Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

BMC Biology

Research Article

Mingrui Xu¹  Zhanghui Zeng²  Ning Han³  Muyuan Zhu³  B. Buerte³  Hongwu Bian³  Calum Watt⁴  Yong Jia⁵  Haifei Hu⁵  Brett Chapman⁵  Chengdao Li⁶ 

[1] College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China;College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China;Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, 310058, Hangzhou, China;Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, 311121, Hangzhou, China;Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, 310058, Hangzhou, China;Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, 6150, Murdoch, WA, Australia;Intergrain Pty Ltd, 6163, Bibra Lake, WA, Australia;Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, 6150, Murdoch, WA, Australia;Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, 6150, Murdoch, WA, Australia;Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, 6150, Murdoch, WA, Australia;Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, 6150, Murdoch, WA, Australia;Department of Primary Industries and Regional Development, 3-Baron-Hay Court, 6151, South Perth, WA, Australia;

关键词: Gene duplication;    Gene retention;    Homogentisate phytyltransferase;    Pangenome;    Plant defense responses;    Positive selection;    Relaxed selection;    Vitamin E;   

DOI  :  10.1186/s12915-022-01503-z

 received in 2022-03-27, accepted in 2022-12-16,  发布年份 2022

来源: Springer

【 摘 要 】

BackgroundGene duplication is a prevalent phenomenon and a major driving force underlying genome evolution. The process leading to the fixation of gene duplicates following duplication is critical to understand how genome evolves but remains fragmentally understood. Most previous studies on gene retention are based on gene duplicate analyses in single reference genome. No population-based comparative gene retention analysis has been performed to date.ResultsTaking advantage of recently published genomic data in Triticeae, we dissected a divergent homogentisate phytyltransferase (HPT2) lineage caught in the middle stage of gene fixation following duplication. The presence/absence of HPT2 in barley (diploid), wild emmer (tetraploid), and bread wheat (hexaploid) pangenome lines appears to be associated with gene dosage constraint and environmental adaption. Based on these observations, we adopted a phylogeny-based orthology inference approach and performed comparative gene retention analyses across barley, wild emmer, and bread wheat. This led to the identification of 326 HPT2-pattern-like genes at whole genome scale, representing a pool of gene duplicates in the middle stage of gene fixation. Majority of these HPT2-pattern-like genes were identified as small-scale duplicates, such as dispersed, tandem, and proximal duplications. Natural selection analyses showed that HPT2-pattern-like genes have experienced relaxed selection pressure, which is generally accompanied with partial positive selection and transcriptional divergence. Functional enrichment analyses showed that HPT2-pattern-like genes are over-represented with molecular-binding and defense response functions, supporting the potential role of environmental adaption during gene retention. We also observed that gene duplicates from larger gene family are more likely to be lost, implying a gene dosage constraint effect. Further comparative gene retention analysis in barley and bread wheat pangenome lines revealed combined effects of species-specific selection and gene dosage constraint.ConclusionsComparative gene retention analyses at the population level support gene dosage constraint, environmental adaption, and species-specific selection as three factors that may affect gene retention following gene duplication. Our findings shed light on the evolutionary process leading to the retention of newly formed gene duplicates and will greatly improve our understanding on genome evolution via duplication.

【 授权许可】

CC BY   
© The Author(s) 2023

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