数字农科院2.0

Diploidization in a wild rice allopolyploid is both episodic and gradual

文献类型： 外文期刊

作者： Xin Wang;Ning Li;Qian Wang;Tian Yu Lei;Ju Zhou;Fu Min Zhang;Xue Zhu Liao;Cheng Gen Qiang;Wen Hao Yu;Jing Dan Han;Ya Rong Ye;Chun Yan Jing;Mei Xia Wang;Qiang Gao;Jin Feng Chen;Yuan Nian Jiao;Zhi Qiang Wu;Ya Long Guo;Rod A. Wing;Jeff J. Doyle;Song Ge;Xin Hui Zou

作者机构：

关键词： allopolyploid;diploidization;parental legacy;population genomic approach

期刊名称： Proceedings of the National Academy of Sciences of the United States of America

ISSN： 1091-6490

年卷期： 2025 年 122 卷 26 期

页码：

收录情况： SCIE（2025版）

摘要： Polyploid organisms evolve from their initial doubled genomic condition through a number of processes collectively termed diploidization, whose tempo and mode remain poorly understood mainly due to the difficulty of discriminating de novo evolution subsequent to polyploidy from variation inherited from progenitors. Here, we generated chromosome-scale genome assemblies for the wild rice allopolyploid Oryza minuta and its two diploid progenitors, Oryza punctata and Oryza officinalis, and employed a population genomic approach to investigate the diploidization process in O. minuta at the sequence and transcriptomic level. We show that this wild rice allopolyploid originated around 0.7 Mya, and during subsequent diploidization, its two subgenomes have retained highly conserved synteny with the genomes of its extant diploid progenitors. This populational approach allowed us to distinguish parental legacy of inherited variation from postpolyploidy evolution, and our analyses revealed that whereas gene fractionation occurred in an early burst, accumulation of transposable elements (TEs) and homoeologous exchanges has been gradual. Patterns of homoeolog expression bias are highly variable across tissues, with no consistent subgenome expression bias. Our assessments of the impact of DNA methylation, TE distribution, and parental legacy on expression patterns provide some support for the TE load theory (the theory that the TE densities in flanking regions surrounding genes strongly influence expression levels), while also illustrating the complexity of transcription regulation.

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