Gene duplication and genetic innovation in cereal genomes
- Hui Guo1,2,3,9,
- Yuannian Jiao1,4,9,
- Xu Tan1,
- Xiyin Wang1,5,
- Xianzhong Huang1,6,
- Huizhe Jin1 and
- Andrew H. Paterson1,2,7,8
- 1Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA;
- 2Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA;
- 3DuPont Pioneer, Data Science and Informatics, Johnston, Iowa 50131, USA;
- 4State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
- 5Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University, Tangshan, Hebei 063000, China;
- 6Plant Genomics Laboratory, College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China;
- 7Department of Crop and Soil Sciences, University of Georgia, Athens, Georgia 30602, USA;
- 8Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
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↵9 These authors contributed equally to this work.
Abstract
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.237511.118.
- Received March 25, 2018.
- Accepted December 14, 2018.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
