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

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 

机构地区：[1]Hubei Hongshan Laboratory,College of Biomedicine and Health,Huazhong Agricultural University,Wuhan 430070,China [2]Hubei Key Laboratory of Agricultural Bioinformatics,College of Life Science and Technology,Huazhong Agricultural University,Wuhan 430070,China [3]Center for Ecological and Environmental Sciences,Northwestern Polytechnical University,Xi’an 710072,China [4]Interdisciplinary Sciences Institute,Huazhong Agricultural University,Wuhan 430070,China [5]Shenzhen Institute of Nutrition and Health,Huazhong Agricultural University,Shenzhen 518000,China [6]Shenzhen Branch,Guangdong Laboratory for Lingnan Modern Agriculture,Genome Analysis Laboratory of the Ministry of Agriculture,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Shenzhen 518000,China

出　　处：《Journal of Genetics and Genomics》2021年第12期1122-1129,共8页遗传学报（英文版）

基　　金：supported by the National Natural Science Foundation of China(31871305);the Fundamental Research Funds for the Central Universities(2662019PY003,2662020PY001);HZAU-AGIS Cooperation Fund(SZYJY2021010);Huazhong Agricultural University Scientific&Technological Self-innovation Foundation(2016RC011)。

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 Gen Origin(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 Gen Origin, 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.

关 键 词：Gene age Gene family Comparative analysis 

分 类 号：Q811.4[生物学—生物工程]