Integration of 1:1 orthology maps and updated datasets into Echinobase

Abstract

Echinobase (https://echinobase.org) is a central online platform that generates, manages and hosts genomic data relevant to echinoderm research. While the resource primarily serves the echinoderm research community, the recent release of an excellent quality genome for the frequently studied purple sea urchin (Strongylocentrotus purpuratus genome, v5.0) has provided an opportunity to adapt to the needs of a broader research community across other model systems. To this end, establishing pipelines to identify orthologous genes between echinoderms and other species has become a priority in many contexts including nomenclature, linking to data in other model organisms, and in internal functionality where data gathered in one hosted species can be associated with genes in other hosted echinoderms. This paper describes the orthology pipelines currently employed by Echinobase and how orthology data are processed to yield 1:1 ortholog mappings between a variety of echinoderms and other model taxa. We also describe functions of interest that have recently been included on the resource, including an updated developmental time course for S.purpuratus, and additional tracks for genome browsing. These data enhancements will increase the accessibility of the resource to non-echinoderm researchers and simultaneously expand the data quality and quantity available to core Echinobase users. Database URL: https://echinobase.org.

Figure 1.

(A) Rationale behind taxon choice for orthology analyses at Echinobase. Black arrows represent analyses that have been performed. We have so far used Anneissia japonica for Crinoidea analysis and both Acanthaster planci and Patiria miniata for Asteroidea. Gray arrows show analyses planned for integration (e.g. between S. purpuratus and Mus musculus, Xenopus tropicalis). This demonstrates our use as S. purpuratus as our reference echinoderm, in that orthologs can be laterally inferred between other echinoderms and non-echinoderms via S. purpuratus. 1:1 ortholog counts for intra-echinoderm analyses are expressed as fractions of the total number of genes in the genome of that species. (B) A species tree, showing the phylogenetic positions of different model metazoan taxa relative to echinoderms (box highlighted in yellow). Branch lengths are not drawn to scale. Numbers beside the nodes are estimated times in millions of years which, along with the topology, are adapted from the studies by Cary and Hinman, Delsuc et al. and Dohrmann and Wörheide (34–36). Echinoderms are an extremely diverse group; different classes of echinoderm are distantly related to each other.

Figure 2.

A sample gene summary page for foxa1. The updated developmental time course is shown in the top right. The ortholog of the gene in different echinoderms, as predicted by our pipeline, is seen under the ‘Echinobase Gene ID’ section. The gene can be viewed in JBrowse by clicking the links under the ‘Genomic’ section. Additional orthologs to non-echinoderm species as predicted by NCBI and are reported under the ‘Orthology’ section.

Figure 3.

A screenshot of the S. purpuratus v5.0 genome browser displaying the labeled 18 hours post-fertilization ATAC-seq peaks and peak scores.