Cytoplasmic male sterility (CMS) is a widely used genetic tool in modern hybrid rice breeding. Most genes conferring rice gametophytic CMS are homologous to orf79 and co‐transcribe with atp6. However, the origin, differentiation and flow of these mitochondrial genes in wild and cultivated rice species remain unclear. In this study, we performed de novo assembly of the mitochondrial genomes of 221 common wild rice (Oryza rufipogon Griff.) and 369 Asian cultivated rice (Oryza sativa L.) accessions, and identified 16 haplotypes of atp6‐orf79‐like structures and 11 orf79 alleles. These homologous structures were classified into 4 distinct groups (AO‐I, AO‐II, AO‐III and AO‐IV), all of which were observed in O. rufipogon but only AO‐I was detected in O. sativa, causing a decrease in the frequency of atp6‐orf79‐like structures from 19.9% to 8.1%. Phylogenetic and biogeographic analyses revealed that the different groups of these gametophytic CMS‐related genes in O. rufipogon evolved in a multicentric pattern. The geographical origin of the atp6‐orf79‐like structures was further traced back, and a candidate region in north‐east of Gangetic Plain on the Indian Peninsula (South Asia) was identified as the origin centre of AO‐I. The orf79 alleles were detected in all three cytoplasmic types (Or‐CT0, Or‐CT1 and Or‐CT2) of O. rufipogon, but only two alleles (orf79a and orf79b) were observed in Or‐CT0 type of O. sativa, while no orf79 allele was found in other types of O. sativa. Our results also revealed that the orf79 alleles in cultivated rice originated from the wild rice population in South and South‐East Asia. In addition, strong positive selection pressure was detected on the sequence variations of orf79 alleles, and a special evolutionary strategy was noted in these gametophytic CMS‐related genes, suggesting that their divergence could be beneficial to their survival in evolution.

中文翻译：

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atp6-orf79-like结构的多中心起源和多样性揭示了水稻Oryza rufipogon和Oryza sativa中的线粒体基因流

细胞质雄性不育（CMS）是现代杂交水稻育种中广泛使用的遗传工具。赋予水稻配子体CMS的大多数基因与orf79同源，并与atp6共转录。然而，这些线粒体基因在野生和栽培稻种中的起源，分化和流动仍不清楚。在这项研究中，我们对221种普通野生稻（Oryza rufipogon Griff。）和369种亚洲栽培稻（Oryza sativa L.）的线粒体基因组进行了从头组装，并鉴定了16种atp6-orf79样结构的单倍型和11种单倍型orf79等位基因。这些同源结构被分为4个不同的组（AO-I，AO-II，AO-III和AO-IV），所有这些组均在rufipogon中观察到，但在O. sativa中仅检测到AO-I ，从而导致atp6-orf79样结构的频率从19.9％降低到8.1％。系统发育和生物地理分析表明，这些配子体CMS相关基因在不同群体野生稻的多中心格局演变。进一步追溯了atp6-orf79样结构的地理起源，并确定了印度半岛（南亚）恒河平原东北部的候选区域为AO-1的起源中心。该orf79rufipogon的所有三种细胞质类型（Or-CT0，Or-CT1和Or-CT2）中均检测到等位基因，但在Or-CT0型水稻中仅观察到两个等位基因（orf79a和orf79b），而没有orf79在其他类型的水稻中也发现了等位基因。我们的结果还显示，栽培稻中的orf79等位基因源自南亚和东南亚的野生稻种群。此外，在orf79的序列变异上检测到较强的正选择压力 等位基因，并在这些配子体CMS相关基因中注意到了一种特殊的进化策略，这表明它们的差异可能有利于它们在进化中的生存。