Gene duplication and genetic innovation in cereal genomes

Guo, Hui; Jiao, Yuannian; Tan, Xu; Wang, Xiyin; Huang, Xianzhong; Jin, Huizhe; Paterson, Andrew H.

doi:10.1101/gr.237511.118

Gene duplication and genetic innovation in cereal genomes

Journal Article · Tue Jan 15 23:00:00 EST 2019 · Genome Research

DOI:https://doi.org/10.1101/gr.237511.118· OSTI ID:1625637

Guo, Hui ^[1]; Jiao, Yuannian ^[2]; Tan, Xu ^[3]; Wang, Xiyin ^[4]; Huang, Xianzhong ^[5]; Jin, Huizhe ^[3]; Paterson, Andrew H. ^[3]

Univ. of Georgia, Athens, GA (United States); DuPont Pioneer, Johnston, IA (United States); OSTI
Univ. of Georgia, Athens, GA (United States); Chinese Academy of Sciences (CAS), Beijing (China)
Univ. of Georgia, Athens, GA (United States)
Univ. of Georgia, Athens, GA (United States); Hebei United Univ. (China)
Univ. of Georgia, Athens, GA (United States); Shihezi Univ. (China)

Organisms continuously require genetic variation to adapt to fluctuating environments, yet major evolutionary events are episodic, making the relationship between genome evolution and organismal adaptation of considerable interest. Here, by genome-wide comparison of sorghum, maize, and rice SNPs, we investigated reservoirs of genetic variations with high precision. For sorghum and rice, which have not experienced whole-genome duplication in 96 million years or more, tandem duplicates accumulate relatively more SNPs than paralogous genes retained from genome duplication. However, maize, which experienced lineage-specific genome duplication and has a relatively larger supply of paralogous duplicates, shows SNP enrichment in paralogous genes. The proportion of genes showing signatures of recent positive selection is higher in small-scale (tandem and transposed) than genome-scale duplicates in sorghum, but the opposite is true in maize. A large proportion of recent duplications in rice are species-specific; however, most recent duplications in sorghum are derived from ancestral gene families. A new retrotransposon family was also a source of many recent sorghum duplications, illustrating a role in providing variation for genetic innovations. This study shows that diverse evolutionary mechanisms provide the raw genetic material for adaptation in taxa with divergent histories of genome evolution.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of California, Oakland, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625637

Journal Information:: Genome Research, Journal Name: Genome Research Journal Issue: 2 Vol. 29; ISSN 1088-9051

Publisher:: Cold Spring Harbor Laboratory PressCopyright Statement

Country of Publication:: United States

Language:: English

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