Data from: NEMBASE4: the nematode transcriptome resource

Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services. The genomics revolution has resulted in the production of many datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, but these are not easily compared. NEMBASE4 presents a single portal onto extensively functionally annotated, EST-derived transcriptomes from over sixty species of nematodes, including plant and animal parasites and free-living taxa. Using the PartiGene suite of tools, we have assembled the ESTs publicly available for each species into a high-quality set of putative transcripts. These transcripts have been translated to produce a protein sequence resource, and each annotated with functional information derived from comparison to well-studied nematode species such as Caenorhabditis elegans and also other non-nematode resources. By cross-comparing the sequences within NEMBASE4, we have also generated a protein family assignment for each translation. The data are presented in an openly-accessible, interactive database. To demonstrate the utility of NEMBASE4, we have used the database to examine the uniqueness of the transcriptomes of major clades of parasitic nematodes, identifying lineage-restricted genes that may underpin particular parasitic phenotypes, possible viral pathogens of nematodes, and nematode-unique protein families that may be developed as drug targets.

线虫寄生虫对人类健康与农业均具有重大意义，而自由生活的线虫物种则提供了不可或缺的生态系统服务。基因组学革命催生了大量来自系统发育跨度极广的线虫物种的表达序列标签（EST）数据集，但这类数据集难以进行跨物种比较分析。NEMBASE4为60余种线虫的源自EST的转录组提供了统一的访问门户，这些转录组均经过全面的功能注释，涵盖了动植物寄生线虫与自由生活线虫类群。研究团队借助PartiGene工具套件，将各物种公开可用的EST序列组装为一套高质量的推定转录本集合。研究团队将上述推定转录本翻译为蛋白质序列，构建了蛋白质序列资源库，并通过与研究较为深入的线虫物种（如秀丽隐杆线虫（Caenorhabditis elegans））及其他非线虫资源进行比对，为每条蛋白质序列添加了功能注释信息。通过对NEMBASE4内部的序列进行跨物种比对分析，研究团队还为每条翻译得到的蛋白质序列分配了对应的蛋白质家族分类。该数据集以开放可访问的交互式数据库形式呈现。为验证NEMBASE4的应用价值，研究团队利用该数据库分析了寄生线虫主要演化支的转录组特异性，鉴定出了可能支撑特定寄生表型的谱系特异性基因、潜在的线虫病毒病原体，以及可作为药物靶点的线虫专属蛋白质家族。