Foley S et al. (2022), Evolutionary analyses of genes in Echinodermata...

ECB-ART-50243

Genomics 2022 Jul 01;1144:110431. doi: 10.1016/j.ygeno.2022.110431.

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Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla.

Foley S , Vlasova A , Marcet-Houben M , Gabaldón T , Hinman VF .

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Despite recent studies discussing the evolutionary impacts of gene duplications and losses among metazoans, the genomic basis for the evolution of phyla remains enigmatic. Here, we employ phylogenomic approaches to search for orthologous genes without known functions among echinoderms, and subsequently use them to guide the identification of their homologs across other metazoans. Our final set of 14 genes was obtained via a suite of homology prediction tools, gene expression data, gene ontology, and generating the Strongylocentrotus purpuratus phylome. The gene set was subjected to selection pressure analyses, which indicated that they are highly conserved and under negative selection. Their presence across broad taxonomic depths suggests that genes required to form a phylum are ancestral to that phylum. Therefore, rather than de novo gene genesis, we posit that evolutionary forces such as selection on existing genomic elements over large timescales may drive divergence and contribute to the emergence of phyla.

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Al-Shahrour, FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. 2004, Pubmed

	Fig. 2. GO term enrichment analysis of the genes duplicated at the S. purpuratus level (age #1) for duplications without large expansions, summarized with the REVIGO server. Panel A covers biological processes, and panel B covers molecular function categories.
	Fig. 3. GO term enrichment analysis of the S. purpuratus orphan (i.e., potentially lineage specific) genes, summarized with the REVIGO server. Panel A covers biological processes, and panel B covers molecular function categories.
	Fig. 4. Gene expression in both embryonic and adult tissues represented as a heatmap. In each case, genes in the green bracket corresponding to the purple sea urchin were only recovered in echinoderms, and genes in the green bracket corresponding to the blue InterPro logo were the only ones to record InterPro domains. Panel A shows the raw TPM values for each key developmental timepoint, ranging from 0 to 72 h post-fertilization. Panel B shows the log expression of those TPM values. Expression of our genes of interest is sustained throughout development, generally peaking at 18-24 h. Panel C shows TPM values across six different adult tissues. Panel D shows the log of those values. Expression is also sustained in adult tissues, particularly in the coelomocyte and testes.