonstrate how intra- and intergenus comparative genomics can be used to drive these investigations forward, illustrate the advantages and limitations of these approaches and review how post genomic technologies offer complementary strategies for genome characterisation. While sequencing and functional characterisation of other schistosome/platyhelminth genomes continues to expedite anthelmintic discovery, we contend that future priorities should equally focus on improving assembly quality, and chromosomal assignment, of existing schistosome/platyhelminth genomes. PMID:22024648

Short and long-term genome stability analysis of prokaryotic genomes.

PubMed

Brilli, Matteo; Liò, Pietro; Lacroix, Vincent; Sagot, Marie-France

2013-05-08

Gene organization dynamics is actively studied because it provides useful evolutionary information, makes functional annotation easier and often enables to characterize pathogens. There is therefore a strong interest in understanding the variability of this trait and the possible correlations with life-style. Two kinds of events affect genome organization: on one hand translocations and recombinations change the relative position of genes shared by two genomes (i.e. the backbone gene order); on the other, insertions and deletions leave the backbone gene order unchanged but they alter the gene neighborhoods by breaking the syntenic regions. A complete picture about genome organization evolution therefore requires to account for both kinds of events. We developed an approach where we model chromosomes as graphs on which we compute different stability estimators; we consider genome rearrangements as well as the effect of gene insertions and deletions. In a first part of the paper, we fit a measure of backbone gene order conservation (hereinafter called backbone stability) against phylogenetic distance for over 3000 genome comparisons, improving existing models for the divergence in time of backbone stability. Intra- and inter-specific comparisons were treated separately to focus on different time-scales. The use of multiple genomes of a same species allowed to identify genomes with diverging gene order with respect to their conspecific. The inter-species analysis indicates that pathogens are more often unstable with respect to non-pathogens. In a second part of the text, we show that in pathogens, gene content dynamics (insertions and deletions) have a much more dramatic effect on genome organization stability than backbone rearrangements. In this work, we studied genome organization divergence taking into account the contribution of both genome order rearrangements and genome content dynamics. By studying species with multiple sequenced genomes available, we were

Rapid construction of genome map for large yellow croaker (Larimichthys crocea) by the whole-genome mapping in BioNano Genomics Irys system.

PubMed

Xiao, Shijun; Li, Jiongtang; Ma, Fengshou; Fang, Lujing; Xu, Shuangbin; Chen, Wei; Wang, Zhi Yong

2015-09-03

Large yellow croaker (Larimichthys crocea) is an important commercial fish in China and East-Asia. The annual product of the species from the aqua-farming industry is about 90 thousand tons. In spite of its economic importance, genetic studies of economic traits and genomic selections of the species are hindered by the lack of genomic resources. Specifically, a whole-genome physical map of large yellow croaker is still missing. The traditional BAC-based fingerprint method is extremely time- and labour-consuming. Here we report the first genome map construction using the high-throughput whole-genome mapping technique by nanochannel arrays in BioNano Genomics Irys system. For an optimal marker density of ~10 per 100 kb, the nicking endonuclease Nt.BspQ1 was chosen for the genome map generation. 645,305 DNA molecules with a total length of ~112 Gb were labelled and detected, covering more than 160X of the large yellow croaker genome. Employing IrysView package and signature patterns in raw DNA molecules, a whole-genome map of large yellow croaker was assembled into 686 maps with a total length of 727 Mb, which was consistent with the estimated genome size. The N50 length of the whole-genome map, including 126 maps, was up to 1.7 Mb. The excellent hybrid alignment with large yellow croaker draft genome validated the consensus genome map assembly and highlighted a promising application of whole-genome mapping on draft genome sequence super-scaffolding. The genome map data of large yellow croaker are accessible on lycgenomics.jmu.edu.cn/pm. Using the state-of-the-art whole-genome mapping technique in Irys system, the first whole-genome map for large yellow croaker has been constructed and thus highly facilitates the ongoing genomic and evolutionary studies for the species. To our knowledge, this is the first public report on genome map construction by the whole-genome mapping for aquatic-organisms. Our study demonstrates a promising application of the whole-genome

Translational genomics for plant breeding with the genome sequence explosion.

PubMed

Kang, Yang Jae; Lee, Taeyoung; Lee, Jayern; Shim, Sangrea; Jeong, Haneul; Satyawan, Dani; Kim, Moon Young; Lee, Suk-Ha

2016-04-01

The use of next-generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies. © 2015 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Deep whole-genome sequencing of 90 Han Chinese genomes.

PubMed

Lan, Tianming; Lin, Haoxiang; Zhu, Wenjuan; Laurent, Tellier Christian Asker Melchior; Yang, Mengcheng; Liu, Xin; Wang, Jun; Wang, Jian; Yang, Huanming; Xu, Xun; Guo, Xiaosen

2017-09-01

Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants. Although whole-exome sequencing is also a viable choice for exome regions, it cannot account for noncoding regions, sometimes resulting in the absence of important, causal variants. For Han Chinese populations, the majority of variants have been discovered based upon low-coverage data from the 1000 Genomes Project. However, high-coverage, whole-genome sequencing data are limited for any population, and a large amount of low-frequency, population-specific variants remain uncharacterized. We have performed whole-genome sequencing at a high depth (∼×80) of 90 unrelated individuals of Chinese ancestry, collected from the 1000 Genomes Project samples, including 45 Northern Han Chinese and 45 Southern Han Chinese samples. Eighty-three of these 90 have been sequenced by the 1000 Genomes Project. We have identified 12 568 804 single nucleotide polymorphisms, 2 074 210 short InDels, and 26 142 structural variations from these 90 samples. Compared to the Han Chinese data from the 1000 Genomes Project, we have found 7 000 629 novel variants with low frequency (defined as minor allele frequency < 5%), including 5 813 503 single nucleotide polymorphisms, 1 169 199 InDels, and 17 927 structural variants. Using deep sequencing data, we have built a greatly expanded spectrum of genetic variation for the Han Chinese genome. Compared to the 1000 Genomes Project, these Han Chinese deep sequencing data enhance the

Whole-genome alignment.

PubMed

Dewey, Colin N

2012-01-01

Whole-genome alignment (WGA) is the prediction of evolutionary relationships at the nucleotide level between two or more genomes. It combines aspects of both colinear sequence alignment and gene orthology prediction, and is typically more challenging to address than either of these tasks due to the size and complexity of whole genomes. Despite the difficulty of this problem, numerous methods have been developed for its solution because WGAs are valuable for genome-wide analyses, such as phylogenetic inference, genome annotation, and function prediction. In this chapter, we discuss the meaning and significance of WGA and present an overview of the methods that address it. We also examine the problem of evaluating whole-genome aligners and offer a set of methodological challenges that need to be tackled in order to make the most effective use of our rapidly growing databases of whole genomes.

