Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310029, China.
BMC Genomics. 2010 Jun 24;11:400. doi: 10.1186/1471-2164-11-400.
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.
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.
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.
烟粉虱（Bemisia tabaci）通过直接取食植物和传播数百种双生病毒，在全世界范围内造成广泛的作物损害。然而，人们对其参与发育、抗药性、宿主范围可塑性和病毒传播的基因知之甚少。
为了促进对烟粉虱的研究，我们提出了一种使用短读测序技术（Illumina）从头组装烟粉虱转录组的方法。在一次运行中，我们产生了超过 4300 万条测序reads。这些reads 被组装成 168900 个独特的序列（平均大小=266bp），代表了 GenBank 中所有烟粉虱序列的 10 倍以上（截至 2010 年 3 月）。基于与已知蛋白质的相似性搜索，这些分析确定了 27290 个具有 10-5 以上 E 值的序列。组装的序列用基因描述、基因本体论和直系同源群术语进行了注释。此外，我们还使用基于标签的数字基因表达（DGE）系统研究了烟粉虱发育过程中的转录组变化。我们每个样本获得了超过 250 万个标签的测序深度，并鉴定出了大量与特定发育阶段和抗药性相关的基因。
我们的数据为烟粉虱研究提供了最全面的序列资源，并表明 Illumina 测序允许在缺乏基因组信息的物种中进行从头转录组组装和基因表达分析。我们预计，下一代测序技术在其他非模式生物的转录组研究中具有巨大潜力。
