数字农科院2.0

GenOrigin: A comprehensive protein-coding gene origination database on the evolutionary timescale of life

文献类型： 外文期刊

作者： Yi Bo Tong;Meng Wei Shi;Sheng Hu Qian;Yu Jie Chen;Zhi Hui Luo;Yi Xuan Tu;Yu Li Xiong;Ying Jie Geng;Chunyan Chen;Zhen Xia Chen

作者机构：

关键词： Comparative analysis;Gene age;Gene family

期刊名称： Journal of Genetics and Genomics

ISSN： 1673-8527

年卷期： 2021 年 48 卷 12 期

页码：

收录情况： JCR（2021版） ; CSCD（2020-2021年度） ; 科技核心（2020版）

摘要： The origination of new genes contributes to the biological diversity of life. New genes may quickly build their network, exert important functions, and generate novel phenotypes. Dating gene age and inferring the origination mechanisms of new genes, like primate-specific genes, 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 date 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 a protein-family-based pipeline with Wagner parsimony algorithm. We also collect gene age estimate data from other studies and uniformly distribute the gene age estimates to time ranges in a million years for comparison across studies. All the data are 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, is provided to researchers for exploring gene functions.

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