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

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

doi:10.1016/j.jgg.2021.03.018

Volume 48 Issue 12

Dec. 2021

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Article Navigation > Journal of Genetics and Genomics > 2021 > 48(12): 1122-1129

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

doi: 10.1016/j.jgg.2021.03.018

a. Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China;
b. Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
c. Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China;
d. Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China;
e. Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China;
f. 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

Funds:

the Fundamental Research Funds for the Central Universities (2662019PY003, 2662020PY001)

and Huazhong Agricultural University Scientific & Technological Self-innovation Foundation (2016RC011). Funding for open access charge:National Natural Science Foundation of China.

We gratefully acknowledge Manyuan Long from the University of Chicago and Yong E. Zhang from the Institute of Zoology, Chinese Academy of Sciences, for the helpful suggestions. We thank Zhongliang Xue for providing the jingwei origin figure on the web page. We are also grateful to our users and all members in our lab for their valuable suggestions and comments. This work was supported by the National Natural Science Foundation of China (31871305)

HZAU-AGIS Cooperation Fund (SZYJY2021010)

Received Date: 2021-03-02
Accepted Date: 2021-03-29
Rev Recd Date: 2021-03-21
Publish Date: 2021-12-20

Abstract

Abstract

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.
- Gene age,
- Gene family,
- Comparative analysis

These authors contributed equally to this work.

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References(39)

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