CrusTome: A transcriptome database resource for large-scale analyses across Crustacea
Jorge L. Pérez-Moreno, Mihika T. Kozma, Danielle M. DeLeo, Heather D. Bracken-Grissom, David S. Durica, and Donald L. Mykles, In review, 2022
Transcriptomes from non-traditional model organisms often harbor a wealth of unexplored data. Examining these datasets 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 non-traditional model organisms remains limited. Crustaceans, for example, being amongst 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 multi-species, multi-tissue, transcriptome database of 201 assembled mRNA transcriptomes (189 crustaceans, 30 of which were previously unpublished, and 12 ecdysozoan outgroups) as an evolving, and publicly available resource. This database is suitable for evolutionary, ecological, and functional studies that employ genomic/transcriptomic techniques and datasets. CrusTome is presented in BLAST and DIAMOND formats, providing robust datasets for sequence similarity searches, orthology assignments, phylogenetic inference, etc., and thus allowing for straight-forward 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.