EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms

Area of Science:

• Marine Biology
• Genomics
• Bioinformatics

Background:

• The echinoderm tree of life project aims to identify orthologs for phylogenetic analysis using next-generation transcriptome data.
• The largest dataset assembled for echinoderm phylogeny and transcriptomics was generated using RNA-Seq on 42 specimens across 24 orders and 37 families.
• Specimens were collected from deep and polar seas to represent key evolutionary divergences.

Purpose of the Study:

• To create a comprehensive, searchable repository of orthologous echinoderm transcripts.
• To make a large dataset available to researchers for diverse interests beyond phylogenetic reconstruction.
• To facilitate comparative biology research through accessible genomic data.

Main Methods:

• RNA-Seq was performed on adult tissues from 42 echinoderm specimens.
• A web-based application, EchinoDB, was developed as a repository for orthologous transcripts.
• EchinoDB allows searching by keywords and sequence similarity.

Main Results:

• Identified 749,397 clusters of orthologous loci from the transcriptome data.
• Developed IT infrastructure to manage and search loci and their annotations against the Sea Urchin genome.
• The data has already supported projects in developmental biology, gene family studies, and neuroscience.

Conclusions:

• EchinoDB serves as a valuable resource for echinoderm research.
• The database facilitates discovery for a wide range of comparative biology questions.
• Researchers are encouraged to utilize EchinoDB for their specific studies.