Genomic Data Commons and Genomic Cloud Pilots - Google Hangout

Cancer.gov

Join us for a live, moderated discussion about two NCI efforts to expand access to cancer genomics data: the Genomic Data Commons and Genomic Cloud Pilots. NCI subject matters experts will include Louis M. Staudt, M.D., Ph.D., Director Center for Cancer Genomics, Warren Kibbe, Ph.D., Director, NCI Center for Biomedical Informatics and Information Technology, and moderated by Anthony Kerlavage, Ph.D., Chief, Cancer Informatics Branch, Center for Biomedical Informatics and Information Technology. We welcome your questions before and during the Hangout on Twitter using the hashtag #AskNCI.

Structural Genomics: Correlation Blocks, Population Structure, and Genome Architecture

PubMed Central

Hu, Xin-Sheng; Yeh, Francis C.; Wang, Zhiquan

2011-01-01

An integration of the pattern of genome-wide inter-site associations with evolutionary forces is important for gaining insights into the genomic evolution in natural or artificial populations. Here, we assess the inter-site correlation blocks and their distributions along chromosomes. A correlation block is broadly termed as the DNA segment within which strong correlations exist between genetic diversities at any two sites. We bring together the population genetic structure and the genomic diversity structure that have been independently built on different scales and synthesize the existing theories and methods for characterizing genomic structure at the population level. We discuss how population structure could shape correlation blocks and their patterns within and between populations. Effects of evolutionary forces (selection, migration, genetic drift, and mutation) on the pattern of genome-wide correlation blocks are discussed. In eukaryote organisms, we briefly discuss the associations between the pattern of correlation blocks and genome assembly features in eukaryote organisms, including the impacts of multigene family, the perturbation of transposable elements, and the repetitive nongenic sequences and GC-rich isochores. Our reviews suggest that the observable pattern of correlation blocks can refine our understanding of the ecological and evolutionary processes underlying the genomic evolution at the population level. PMID:21886455

The genomes and comparative genomics of Lactobacillus delbrueckii phages.

PubMed

Riipinen, Katja-Anneli; Forsman, Päivi; Alatossava, Tapani

2011-07-01

Lactobacillus delbrueckii phages are a great source of genetic diversity. Here, the genome sequences of Lb. delbrueckii phages LL-Ku, c5 and JCL1032 were analyzed in detail, and the genetic diversity of Lb. delbrueckii phages belonging to different taxonomic groups was explored. The lytic isometric group b phages LL-Ku (31,080 bp) and c5 (31,841 bp) showed a minimum nucleotide sequence identity of 90% over about three-fourths of their genomes. The genomic locations of their lysis modules were unique, and the genomes featured several putative overlapping transcription units of genes. LL-Ku and c5 virions displayed peptidoglycan hydrolytic activity associated with a ~36-kDa protein similar in size to the endolysin. Unexpectedly, the 49,433-bp genome of the prolate phage JCL1032 (temperate, group c) revealed a conserved gene order within its structural genes. Lb. delbrueckii phages representing groups a (a phage LL-H), b and c possessed only limited protein sequence homology. Genomic comparison of LL-Ku and c5 suggested that diversification of Lb. delbrueckii phages is mainly due to insertions, deletions and recombination. For the first time, the complete genome sequences of group b and c Lb. delbrueckii phages are reported.

Evolution of genome size and genomic GC content in carnivorous holokinetics (Droseraceae).

PubMed

Veleba, Adam; Šmarda, Petr; Zedek, František; Horová, Lucie; Šmerda, Jakub; Bureš, Petr

2017-02-01

Studies in the carnivorous family Lentibulariaceae in the last years resulted in the discovery of the smallest plant genomes and an unusual pattern of genomic GC content evolution. However, scarcity of genomic data in other carnivorous clades still prevents a generalization of the observed patterns. Here the aim was to fill this gap by mapping genome evolution in the second largest carnivorous family, Droseraceae, where this evolution may be affected by chromosomal holokinetism in Drosera METHODS: The genome size and genomic GC content of 71 Droseraceae species were measured by flow cytometry. A dated phylogeny was constructed, and the evolution of both genomic parameters and their relationship to species climatic niches were tested using phylogeny-based statistics. The 2C genome size of Droseraceae varied between 488 and 10 927 Mbp, and the GC content ranged between 37·1 and 44·7 %. The genome sizes and genomic GC content of carnivorous and holocentric species did not differ from those of their non-carnivorous and monocentric relatives. The genomic GC content positively correlated with genome size and annual temperature fluctuations. The genome size and chromosome numbers were inversely correlated in the Australian clade of Drosera CONCLUSIONS: Our results indicate that neither carnivory (nutrient scarcity) nor the holokinetism have a prominent effect on size and DNA base composition of Droseraceae genomes. However, the holokinetic drive seems to affect karyotype evolution in one of the major clades of Drosera Our survey confirmed that the evolution of GC content is tightly connected with the evolution of genome size and also with environmental conditions. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Rewriting the blueprint of life by synthetic genomics and genome engineering.

PubMed

Annaluru, Narayana; Ramalingam, Sivaprakash; Chandrasegaran, Srinivasan

2015-06-16

Advances in DNA synthesis and assembly methods over the past decade have made it possible to construct genome-size fragments from oligonucleotides. Early work focused on synthesis of small viral genomes, followed by hierarchical synthesis of wild-type bacterial genomes and subsequently on transplantation of synthesized bacterial genomes into closely related recipient strains. More recently, a synthetic designer version of yeast Saccharomyces cerevisiae chromosome III has been generated, with numerous changes from the wild-type sequence without having an impact on cell fitness and phenotype, suggesting plasticity of the yeast genome. A project to generate the first synthetic yeast genome--the Sc2.0 Project--is currently underway.

Genome-wide characterization of centromeric satellites from multiple mammalian genomes.

PubMed

Alkan, Can; Cardone, Maria Francesca; Catacchio, Claudia Rita; Antonacci, Francesca; O'Brien, Stephen J; Ryder, Oliver A; Purgato, Stefania; Zoli, Monica; Della Valle, Giuliano; Eichler, Evan E; Ventura, Mario

2011-01-01

Despite its importance in cell biology and evolution, the centromere has remained the final frontier in genome assembly and annotation due to its complex repeat structure. However, isolation and characterization of the centromeric repeats from newly sequenced species are necessary for a complete understanding of genome evolution and function. In recent years, various genomes have been sequenced, but the characterization of the corresponding centromeric DNA has lagged behind. Here, we present a computational method (RepeatNet) to systematically identify higher-order repeat structures from unassembled whole-genome shotgun sequence and test whether these sequence elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes. Our analysis revealed the greatest diversity of centromeric sequences in horse and dog in contrast to elephant and armadillo, which showed high-centromeric sequence homogeneity. We could not isolate centromeric sequences within the platypus genome, suggesting that centromeres in platypus are not enriched in satellite DNA. Our method can be applied to the characterization of thousands of other vertebrate genomes anticipated for sequencing in the near future, providing an important tool for annotation of centromeres.

