Wang Xin, Li Ning, Wang Qian, Lei Tian-Yu, Zhou Ju, Zhang Fu-Min, Liao Xue-Zhu, Qiang Cheng-Gen, Yu Wen-Hao, Han Jing-Dan, Ye Ya-Rong, Jing Chun-Yan, Wang Mei-Xia, Gao Qiang, Chen Jin-Feng, Jiao Yuan-Nian, Wu Zhi-Qiang, Guo Ya-Long, Wing Rod A, Doyle Jeff J, Ge Song, Zou Xin-Hui
State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
China National Botanical Garden, Beijing 100093, China.
Proc Natl Acad Sci U S A. 2025 Jul;122(26):e2424854122. doi: 10.1073/pnas.2424854122. Epub 2025 Jun 26.
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 and its two diploid progenitors, and , and employed a population genomic approach to investigate the diploidization process in 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.
多倍体生物从其最初的基因组加倍状态通过一系列统称为二倍体化的过程进化而来，其速度和模式仍知之甚少，主要是因为难以区分多倍体后的从头进化与从祖先遗传的变异。在这里，我们为野生稻异源多倍体及其两个二倍体祖先物种和生成了染色体水平的基因组组装，并采用群体基因组方法在序列和转录组水平上研究中的二倍体化过程。我们表明，这种野生稻异源多倍体起源于约70万年前，在随后的二倍体化过程中，其两个亚基因组与现存二倍体祖先的基因组保持了高度保守的同线性。这种群体方法使我们能够区分遗传变异的亲本遗留和多倍体后进化，我们的分析表明，虽然基因分馏在早期爆发中发生，但转座元件（TEs）的积累和同源交换是渐进的。同源基因表达偏向模式在不同组织中高度可变，没有一致的亚基因组表达偏向。我们对DNA甲基化、TE分布和亲本遗留在表达模式上的影响的评估为TE负荷理论（即基因侧翼区域中的TE密度强烈影响表达水平的理论）提供了一些支持，同时也说明了转录调控的复杂性。
