GenOrigin: A Comprehensive Protein-coding Gene Origination Database on the Evolutionary Timescale of Life

Abstract

The origination of new genes contributes to the biological diversity of life. New genes may quickly build their own network in the genomes, exert important functions, and generate novel phenotypes. Dating gene age and inferring the origination mechanisms of new genes, like primate-specific gene, is the basis for the functional study of the genes. However, no comprehensive resource of gene age estimates across species is available. Here, we systematically dated the age of 9,102,113 protein-coding genes from 565 species in the Ensembl and Ensembl Genomes databases, including 82 bacteria, 57 protists, 134 fungi, 58 plants, 56 metazoa, and 178 vertebrates, using protein-family-based pipeline with Wagner parsimony algorithm. We also collected gene age estimate data from other studies and uniformed the gene age estimates to time ranges in million years for comparison across studies. All the data were cataloged into GenOrigin (http://genorigin.chenzxlab.cn/), a user-friendly new database of gene age estimates, where users can browse gene age estimates by species, age and gene ontology. In GenOrigin, the information such as gene age estimates, annotation, gene ontology, ortholog and paralog, as well as detailed gene presence/absence views for gene age inference based on the species tree with evolutionary timescale, was provided to researchers for exploring gene functions.

Evolution and function of developmentally dynamic pseudogenes in mammals

“…We also observed the DDPs were more conserved than non-dynamic ones and exhibited a remarkable increase in the proportion of evolutionarily old pseudogenes (Spearman correlation rho = 0.94, P < 2 × 10 −16 ) (Additional file 1: Figs. S25-S26), indicating that it took time, albeit short, for pseudogenes to acquire dynamic expression and to interact with more genes, thus integrating into pre-existing networks after birth [50,51]. Overall, the above patterns across multiple regulatory layers provided functional evidences for DDPs.…”

Histone H3K27 Methylation Perturbs Transcriptional Robustness and Underpins Dispensability of Highly Conserved Genes in Fungi

“…The outline of the data sets used in the study based on orthology conservation is available in figure 1 B . To infer the age of highly conserved genes in Fusarium , we used the F. oxysporum gene set available from the Geneorigin database covering 565 species from Ensembl and Ensembl Genomes databases following the protein family-based pipeline based on the Wagner parsimony algorithm ( Tong et al 2020 ). Data set and sequence accessions are listed in supplementary table S1, Supplementary Material online.…”