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.

PubMed

Mende, Daniel R; Letunic, Ivica; Huerta-Cepas, Jaime; Li, Simone S; Forslund, Kristoffer; Sunagawa, Shinichi; Bork, Peer

2017-01-04

The availability of microbial genomes has opened many new avenues of research within microbiology. This has been driven primarily by comparative genomics approaches, which rely on accurate and consistent characterization of genomic sequences. It is nevertheless difficult to obtain consistent taxonomic and integrated functional annotations for defined prokaryotic clades. Thus, we developed proGenomes, a resource that provides user-friendly access to currently 25 038 high-quality genomes whose sequences and consistent annotations can be retrieved individually or by taxonomic clade. These genomes are assigned to 5306 consistent and accurate taxonomic species clusters based on previously established methodology. proGenomes also contains functional information for almost 80 million protein-coding genes, including a comprehensive set of general annotations and more focused annotations for carbohydrate-active enzymes and antibiotic resistance genes. Additionally, broad habitat information is provided for many genomes. All genomes and associated information can be downloaded by user-selected clade or multiple habitat-specific sets of representative genomes. We expect that the availability of high-quality genomes with comprehensive functional annotations will promote advances in clinical microbial genomics, functional evolution and other subfields of microbiology. proGenomes is available at http://progenomes.embl.de. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Brief Guide to Genomics: DNA, Genes and Genomes

MedlinePlus

... Sheets A Brief Guide to Genomics About NHGRI Research About the International HapMap Project Biological Pathways Chromosome Abnormalities Chromosomes Cloning Comparative Genomics DNA Microarray Technology DNA Sequencing Deoxyribonucleic Acid ( ...

Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria.

PubMed

Zhao, Meicheng; Zhi, Hui; Doust, Andrew N; Li, Wei; Wang, Yongfang; Li, Haiquan; Jia, Guanqing; Wang, Yongqiang; Zhang, Ning; Diao, Xianmin

2013-04-11

The Setaria genus is increasingly of interest to researchers, as its two species, S. viridis and S. italica, are being developed as models for understanding C4 photosynthesis and plant functional genomics. The genome constitution of Setaria species has been studied in the diploid species S. viridis, S. adhaerans and S. grisebachii, where three genomes A, B and C were identified respectively. Two allotetraploid species, S. verticillata and S. faberi, were found to have AABB genomes, and one autotetraploid species, S. queenslandica, with an AAAA genome, has also been identified. The genomes and genome constitutions of most other species remain unknown, even though it was thought there are approximately 125 species in the genus distributed world-wide. GISH was performed to detect the genome constitutions of Eurasia species of S. glauca, S. plicata, and S. arenaria, with the known A, B and C genomes as probes. No or very poor hybridization signal was detected indicating that their genomes are different from those already described. GISH was also performed reciprocally between S. glauca, S. plicata, and S. arenaria genomes, but no hybridization signals between each other were found. The two sets of chromosomes of S. lachnea both hybridized strong signals with only the known C genome of S. grisebachii. Chromosomes of Qing 9, an accession formerly considered as S. viridis, hybridized strong signal only to B genome of S. adherans. Phylogenetic trees constructed with 5S rDNA and knotted1 markers, clearly classify the samples in this study into six clusters, matching the GISH results, and suggesting that the F genome of S. arenaria is basal in the genus. Three novel genomes in the Setaria genus were identified and designated as genome D (S. glauca), E (S. plicata) and F (S. arenaria) respectively. The genome constitution of tetraploid S. lachnea is putatively CCC'C'. Qing 9 is a B genome species indigenous to China and is hypothesized to be a newly identified species. The

Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria

PubMed Central

2013-01-01

Background The Setaria genus is increasingly of interest to researchers, as its two species, S. viridis and S. italica, are being developed as models for understanding C4 photosynthesis and plant functional genomics. The genome constitution of Setaria species has been studied in the diploid species S. viridis, S. adhaerans and S. grisebachii, where three genomes A, B and C were identified respectively. Two allotetraploid species, S. verticillata and S. faberi, were found to have AABB genomes, and one autotetraploid species, S. queenslandica, with an AAAA genome, has also been identified. The genomes and genome constitutions of most other species remain unknown, even though it was thought there are approximately 125 species in the genus distributed world-wide. Results GISH was performed to detect the genome constitutions of Eurasia species of S. glauca, S. plicata, and S. arenaria, with the known A, B and C genomes as probes. No or very poor hybridization signal was detected indicating that their genomes are different from those already described. GISH was also performed reciprocally between S. glauca, S. plicata, and S. arenaria genomes, but no hybridization signals between each other were found. The two sets of chromosomes of S. lachnea both hybridized strong signals with only the known C genome of S. grisebachii. Chromosomes of Qing 9, an accession formerly considered as S. viridis, hybridized strong signal only to B genome of S. adherans. Phylogenetic trees constructed with 5S rDNA and knotted1 markers, clearly classify the samples in this study into six clusters, matching the GISH results, and suggesting that the F genome of S. arenaria is basal in the genus. Conclusions Three novel genomes in the Setaria genus were identified and designated as genome D (S. glauca), E (S. plicata) and F (S. arenaria) respectively. The genome constitution of tetraploid S. lachnea is putatively CCC’C’. Qing 9 is a B genome species indigenous to China and is hypothesized to be

Ensembl Genomes 2013: scaling up access to genome-wide data

USDA-ARS?s Scientific Manuscript database

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provi...

Bacterial Genome Instability

PubMed Central

Darmon, Elise

2014-01-01

SUMMARY Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease. PMID:24600039

Genome-derived vaccines.

PubMed

De Groot, Anne S; Rappuoli, Rino

2004-02-01

Vaccine research entered a new era when the complete genome of a pathogenic bacterium was published in 1995. Since then, more than 97 bacterial pathogens have been sequenced and at least 110 additional projects are now in progress. Genome sequencing has also dramatically accelerated: high-throughput facilities can draft the sequence of an entire microbe (two to four megabases) in 1 to 2 days. Vaccine developers are using microarrays, immunoinformatics, proteomics and high-throughput immunology assays to reduce the truly unmanageable volume of information available in genome databases to a manageable size. Vaccines composed by novel antigens discovered from genome mining are already in clinical trials. Within 5 years we can expect to see a novel class of vaccines composed by genome-predicted, assembled and engineered T- and Bcell epitopes. This article addresses the convergence of three forces--microbial genome sequencing, computational immunology and new vaccine technologies--that are shifting genome mining for vaccines onto the forefront of immunology research.

