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

Abstract

BackgroundWhitefly (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.ResultsTo 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.ConclusionOur 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.

De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology

“…Of all the unigenes, 33 276 (45.0%) had BLAST hits in the Swiss-Prot database. Compared with Wang et al (2010b), in which only 16.2% had BLAST hits in Nr database, the higher percentage in the present study was partially ascribed to the higher frequency of long sequences (Wang et al, 2010b). As reported by Parchman et al (2010), longer contigs were more likely to have BLAST matches in the protein database.…”

“…A primary platform being used to generate transcriptomic resources is the Illumina short read sequencing platform, followed by de-novo assembly of sequence reads. This approach has been used to characterize transcriptomes of diverse taxa, including plants (Chang et al, 2011;Garg et al, 2011), insects (Wang et al, 2010b;Xue et al, 2010), mollusks (Feldmeyer et al, 2011), fish (Xiang et al, 2010), and mammals (Yao et al, 2012a;2012b). Despite their obvious benefits, NGS methods have not yet been applied to turtle research.…”

Analysis of alterations to the transcriptome of Loquat (Eriobotrya japonica Lindl.) under low temperature stress via de novo sequencing

“…Chilling injury occurs in loquat fruit when they are stored at temperatures lower than 5°C, and fruit stored at 0°C exhibits severe symptoms of lignification and tissue browning, and a decrease in the percentage of juice (Cai et al, 2006c). Wang et al (2010) identified five components of the ethylene signal transduction pathway from ripening loquat fruit and found that the EjETR1 and EjEIL1 genes may be involved in chilling injury development. However, the expression profiles of these genes under low temperature stress are unknown.…”

De Novo Assembly and Analysis of the Testes Transcriptome from the Menhaden, Bervoortia tyrannus

“…Transcriptome analyses are a cost-effective method for the characterization of species that lack a fully sequenced genome [7,8]. The short reads from Illumina paired-end sequencing can provide a deep sequencing coverage for the accurate base calling in de-novo transcriptome assembly and has been utilized to characterize many non-model species [37][38][39][40]. However, no transcriptome sequencing data is available for menhaden.…”