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CrusTome: a transcriptome database resource for large-scale analyses across Crustacea
Jorge L Pérez-Moreno1, Mihika T Kozma1, Danielle M DeLeo2
1Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
G3 (Bethesda, Md.)
|May 2, 2023
Summary
CrusTome is a new database of crustacean transcriptomes, offering valuable data for evolutionary and ecological research. This resource enhances understanding of diverse species and their genetic makeup.
Area of Science:
- Genomics and Bioinformatics
- Evolutionary Biology
- Marine Biology
Background:
- Nontraditional model organisms, like crustaceans, possess vast unexplored genomic and transcriptomic data.
- Limited availability of genomic and transcriptomic resources hinders research in diverse taxa.
- Crustaceans are ecologically significant and economically important but underrepresented in sequence databases.
Purpose of the Study:
- To develop and present CrusTome, a comprehensive, publicly available transcriptome database for crustaceans.
- To provide a robust resource for evolutionary, ecological, and functional studies using genomic and transcriptomic data.
- To demonstrate the utility of CrusTome through phylogenetic analysis of cryptochrome/photolyase proteins.
Main Methods:
- Assembly of 201 mRNA transcriptomes (189 crustaceans, 12 ecdysozoans).
- Inclusion of 30 previously unpublished crustacean transcriptomes.
- Database formatted for BLAST and DIAMOND for sequence similarity searches and orthology assignments.
Main Results:
- Creation of CrusTome, a multispecies, multitissue transcriptome database.
- Database suitable for high-throughput analyses and phylogenetic inference.
- Phylogenetic analysis revealed insights into the evolution of cryptochrome/photolyase proteins in crustaceans.
Conclusions:
- CrusTome serves as an evolving, publicly accessible resource for diverse biological studies.
- The database facilitates comparative genomics and evolutionary research across crustacean species.
- CrusTome empowers researchers to explore the genetic underpinnings of crustacean diversity and function.
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