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

Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms

“…Echinobase adopted the methods and best practices developed by the DIOPT consortia to predict orthology, as described in detail by Foley et al. ( 25 ). These are used in two ways; to assign gene names consistent with human nomenclature according to HUGO Gene Nomenclature Committee (HGNC), and to map relationships between genomes in different echinoderm species.…”

“…We also run the DIOPT tool set internally to build pairwise orthology sets between echinoderm species. To date, Echinobase has integrated seven different methods for inferring such orthologies: InParanoid v4.1 ( 28 , 29 ), PhylomeDB as described in ( 25 ) ProteinOrtho ( 30 ), SwiftOrtho ( 31 ) and FastOrtho ( https://github.com/olsonanl/FastOrtho ) are run with e -values set to 1e–40, with FastOrtho, OMA ( 32 ) and OrthoFinder ( 33 ) run with default settings. RefSeq identifiers for each hit are converted to Entrez IDs, and outputs are subsequently pooled.…”

New hypotheses of cell type diversity and novelty from comparative single cell and nuclei transcriptomics in echinoderms

“…In order to directly compare sea star and sea urchin cell types, we projected the datasets from the two species into a single shared space (Figure 8.B). We took advantage of extensive orthology analysis that has identified 1:1 orthologs between P. miniata and S. purpuratus , using a DIOPT-like system (Foley et al, 2021) and subsetted the datasets to only include 1:1 orthologs that are expressed in both datasets (see methods). This filtered gene set had 5,790 genes (28.3% of P. miniata’s total genes, 21.7% of S. purpuratus’ total genes), removing species-specific genes and genes with 1:many orthologs from our analysis.…”

“…1:1 orthologs were identified between S. purpuratus genome V 5.0 and P. miniata genome V3.0 and named according to orthologs identified in the human genome. For a full description of ortholog identification see Foley et al, 2021. To facilitate dataset integration, where applicable, the gene IDs in P. miniata datasets were converted to their orthologous S. purpuratus gene IDs.…”

“…Ortholog identification and multi-species integration 1:1 orthologs were identified between S. purpuratus genome V 5.0 and P. miniata genome V3.0 and named according to orthologs identified in the human genome. For a full description of ortholog identification see Foley et al, 2021. To facilitate dataset integration, where applicable, the gene IDs in P. miniata datasets were converted to their orthologous S. purpuratus gene IDs. In total, 5790 of the 5935 1:1 orthologous genes identified between both species were expressed in at least 2 cells/nuclei in a dataset.…”