De novo characterization of a whitefly transcriptome and analysis of its gene expression during development

BMC Genomics, Jun 2010

Background Whitefly (Bemisia tabaci) causes extensive crop damage throughout the world by feeding directly on plants and by vectoring hundreds of species of begomoviruses. Yet little is understood about its genes involved in development, insecticide resistance, host range plasticity and virus transmission. Results To facilitate research on whitefly, we present a method for de novo assembly of whitefly transcriptome using short read sequencing technology (Illumina). In a single run, we produced more than 43 million sequencing reads. These reads were assembled into 168,900 unique sequences (mean size = 266 bp) which represent more than 10-fold of all the whitefly sequences deposited in the GenBank (as of March 2010). Based on similarity search with known proteins, these analyses identified 27,290 sequences with a cut-off E-value above 10-5. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. In addition, we investigated the transcriptome changes during whitefly development using a tag-based digital gene expression (DGE) system. We obtained a sequencing depth of over 2.5 million tags per sample and identified a large number of genes associated with specific developmental stages and insecticide resistance. Conclusion Our data provides the most comprehensive sequence resource available for whitefly study and demonstrates that the Illumina sequencing allows de novo transcriptome assembly and gene expression analysis in a species lacking genome information. We anticipate that next generation sequencing technologies hold great potential for the study of the transcriptome in other non-model organisms.

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De novo characterization of a whitefly transcriptome and analysis of its gene expression during development

BMC Genomics RDeseearnchoarvtiocle characterization of a whitefly transcriptome and analysis of its gene expression during development Xiao-Wei Wang 0 Jun-Bo Luan 0 Jun-Min Li 0 Yan-Yuan Bao 0 Chuan-Xi Zhang 0 Shu-Sheng Liu 0 0 Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University , Hangzhou 310029 , China Background: Whitefly (Bemisia tabaci) causes extensive crop damage throughout the world by feeding directly on plants and by vectoring hundreds of species of begomoviruses. Yet little is understood about its genes involved in development, insecticide resistance, host range plasticity and virus transmission. Results: To facilitate research on whitefly, we present a method for de novo assembly of whitefly transcriptome using short read sequencing technology (Illumina). In a single run, we produced more than 43 million sequencing reads. These reads were assembled into 168,900 unique sequences (mean size = 266 bp) which represent more than 10-fold of all the whitefly sequences deposited in the GenBank (as of March 2010). Based on similarity search with known proteins, these analyses identified 27,290 sequences with a cut-off E-value above 10-5. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. In addition, we investigated the transcriptome changes during whitefly development using a tag-based digital gene expression (DGE) system. We obtained a sequencing depth of over 2.5 million tags per sample and identified a large number of genes associated with specific developmental stages and insecticide resistance. Conclusion: Our data provides the most comprehensive sequence resource available for whitefly study and demonstrates that the Illumina sequencing allows de novo transcriptome assembly and gene expression analysis in a species lacking genome information. We anticipate that next generation sequencing technologies hold great potential for the study of the transcriptome in other non-model organisms. - Background The whitefly Bemisia tabaci (Gennadius) is a genetically diverse complex containing some of the most destructive invasive pests of many ornamental and glasshouse crops worldwide [1,2]. The species complex colonizes more than 600 different species of plants, transmits many plant viruses, feeds on phloem sap, and promotes the growth of damaging fungi on honeydew excretions deposited on plants [3-6]. Recent phylogenetic analysis combined with a pattern of reproductive isolation among genetic groups within B. tabaci indicate that the complex contains at least 24 cryptic species, some of which have been referred to as "biotypes" in the last 20 years [7,8]. As the separation at the species level within the B. tabaci complex is yet to be fully resolved, we have retained the commonly used term "biotype" to link this study with existing literature. The most predominant and damaging biotypes of B. tabaci are the B and Q biotypes [9,10]. While the former is known for its high fitness parameters, the Q biotype whitefly has a unique ability to develop and maintain high levels of resistance to major classes of insecticides owing to biological and genetic factors [11,12]. Despite its global importance, genomic sequence resources available for the whitefly are scarce, especially for the Q biotype. Currently (March 30th, 2010), there are about 9110 EST and 762 nucleotide sequences available on NCBI for the B biotype whitefly, and only 683 nucleotide sequences have been deposited for the Q biotype whitefly. The previous EST sequencing efforts for the B biotype whitefly have allowed the development of smallscale microarrays for gene expression analysis in the context of insecticide resistance and parasitoid-whitefly interactions [13-15]. While these studies have highlighted the utility of cDNA sequencing for candidate gene discovery in the absence of a genome sequence, a comprehensive description of the genes expressed in insecticideresistant Q biotype whitefly remains unavailable. Over the past several years, the next generation sequencing technology has emerged as a cutting edge approach for high-throughput sequence determination and this has dramatically improved the efficiency and speed of gene discovery [16,17]. For example, the Illumina sequencing technology is able to generate over one billion bases of high-quality DNA sequence per run at less than 1% of the cost of capillary-based methods [18]. Furthermore, this next generation sequencing has also significantly accelerated and improved the sensitivity of gene-expression profiling and, is expected to boost collaborative and comparative genomics studies [19,20]. Previously, Illumina sequencing of transcriptomes for organisms with completed genomes confirmed that the relatively short reads produced can be effectively assembled and used for gene discovery and comparison of gene expression profiles [21,22]. Despi (...truncated)


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Xiao-Wei Wang, Jun-Bo Luan, Jun-Min Li, Yan-Yuan Bao, Chuan-Xi Zhang, Shu-Sheng Liu. De novo characterization of a whitefly transcriptome and analysis of its gene expression during development, BMC Genomics, 2010, pp. 400, 11, DOI: 10.1186/1471-2164-11-400