Institution of Genomics and Bioinformatics, South China Agricultural University, 510642, Guangzhou, China.
Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern, Kunming Institute of Botany, Chinese Academy of Sciences, 650204, Kunming, China.
Commun Biol. 2020 Apr 7;3(1):167. doi: 10.1038/s42003-020-0890-8.
Asian cultivated rice is believed to have been domesticated from a wild progenitor, Oryza rufipogon, offering promising sources of alleles for world rice improvement. Here we first present a high-quality chromosome-scale genome of the typical O. rufipogon. Comparative genomic analyses of O. sativa and its two wild progenitors, O. nivara and O. rufipogon, identified many dispensable genes functionally enriched in the reproductive process. We detected millions of genomic variants, of which large-effect mutations could affect agronomically relevant traits. We demonstrate how lineage-specific expansion of gene families may have contributed to the formation of reproduction isolation. We document thousands of genes with signatures of positive selection that are mainly involved in the reproduction and response to biotic- and abiotic stresses. We show that selection pressures may serve as forces to govern substantial genomic alterations that form the genetic basis of rapid evolution of mating and reproductive systems under diverse habitats.
亚洲栽培稻被认为是由野生祖先进化而来的，为世界水稻改良提供了有希望的等位基因来源。在这里，我们首先呈现了一个高质量的典型 O. rufipogon 染色体水平的基因组。对 O. sativa 及其两个野生祖先进化的比较基因组分析，鉴定出了许多在生殖过程中功能丰富的非必需基因。我们检测到了数百万个基因组变异，其中大效应突变可能会影响农艺相关性状。我们展示了基因家族的谱系特异性扩张如何可能有助于生殖隔离的形成。我们记录了数千个具有正选择特征的基因，这些基因主要涉及繁殖和对生物及非生物胁迫的反应。我们表明，选择压力可能是控制重大基因组改变的力量，这些改变构成了在不同生境下交配和生殖系统快速进化的遗传基础。
