High-speed rail model reveals the gene tandem amplification mediated by short repeated sequence in eukaryote

Haidi Chen; Jingwen Xue; Zhenghou Zhang; Geyu Zhang; Xinyuan Xu; He Li; Ruxue Zhang; Najeeb Ullah; Lvxing Chen; Amanullah; Zhuqing Zang; Shanshan Lai; Ximiao He; Wei Li; Miao Guan; Jingyi Li; Liangbiao Chen; Cheng Deng

doi:10.1038/s41598-022-06250-3

High-speed rail model reveals the gene tandem amplification mediated by short repeated sequence in eukaryote

Sci Rep. 2022 Feb 10;12(1):2289. doi: 10.1038/s41598-022-06250-3.

Authors

Haidi Chen^#¹, Jingwen Xue^#¹, Zhenghou Zhang^#², Geyu Zhang^#¹, Xinyuan Xu¹, He Li¹, Ruxue Zhang¹, Najeeb Ullah¹, Lvxing Chen¹, Amanullah¹, Zhuqing Zang¹, Shanshan Lai¹, Ximiao He^{3

4

5}, Wei Li⁶, Miao Guan⁷, Jingyi Li⁸, Liangbiao Chen⁹, Cheng Deng¹⁰

Affiliations

¹ Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China.
² The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China.
³ Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
⁴ Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
⁵ Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
⁶ Department of Dermatovenereology, Institutes for Systems Genetics, Rare Disease Center, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang Street, Chengdu, 610041, Sichuan, China.
⁷ Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China. xiaoniao8911@126.com.
⁸ M.D. Department of Dermatology and Venereology, West China Hospital of Sichuan University, No. 37 Guo Xue Lane, Chengdu, 610041, China. ljy7733@163.com.
⁹ Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Institute of Experimental Pathology, Shanghai Ocean University, Shanghai, 201306, China. lbchen@shou.edu.cn.
¹⁰ Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China. dengcheng2014@126.com.

^# Contributed equally.

Abstract

The occurrence of gene duplication/amplification (GDA) provide potential material for adaptive evolution with environmental stress. Several molecular models have been proposed to explain GDA, recombination via short stretches of sequence similarity plays a crucial role. By screening genomes for such events, we propose a "SRS (short repeated sequence) *N + unit + SRS*N" amplified unit under USCE (unequal sister-chromatid exchange) for tandem amplification mediated by SRS with different repeat numbers in eukaryotes. The amplified units identified from 2131 well-organized amplification events that generate multi gene/element copy amplified with subsequent adaptive evolution in the respective species. Genomic data we analyzed showed dynamic changes among related species or subspecies or plants from different ecotypes/strains. This study clarifies the characteristics of variable copy number SRS on both sides of amplified unit under USCE mechanism, to explain well-organized gene tandem amplification under environmental stress mediated by SRS in all eukaryotes.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adaptation, Biological / genetics
Biological Evolution
Environment
Eukaryota / genetics*
Gene Amplification*
Models, Molecular*
Repetitive Sequences, Nucleic Acid*