Comparative genomics of Lactobacillus

PubMed Central

Kant, Ravi; Blom, Jochen; Palva, Airi; Siezen, Roland J.; de Vos, Willem M.

2011-01-01

Summary The genus Lactobacillus includes a diverse group of bacteria consisting of many species that are associated with fermentations of plants, meat or milk. In addition, various lactobacilli are natural inhabitants of the intestinal tract of humans and other animals. Finally, several Lactobacillus strains are marketed as probiotics as their consumption can confer a health benefit to host. Presently, 154 Lactobacillus species are known and a growing fraction of these are subject to draft genome sequencing. However, complete genome sequences are needed to provide a platform for detailed genomic comparisons. Therefore, we selected a total of 20 genomes of various Lactobacillus strains for which complete genomic sequences have been reported. These genomes had sizes varying from 1.8 to 3.3 Mb and other characteristic features, such as G+C content that ranged from 33% to 51%. The Lactobacillus pan genome was found to consist of approximately 14 000 protein‐encoding genes while all 20 genomes shared a total of 383 sets of orthologous genes that defined the Lactobacillus core genome (LCG). Based on advanced phylogeny of the proteins encoded by this LCG, we grouped the 20 strains into three main groups and defined core group genes present in all genomes of a single group, signature group genes shared in all genomes of one group but absent in all other Lactobacillus genomes, and Group‐specific ORFans present in core group genes of one group and absent in all other complete genomes. The latter are of specific value in defining the different groups of genomes. The study provides a platform for present individual comparisons as well as future analysis of new Lactobacillus genomes. PMID:21375712

PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

PubMed Central

Fong, Christine; Rohmer, Laurence; Radey, Matthew; Wasnick, Michael; Brittnacher, Mitchell J

2008-01-01

Background The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT) is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes. Results PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function. Conclusion PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any web browser with no client

Inverse Symmetry in Complete Genomes and Whole-Genome Inverse Duplication

PubMed Central

Kong, Sing-Guan; Fan, Wen-Lang; Chen, Hong-Da; Hsu, Zi-Ting; Zhou, Nengji; Zheng, Bo; Lee, Hoong-Chien

2009-01-01

The cause of symmetry is usually subtle, and its study often leads to a deeper understanding of the bearer of the symmetry. To gain insight into the dynamics driving the growth and evolution of genomes, we conducted a comprehensive study of textual symmetries in 786 complete chromosomes. We focused on symmetry based on our belief that, in spite of their extreme diversity, genomes must share common dynamical principles and mechanisms that drive their growth and evolution, and that the most robust footprints of such dynamics are symmetry related. We found that while complement and reverse symmetries are essentially absent in genomic sequences, inverse–complement plus reverse–symmetry is prevalent in complex patterns in most chromosomes, a vast majority of which have near maximum global inverse symmetry. We also discovered relations that can quantitatively account for the long observed but unexplained phenomenon of -mer skews in genomes. Our results suggest segmental and whole-genome inverse duplications are important mechanisms in genome growth and evolution, probably because they are efficient means by which the genome can exploit its double-stranded structure to enrich its code-inventory. PMID:19898631

Genomic Data Commons | Office of Cancer Genomics

Cancer.gov

The NCI’s Center for Cancer Genomics launches the Genomic Data Commons (GDC), a unified data sharing platform for the cancer research community. The mission of the GDC is to enable data sharing across the entire cancer research community, to ultimately support precision medicine in oncology.

Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuo, Alan; Grigoriev, Igor

2009-04-17

Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentousmore » ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.« less

Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays.

PubMed

Mak, Angel C Y; Lai, Yvonne Y Y; Lam, Ernest T; Kwok, Tsz-Piu; Leung, Alden K Y; Poon, Annie; Mostovoy, Yulia; Hastie, Alex R; Stedman, William; Anantharaman, Thomas; Andrews, Warren; Zhou, Xiang; Pang, Andy W C; Dai, Heng; Chu, Catherine; Lin, Chin; Wu, Jacob J K; Li, Catherine M L; Li, Jing-Woei; Yim, Aldrin K Y; Chan, Saki; Sibert, Justin; Džakula, Željko; Cao, Han; Yiu, Siu-Ming; Chan, Ting-Fung; Yip, Kevin Y; Xiao, Ming; Kwok, Pui-Yan

2016-01-01

Comprehensive whole-genome structural variation detection is challenging with current approaches. With diploid cells as DNA source and the presence of numerous repetitive elements, short-read DNA sequencing cannot be used to detect structural variation efficiently. In this report, we show that genome mapping with long, fluorescently labeled DNA molecules imaged on nanochannel arrays can be used for whole-genome structural variation detection without sequencing. While whole-genome haplotyping is not achieved, local phasing (across >150-kb regions) is routine, as molecules from the parental chromosomes are examined separately. In one experiment, we generated genome maps from a trio from the 1000 Genomes Project, compared the maps against that derived from the reference human genome, and identified structural variations that are >5 kb in size. We find that these individuals have many more structural variants than those published, including some with the potential of disrupting gene function or regulation. Copyright © 2016 by the Genetics Society of America.

JGI Fungal Genomics Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grigoriev, Igor V.

2011-03-14

Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functionalmore » genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here« less

Genomic Encyclopedia of Fungi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grigoriev, Igor

Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supportedmore » by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.« less

The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes.

PubMed

Mao, Qing; Ciotlos, Serban; Zhang, Rebecca Yu; Ball, Madeleine P; Chin, Robert; Carnevali, Paolo; Barua, Nina; Nguyen, Staci; Agarwal, Misha R; Clegg, Tom; Connelly, Abram; Vandewege, Ward; Zaranek, Alexander Wait; Estep, Preston W; Church, George M; Drmanac, Radoje; Peters, Brock A

2016-10-11

Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. However, most of these were sequenced without experimental haplotype data and are therefore missing an important aspect of genome biology. In addition, much of the genomic data is not available to the public and lacks phenotypic information. As part of the Personal Genome Project, blood samples from 184 participants were collected and processed using Complete Genomics' Long Fragment Read technology. Here, we present the experimental whole genome haplotyping and sequencing of these samples to an average read coverage depth of 100X. This is approximately three-fold higher than the read coverage applied to most whole human genome assemblies and ensures the highest quality results. Currently, 114 genomes from this dataset are freely available in the GigaDB repository and are associated with rich phenotypic data; the remaining 70 should be added in the near future as they are approved through the PGP data release process. For reproducibility analyses, 20 genomes were sequenced at least twice using independent LFR barcoded libraries. Seven genomes were also sequenced using Complete Genomics' standard non-barcoded library process. In addition, we report 2.6 million high-quality, rare variants not previously identified in the Single Nucleotide Polymorphisms database or the 1000 Genomes Project Phase 3 data. These genomes represent a unique source of haplotype and phenotype data for the scientific community and should help to expand our understanding of human genome evolution and function.

Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia.

PubMed

Campbell, Matthew A; Van Leuven, James T; Meister, Russell C; Carey, Kaitlin M; Simon, Chris; McCutcheon, John P

2015-08-18

Comparative genomics from mitochondria, plastids, and mutualistic endosymbiotic bacteria has shown that the stable establishment of a bacterium in a host cell results in genome reduction. Although many highly reduced genomes from endosymbiotic bacteria are stable in gene content and genome structure, organelle genomes are sometimes characterized by dramatic structural diversity. Previous results from Candidatus Hodgkinia cicadicola, an endosymbiont of cicadas, revealed that some lineages of this bacterium had split into two new cytologically distinct yet genetically interdependent species. It was hypothesized that the long life cycle of cicadas in part enabled this unusual lineage-splitting event. Here we test this hypothesis by investigating the structure of the Ca. Hodgkinia genome in one of the longest-lived cicadas, Magicicada tredecim. We show that the Ca. Hodgkinia genome from M. tredecim has fragmented into multiple new chromosomes or genomes, with at least some remaining partitioned into discrete cells. We also show that this lineage-splitting process has resulted in a complex of Ca. Hodgkinia genomes that are 1.1-Mb pairs in length when considered together, an almost 10-fold increase in size from the hypothetical single-genome ancestor. These results parallel some examples of genome fragmentation and expansion in organelles, although the mechanisms that give rise to these extreme genome instabilities are likely different.

Primer in Genetics and Genomics, Article 2-Advancing Nursing Research With Genomic Approaches.

PubMed

Lee, Hyunhwa; Gill, Jessica; Barr, Taura; Yun, Sijung; Kim, Hyungsuk

2017-03-01

Nurses investigate reasons for variable patient symptoms and responses to treatments to inform how best to improve outcomes. Genomics has the potential to guide nursing research exploring contributions to individual variability. This article is meant to serve as an introduction to the novel methods available through genomics for addressing this critical issue and includes a review of methodological considerations for selected genomic approaches. This review presents essential concepts in genetics and genomics that will allow readers to identify upcoming trends in genomics nursing research and improve research practice. It introduces general principles of genomic research and provides an overview of the research process. It also highlights selected nursing studies that serve as clinical examples of the use of genomic technologies. Finally, the authors provide suggestions about how to apply genomic technology in nursing research along with directions for future research. Using genomic approaches in nursing research can advance the understanding of the complex pathophysiology of disease susceptibility and different patient responses to interventions. Nurses should be incorporating genomics into education, clinical practice, and research as the influence of genomics in health-care research and practice continues to grow. Nurses are also well placed to translate genomic discoveries into improved methods for patient assessment and intervention.

Genomics for Everyone

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chain, Patrick

Genomics — the genetic mapping and DNA sequencing of sets of genes or the complete genomes of organisms, along with related genome analysis and database work — is emerging as one of the transformative sciences of the 21st century. But current bioinformatics tools are not accessible to most biological researchers. Now, a new computational and web-based tool called EDGE Bioinformatics is working to fulfill the promise of democratizing genomics.

Enabling responsible public genomics.

PubMed

Conley, John M; Doerr, Adam K; Vorhaus, Daniel B

2010-01-01

As scientific understandings of genetics advance, researchers require increasingly rich datasets that combine genomic data from large numbers of individuals with medical and other personal information. Linking individuals' genetic data and personal information precludes anonymity and produces medically significant information--a result not contemplated by the established legal and ethical conventions governing human genomic research. To pursue the next generation of human genomic research and commerce in a responsible fashion, scientists, lawyers, and regulators must address substantial new issues, including researchers' duties with respect to clinically significant data, the challenges to privacy presented by genomic data, the boundary between genomic research and commerce, and the practice of medicine. This Article presents a new model for understanding and addressing these new challenges--a "public genomics" premised on the idea that ethically, legally, and socially responsible genomics research requires openness, not privacy, as its organizing principle. Responsible public genomics combines the data contributed by informed and fully consenting information altruists and the research potential of rich datasets in a genomic commons that is freely and globally available. This Article examines the risks and benefits of this public genomics model in the context of an ambitious genetic research project currently under way--the Personal Genome Project. This Article also (i) demonstrates that large-scale genomic projects are desirable, (ii) evaluates the risks and challenges presented by public genomics research, and (iii) determines that the current legal and regulatory regimes restrict beneficial and responsible scientific inquiry while failing to adequately protect participants. The Article concludes by proposing a modified normative and legal framework that embraces and enables a future of responsible public genomics.

Breeding-assisted genomics.

PubMed

Poland, Jesse

2015-04-01

The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition. Copyright © 2015 Elsevier Ltd. All rights reserved.

Understanding cross-communication between aboveground and belowground tissues via transcriptome analysis of a sucking insect whitefly-infested pepper plants.

PubMed

Park, Yong-Soon; Ryu, Choong-Min

2014-01-03

Plants have developed defensive machinery to protect themselves against herbivore and pathogen attacks. We previously reported that aboveground whitefly (Bemisia tabaci Genn.) infestation elicited induced resistance in leaves and roots and influenced the modification of the rhizosphere microflora. In this study, to obtain molecular evidence supporting these plant fitness strategies against whitefly infestation, we performed a 300 K pepper microarray analysis using leaf and root tissues of pepper (Capsicum annuum L.) applied with whitefly, benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH), and the combination of BTH+whitefly. We defined differentially expressed genes (DEGs) as genes exhibiting more than 2-fold change (1.0 based on log2 values) in expression in leaves and roots in response to each treatment compared to the control. We identified a total of 16,188 DEGs in leaves and roots. Of these, 6685, 6752, and 4045 DEGs from leaf tissue and 6768, 7705, and 7667 DEGs from root tissue were identified in the BTH, BTH+whitefly, and whitefly treatment groups, respectively. The total number of DEGs was approximately two-times higher in roots than in whitefly-infested leaves subjected to whitefly infestation. Among DEGs, whitefly feeding induced salicylic acid and jasmonic acid/ethylene-dependent signaling pathways in leaves and roots. Several transporters and auxin-responsive genes were upregulated in roots, which can explain why biomass increase is facilitated. Using transcriptome analysis, our study provides new insights into the molecular basis of whitefly-mediated intercommunication between aboveground and belowground plant tissues and provides molecular evidence that may explain the alteration of rhizosphere microflora and root biomass by whitefly infestation. Copyright © 2013 Elsevier Inc. All rights reserved.

