EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms

Area of Science:

• Genomics
• Developmental Biology
• Echinoderm Research

Background:

• EchinoDB is a database for echinoderm genomic and transcriptomic data.
• The initial version contained 749,397 orthologous and paralogous transcripts.
• It was first released in 2016 and implemented in GO on a local server.

Purpose of the Study:

• To release an updated version of EchinoDB (v2.0) with enhanced features and data.
• To provide researchers with improved access to echinoderm genomic and transcriptomic information.
• To facilitate research in areas such as phylogenetics, developmental biology, and regeneration.

Main Methods:

• Incorporated new RNA-Seq data for Ophioderma brevispinum and genomic assembly data for Lytechinus variegatus.
• Enabled keyword searches for annotated data and updated SequenceServer for Basic Local Alignment Search Tool (BLAST) searches.
• Re-implemented the database using R Shiny and migrated to a cloud-based infrastructure for improved reliability and scalability.

Main Results:

• EchinoDB v2.0 now includes comprehensive genomic and transcriptomic data for key echinoderm species.
• Enhanced search functionalities (keyword and BLAST) and data download in FASTA format are available.
• The database runs on a cloud platform, ensuring better accessibility and performance.

Conclusions:

• EchinoDB v2.0 supports diverse research fields including phylogenetics, developmental biology, genomics, physiology, neurobiology, and regeneration.
• The database aids in studying signaling pathways in tissue regeneration and the conservation of echinoderm-specific proteins.
• It enables investigation into the presence of biomineralization proteins and tensilin across the echinoderm phylum.