Hainan Institute of Zhejiang University, Sanya, 572025, China.
Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
Genome Biol. 2023 Aug 3;24(1):179. doi: 10.1186/s13059-023-03017-5.
Asian rice is one of the world's most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the evolution of rice is still under debate.
Here, we construct a syntelog-based rice pan-genome by integrating and merging 74 high-accuracy genomes based on long-read sequencing, encompassing all ecotypes and taxa of Oryza sativa and Oryza rufipogon. Analyses of syntelog groups illustrate subspecies divergence in gene presence-and-absence and haplotype composition and identify massive genomic regions putatively introgressed from ancient Geng/japonica to ancient Xian/indica or its wild ancestor, including almost all well-known domestication genes and a 4.5-Mbp centromere-spanning block, supporting a single domestication event in main rice subspecies. Genomic comparisons between weedy and cultivated rice highlight the contribution from wild introgression to the emergence of de-domestication syndromes in weedy rice.
This work highlights the significance of inter-taxa introgression in shaping diversification and divergence in rice evolution and provides an exploratory attempt by utilizing the advantages of pan-genomes in evolutionary studies.
亚洲稻是世界上种植最广泛的作物之一。为了探索亚洲稻的驯化和去驯化基因组历史，已经进行了大规模的重测序分析，但水稻的进化仍存在争议。
在这里，我们通过整合和合并基于长读测序的 74 个高精度基因组，构建了基于 syntelog 的水稻泛基因组，涵盖了 Oryza sativa 和 Oryza rufipogon 的所有生态型和分类群。对 syntelog 组的分析说明了亚种在基因存在和缺失以及单倍型组成上的分歧，并确定了大量可能从古代粳稻/日本稻或其野生祖先中渗入的基因组区域，包括几乎所有著名的驯化基因和一个 4.5-Mbp 的着丝粒跨越的块，支持主要稻亚种的单次驯化事件。杂草稻和栽培稻之间的基因组比较突出了野生基因渗入对杂草稻去驯化综合征出现的贡献。
这项工作强调了种间基因渗入在塑造水稻进化中的多样化和分化方面的重要性，并通过利用泛基因组在进化研究中的优势进行了探索性尝试。