Rapid assessment of insect fauna based on local knowledge: comparing ecological and ethnobiological methods.

PubMed

Lima, Daniele Cristina de Oliveira; Ramos, Marcelo Alves; da Silva, Henrique Costa Hermenegildo; Alves, Angelo Giuseppe Chaves

2016-03-01

The rapid assessment of biodiversity making use of surveys of local knowledge has been successful for different biological taxa. However, there are no reports on the testing of such tools for sampling insect fauna. The present study aimed to evaluate the efficiency of different ethnobiological techniques for rapid sampling of insect fauna. Field research for the conventional survey of insect fauna was conducted on a private farm (9 ° 43'38.95 "S, 37 ° 45'11.97" W) , where there was intensive cultivation of okra (Abelmoschus esculentus L. (Moench)). The survey of local entomological knowledge was conducted among all the producers of okra living in the rural villages Pereira, Santa Luzia, and Nassau de Souza, within the Jacaré Curituba irrigated settlement scheme. The combined use of the techniques "free list" and projective interviews was analyzed, using two types of visual stimuli: stock photos and an entomological box. During the conventional survey of insect fauna, the species Bemisia tabaci biotype B, Aphis gossypii, Phenacoccus sp., Icerya purchasi and Lagria villosa were the primary pests found in the okra crop. Regarding the survey of insect pests, the results were convergent  in both techniques (conventional sampling and free list). Comparing the interview with visual stimuli (pictures) and specimen witnesses (entomological box) revealed that the latter was more effective. Techniques based on the recording and analysis of local knowledge about insects are effective for quick sampling of pest insects, but ineffective in sampling predator insects. The utilization of collected insects, infested branches, or photos of the symptoms of damage caused by pests in projective interviews is recommended.

New cost-effective bioconversion process of palm kernel cake into bioinsecticides based on Beauveria bassiana and Isaria javanica.

PubMed

do Nascimento Silva, Jaqueline; Mascarin, Gabriel Moura; Dos Santos Gomes, Isabel Cristina; Tinôco, Ricardo Salles; Quintela, Eliane Dias; Dos Reis Castilho, Leda; Freire, Denise Maria Guimarães

2018-03-01

The present study aimed to add value to palm oil by-products as substrates to efficiently produce conidia of Beauveria bassiana and Isaria javanica (Hypocreales: Cordycipitaceae) for biological control of the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae), through a solid-state fermentation process using palm kernel cake and palm fiber as nutrient source and solid matrix, respectively. The optimum culture conditions yielded high concentrations of viable conidia after air-drying, when the fungi were grown on palm kernel cake (B. bassiana 7.65 × 10 9 and I. javanica 2.91 × 10 9  conidia g -1 dry substrate) after 6 days under optimal growth conditions set to 60% substrate moisture and 32 °C. Both fungal strains exhibited high efficacy against third-instar whitefly nymphs, inducing mortality up to 62.9 and 56.6% by B. bassiana and I. javanica, respectively, assessed after 9 days post-application in a screenhouse. Furthermore, we noted that insect mortality was strongly correlated with high atmospheric moisture, while B. bassiana appeared to require shorter accumulative hours under high moisture to kill whitefly nymphs compared to I. javanica. Our results underpin a feasible and cost-effective mass production method for aerial conidia, using palm kernel as the main substrate in order to produce efficacious fungal bioinsecticides against an invasive whitefly species in Brazil. Finally, our fermentation process may offer a sustainable and cost-effective means to produce eco-friendly mycoinsecticides, using an abundant agro-industrial by-product from Brazil that will ultimately assist in the integrated management of agricultural insect pests.

Improved shelf life of dried Beauveria bassiana blastospores using convective drying and active packaging processes.

PubMed

Mascarin, Gabriel Moura; Jackson, Mark A; Behle, Robert W; Kobori, Nilce N; Júnior, Ítalo Delalibera

2016-10-01

The yeast form (blastospore) of the dimorphic insect-pathogenic fungus Beauveria bassiana can be rapidly produced using liquid fermentation methods but is generally unable to survive rapid dehydration processes or storage under non-refrigerated conditions. In this study, we evaluated the influence of two convective drying methods, various modified atmosphere packaging systems, and storage temperatures on the desiccation tolerance, storage stability, and virulence of blastospores of B. bassiana ESALQ 1432. All blastospore formulations were dried to <5 % water content equivalent to aw < 0.3. The viability of B. bassiana blastospores after air drying and spray drying was greater than 80 %. Vacuum-packaged blastospores remained viable longer when stored at 4 °C compared with 28 °C with virtually no loss in viability over 9 months regardless the drying method. When both oxygen and moisture scavengers were added to sealed packages of dried blastospore formulations stored at 28 °C, viability was significantly prolonged for both air- and spray-dried blastospores. The addition of ascorbic acid during spray drying did not improve desiccation tolerance but enhanced cell stability (∼twofold higher half-life) when stored at 28 °C. After storage for 4 months at 28 °C, air-dried blastospores produced a lower LC80 and resulted in higher mortality to whitefly nymphs (Bemisia tabaci) when compared with spray-dried blastospores. These studies identified key storage conditions (low aw and oxygen availability) that improved blastospore storage stability at 28 °C and will facilitate the commercial development of blastospores-based bioinsecticides.

Members of WRKY Group III transcription factors are important in TYLCV defense signaling pathway in tomato (Solanum lycopersicum).

PubMed

Huang, Ying; Li, Meng-Yao; Wu, Peng; Xu, Zhi-Sheng; Que, Feng; Wang, Feng; Xiong, Ai-Sheng

2016-10-07

Transmitted by the whitefly Bemisia tabaci, tomato yellow leaf curly virus (TYLCV) has posed serious threats to plant growth and development. Plant innate immune systems against various threats involve WRKY Group III transcription factors (TFs). This group participates as a major component of biological processes in plants. In this study, 6 WRKY Group III TFs (SolyWRKY41, SolyWRKY42, SolyWRKY53, SolyWRKY54, SolyWRKY80, and SolyWRKY81) were identified, and these TFs responded to TYLCV infection. Subcellular localization analysis indicated that SolyWRKY41 and SolyWRKY54 were nuclear proteins in vivo. Many elements, including W-box, were found in the promoter region of Group III TFs. Interaction network analysis revealed that Group III TFs could interact with other proteins, such as mitogen-activated protein kinase 5 (MAPK) and isochorismate synthase (ICS), to respond to biotic and abiotic stresses. Positive and negative expression patterns showed that WRKY Group III genes could also respond to TYLCV infection in tomato. The DNA content of TYLCV resistant lines after SolyWRKY41 and SolyWRKY54 were subjected to virus-induced gene silencing (VIGS) was lower than that of the control lines. In the present study, 6 WRKY Group III TFs in tomato were identified to respond to TYLCV infection. Quantitative real-time-polymerase chain reaction (RT-qPCR) and VIGS analyses demonstrated that Group III genes served as positive and negative regulators in tomato-TYLCV interaction. WRKY Group III TFs could interact with other proteins by binding to cis elements existing in the promoter regions of other genes to regulate pathogen-related gene expression.

