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生产具有重大意义，而自由生活的线虫物种则提供了至关重要的生态系统服务。基因组学领域的革新催生了大量涵盖多个系统发育类群线虫物种的表达序列标签（expressed sequence tags, EST）数据集，但此类数据集难以实现跨物种比较。NEMBASE4作为统一的检索门户，整合了60余种线虫（包含动植物寄生虫与自由生活类群）的经广泛功能注释的EST来源转录组数据。研究团队借助PartiGene工具套件，将各物种公开可得的EST序列组装为一套高质量的推定转录本集合。随后将这些转录本翻译为蛋白质序列资源，并通过与模式线虫物种（如秀丽隐杆线虫（Caenorhabditis elegans））及其他非线虫参考资源的比对，为每条蛋白质序列添加了功能注释信息。通过对NEMBASE4内部的序列开展跨物种交叉比对，研究团队还为每个翻译得到的蛋白质序列分配了蛋白家族分类。该数据集以开放可访问的交互式数据库形式对外发布。为验证NEMBASE4的应用价值，研究团队利用该数据库分析了主要演化支寄生线虫的转录组特异性，鉴定出了可能支撑特定寄生表型的支系限制性基因、潜在的线虫病毒病原体，以及可开发为药物靶点的线虫专属蛋白家族。