CrusTome: a transcriptome database resource for large-scale analyses across Crustacea.
CrusTome: a transcriptome database resource for large-scale analyses across Crustacea.
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DOI：
10.1093/g3journal/jkad098
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发表时间：
2023-07-05
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来自非传统模式生物的转录组通常包含大量未探索的数据。检查这些数据集可以在传统系统中获得清晰和新颖的见解，以及在众多领域中的发现。尽管在DNA测序技术及其采用方面取得了重大进展，但获得非传统模式生物的基因组和转录组资源仍然有限。例如，甲壳类动物是地球上数量最多、种类最多、分布最广的类群之一，常常是解决生态、进化和有机体问题的优秀系统。虽然它们在各种环境中普遍存在，并且具有经济和粮食安全的重要性，但它们在公开可用的序列数据库中仍然严重不足。在这里，我们提出CrusTome，一个多物种，多组织，转录组数据库的201组装mRNA转录组（189甲壳类动物，其中30个是以前未发表的，和12蜕皮动物的系统发育背景）作为一个不断发展和公开可用的资源。该数据库适用于采用基因组/转录组技术和数据集的进化，生态和功能研究。CrusTome以BLAST和DIAMOND格式呈现，为序列相似性搜索、同源性分配、系统发育推断等提供了强大的数据集，从而允许直接并入现有的自定义管道以进行高通量分析。此外，为了说明CrusTome的用途和潜力，我们进行了系统发育分析，阐明了隐花色素/光解酶家族蛋白质在甲壳类动物中的身份和进化。
Transcriptomes from nontraditional model organisms often harbor a wealth of unexplored data. Examining these data sets can lead to clarity and novel insights in traditional systems, as well as to discoveries across a multitude of fields. Despite significant advances in DNA sequencing technologies and in their adoption, access to genomic and transcriptomic resources for nontraditional model organisms remains limited. Crustaceans, for example, being among the most numerous, diverse, and widely distributed taxa on the planet, often serve as excellent systems to address ecological, evolutionary, and organismal questions. While they are ubiquitously present across environments, and of economic and food security importance, they remain severely underrepresented in publicly available sequence databases. Here, we present CrusTome, a multispecies, multitissue, transcriptome database of 201 assembled mRNA transcriptomes (189 crustaceans, 30 of which were previously unpublished, and 12 ecdysozoans for phylogenetic context) as an evolving and publicly available resource. This database is suitable for evolutionary, ecological, and functional studies that employ genomic/transcriptomic techniques and data sets. CrusTome is presented in BLAST and DIAMOND formats, providing robust data sets for sequence similarity searches, orthology assignments, phylogenetic inference, etc. and thus allowing for straightforward incorporation into existing custom pipelines for high-throughput analyses. In addition, to illustrate the use and potential of CrusTome, we conducted phylogenetic analyses elucidating the identity and evolution of the cryptochrome/photolyase family of proteins across crustaceans.
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