Toxicity of seven foliar insecticides to four insect parasitoids attacking citrus and cotton pests.

PubMed

Prabhaker, Nilima; Morse, J G; Castle, S J; Naranjo, S E; Henneberry, T J; Toscano, N C

2007-08-01

Laboratory studies were carried out to compare the toxicity of seven foliar insecticides to four species of adult beneficial insects representing two families of Hymenoptera: Aphelinidae (Aphytis melinus Debach, Eretmocerus eremicus Rose & Zolnerowich, and Encarsiaformosa Gahan) and Mymaridae (Gonatocerus ashmeadi Girault) that attack California red scale, Aonidiella aurantii (Maskell); sweetpotato whitefly, Bemisia tabaci (Gennadius) (both E. eremicus and E. formosa); and glassy-winged sharpshooter, Homalodisca vitripennis (Germar), respectively. Insecticides from four pesticide classes were evaluated using a petri dish bioassay technique across a range of concentrations to develop dosage-mortality regressions. Insecticides tested included acetamiprid (neonicotinoid); chlorpyrifos (organophosphate); bifenthrin, cyfluthrin, and fenpropathrin (pyrethroids); and buprofezin and pyriproxyfen (insect growth regulators [IGRs]). Chlorpyrifos was consistently the most toxic pesticide to all four species of beneficial insects tested based on LC50 values recorded 24 h posttreatment compared with 48-h LC50 values with the neonicotinoid and pyrethroids or 96 h with the IGRs. Among the three pyrethroids, fenpropathrin was usually less toxic (except similar toxicity to A. melinus) than was cyfluthrin, and it was normally less toxic (except similar toxicity with E. formosa) than was bifenthrin. Acetamiprid was generally less toxic than bifenthrin (except similar toxicity with G. ashmeadi). The IGRs buprofezin and pyriproxyfen were usually less toxic than the contact pesticides, but we did not test for possible impacts on female fecundity. For all seven pesticides tested, A. melinus was the most susceptible parasitoid of the four test species. The data presented here will provide pest managers with specific information on the compatibility of select insecticides with natural enemies attacking citrus and cotton, Gossypium hirsutum L., pests.

Fifty years of the integrated control concept: moving the model and implementation forward in Arizona††

PubMed Central

Naranjo, Steven E; Ellsworth, Peter C

2009-01-01

Fifty years ago, Stern, Smith, van den Bosch and Hagen outlined a simple but sophisticated idea of pest control predicated on the complementary action of chemical and biological control. This integrated control concept has since been a driving force and conceptual foundation for all integrated pest management (IPM) programs. The four basic elements include thresholds for determining the need for control, sampling to determine critical densities, understanding and conserving the biological control capacity in the system and the use of selective insecticides or selective application methods, when needed, to augment biological control. Here we detail the development, evolution, validation and implementation of an integrated control (IC) program for whitefly, Bemisia tabaci (Genn.), in the Arizona cotton system that provides a rare example of the vision of Stern and his colleagues. Economic thresholds derived from research-based economic injury levels were developed and integrated with rapid and accurate sampling plans into validated decision tools widely adopted by consultants and growers. Extensive research that measured the interplay among pest population dynamics, biological control by indigenous natural enemies and selective insecticides using community ordination methods, predator:prey ratios, predator exclusion and demography validated the critical complementary roles played by chemical and biological control. The term ‘bioresidual’ was coined to describe the extended environmental resistance from biological control and other forces possible when selective insecticides are deployed. The tangible benefits have been a 70% reduction in foliar insecticides, a >$200 million saving in control costs and yield, along with enhanced utilization of ecosystem services over the last 14 years. Published in 2009 by John Wiley & Sons, Ltd. PMID:19834884

Complete Genome Sequence and Comparative Genomics of a Novel Myxobacterium Myxococcus hansupus

PubMed Central

Sharma, Gaurav; Narwani, Tarun; Subramanian, Srikrishna

2016-01-01

Myxobacteria, a group of Gram-negative aerobes, belong to the class δ-proteobacteria and order Myxococcales. Unlike anaerobic δ-proteobacteria, they exhibit several unusual physiogenomic properties like gliding motility, desiccation-resistant myxospores and large genomes with high coding density. Here we report a 9.5 Mbp complete genome of Myxococcus hansupus that encodes 7,753 proteins. Phylogenomic and genome-genome distance based analysis suggest that Myxococcus hansupus is a novel member of the genus Myxococcus. Comparative genome analysis with other members of the genus Myxococcus was performed to explore their genome diversity. The variation in number of unique proteins observed across different species is suggestive of diversity at the genus level while the overrepresentation of several Pfam families indicates the extent and mode of genome expansion as compared to non-Myxococcales δ-proteobacteria. PMID:26900859

MIPS plant genome information resources.

PubMed

Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

2007-01-01

The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

Genomic Advances to Improve Biomass for Biofuels (Genomics and Bioenergy)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rokhsar, Daniel

2008-02-11

Lawrence Berkeley National Lab bioscientist Daniel Rokhsar discusses genomic advances to improve biomass for biofuels. He presented his talk Feb. 11, 2008 in Berkeley, California as part of Berkeley Lab's community lecture series. Rokhsar works with the U.S. Department of Energy's Joint Genome Institute and Berkeley Lab's Genomics Division.

New Implications on Genomic Adaptation Derived from the Helicobacter pylori Genome Comparison

PubMed Central

Lara-Ramírez, Edgar Eduardo; Segura-Cabrera, Aldo; Guo, Xianwu; Yu, Gongxin; García-Pérez, Carlos Armando; Rodríguez-Pérez, Mario A.

2011-01-01

Background Helicobacter pylori has a reduced genome and lives in a tough environment for long-term persistence. It evolved with its particular characteristics for biological adaptation. Because several H. pylori genome sequences are available, comparative analysis could help to better understand genomic adaptation of this particular bacterium. Principal Findings We analyzed nine H. pylori genomes with emphasis on microevolution from a different perspective. Inversion was an important factor to shape the genome structure. Illegitimate recombination not only led to genomic inversion but also inverted fragment duplication, both of which contributed to the creation of new genes and gene family, and further, homological recombination contributed to events of inversion. Based on the information of genomic rearrangement, the first genome scaffold structure of H. pylori last common ancestor was produced. The core genome consists of 1186 genes, of which 22 genes could particularly adapt to human stomach niche. H. pylori contains high proportion of pseudogenes whose genesis was principally caused by homopolynucleotide (HPN) mutations. Such mutations are reversible and facilitate the control of gene expression through the change of DNA structure. The reversible mutations and a quasi-panmictic feature could allow such genes or gene fragments frequently transferred within or between populations. Hence, pseudogenes could be a reservoir of adaptation materials and the HPN mutations could be favorable to H. pylori adaptation, leading to HPN accumulation on the genomes, which corresponds to a special feature of Helicobacter species: extremely high HPN composition of genome. Conclusion Our research demonstrated that both genome content and structure of H. pylori have been highly adapted to its particular life style. PMID:21387011

Genomics for Everyone

ScienceCinema

Chain, Patrick

2018-05-31

Genomics — the genetic mapping and DNA sequencing of sets of genes or the complete genomes of organisms, along with related genome analysis and database work — is emerging as one of the transformative sciences of the 21st century. But current bioinformatics tools are not accessible to most biological researchers. Now, a new computational and web-based tool called EDGE Bioinformatics is working to fulfill the promise of democratizing genomics.

Ensembl Genomes 2013: scaling up access to genome-wide data.

PubMed

Kersey, Paul Julian; Allen, James E; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Hughes, Daniel Seth Toney; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Langridge, Nicholas; McDowall, Mark D; Maheswari, Uma; Maslen, Gareth; Nuhn, Michael; Ong, Chuang Kee; Paulini, Michael; Pedro, Helder; Toneva, Iliana; Tuli, Mary Ann; Walts, Brandon; Williams, Gareth; Wilson, Derek; Youens-Clark, Ken; Monaco, Marcela K; Stein, Joshua; Wei, Xuehong; Ware, Doreen; Bolser, Daniel M; Howe, Kevin Lee; Kulesha, Eugene; Lawson, Daniel; Staines, Daniel Michael

2014-01-01

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.

Toward genome-enabled mycology.

PubMed

Hibbett, David S; Stajich, Jason E; Spatafora, Joseph W

2013-01-01

Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.

The Genome Portal of the Department of Energy Joint Genome Institute

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nordberg, Henrik; Cantor, Michael; Dushekyo, Serge

2014-03-14

The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. Genome Portal in the past 2 years was significantly updated, with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI. A critical aspect of handling big data in genomics is the development of visualization and analysis tools that allow scientists to derive meaning from what are otherwise terrabases ofmore » inert sequence. An interactive visualization tool developed in the group allows us to explore contigs resulting from a single metagenome assembly. Implemented with modern web technologies that take advantage of the power of the computer's graphical processing unit (gpu), the tool allows the user to easily navigate over a 100,000 data points in multiple dimensions, among many biologically meaningful parameters of a dataset such as relative abundance, contig length, and G+C content.« less

Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.

PubMed

Puigbò, Pere; Lobkovsky, Alexander E; Kristensen, David M; Wolf, Yuri I; Koonin, Eugene V

2014-08-21

Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. pools of genes that are accessible to the given microbial species. We performed a comprehensive analysis of the genome dynamics in 35 groups (34 bacterial and one archaeal) of closely related microbial genomes using a phylogenetic birth-and-death maximum likelihood model to quantify the rates of gene family gain and loss, as well as expansion and reduction. The results show that loss of gene families dominates the evolution of prokaryotes, occurring at approximately three times the rate of gain. The rates of gene family expansion and reduction are typically seven and twenty times less than the gain and loss rates, respectively. Thus, the prevailing mode of evolution in bacteria and archaea is genome contraction, which is partially compensated by the gain of new gene families via horizontal gene transfer. However, the rates of gene family gain, loss, expansion and reduction vary within wide ranges, with the most stable genomes showing rates about 25 times lower than the most dynamic genomes. For many groups, the supergenome estimated from the fraction of repetitive gene family gains includes about tenfold more gene families than the typical genome in the group although some groups appear to have vast, 'open' supergenomes. Reconstruction of evolution for groups of closely related bacteria and archaea reveals an extremely rapid and highly variable flux of genes in evolving microbial genomes, demonstrates that extensive gene loss and horizontal gene transfer leading to innovation are the two dominant evolutionary processes, and yields robust estimates of the supergenome size.

From genomics to chemical genomics: new developments in KEGG

PubMed Central

Kanehisa, Minoru; Goto, Susumu; Hattori, Masahiro; Aoki-Kinoshita, Kiyoko F.; Itoh, Masumi; Kawashima, Shuichi; Katayama, Toshiaki; Araki, Michihiro; Hirakawa, Mika

2006-01-01

The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource () provides a reference knowledge base for linking genomes to biological systems, categorized as building blocks in the genomic space (KEGG GENES) and the chemical space (KEGG LIGAND), and wiring diagrams of interaction networks and reaction networks (KEGG PATHWAY). A fourth component, KEGG BRITE, has been formally added to the KEGG suite of databases. This reflects our attempt to computerize functional interpretations as part of the pathway reconstruction process based on the hierarchically structured knowledge about the genomic, chemical and network spaces. In accordance with the new chemical genomics initiatives, the scope of KEGG LIGAND has been significantly expanded to cover both endogenous and exogenous molecules. Specifically, RPAIR contains curated chemical structure transformation patterns extracted from known enzymatic reactions, which would enable analysis of genome-environment interactions, such as the prediction of new reactions and new enzyme genes that would degrade new environmental compounds. Additionally, drug information is now stored separately and linked to new KEGG DRUG structure maps. PMID:16381885

SMART on FHIR Genomics: facilitating standardized clinico-genomic apps.

PubMed

Alterovitz, Gil; Warner, Jeremy; Zhang, Peijin; Chen, Yishen; Ullman-Cullere, Mollie; Kreda, David; Kohane, Isaac S

2015-11-01

Supporting clinical decision support for personalized medicine will require linking genome and phenome variants to a patient's electronic health record (EHR), at times on a vast scale. Clinico-genomic data standards will be needed to unify how genomic variant data are accessed from different sequencing systems. A specification for the basis of a clinic-genomic standard, building upon the current Health Level Seven International Fast Healthcare Interoperability Resources (FHIR®) standard, was developed. An FHIR application protocol interface (API) layer was attached to proprietary sequencing platforms and EHRs in order to expose gene variant data for presentation to the end-user. Three representative apps based on the SMART platform were built to test end-to-end feasibility, including integration of genomic and clinical data. Successful design, deployment, and use of the API was demonstrated and adopted by HL7 Clinical Genomics Workgroup. Feasibility was shown through development of three apps by various types of users with background levels and locations. This prototyping work suggests that an entirely data (and web) standards-based approach could prove both effective and efficient for advancing personalized medicine. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Impact of straw mulch on populations of onion thrips (Thysanoptera: Thripidae) in onion.