Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China.
State Key Laboratory for Agrobiotechnology, National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China.
Cell Res. 2022 Oct;32(10):878-896. doi: 10.1038/s41422-022-00685-z. Epub 2022 Jul 12.
Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. Our pan-genome reveals extensive structural variations (SVs) and gene presence/absence variations. Additionally, our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter- and intraspecific diversity. Moreover, we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes. We characterized genetic variants associated with submergence tolerance, seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice. This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species.
大规模自然群体的泛基因组可以捕获遗传多样性并揭示基因组的复杂性。我们使用从头长读长组装技术，生成了一个基于图的超级泛基因组，其中包含了一个由 251 个亚洲和非洲水稻栽培和野生种组成的面板。我们的泛基因组揭示了广泛的结构变异（SVs）和基因存在/缺失变异。此外，我们的泛基因组能够准确识别核苷酸结合亮氨酸重复基因，并对其种间和种内多样性进行特征描述。此外，我们发现了与粒重相关的 SVs，这些 SVs 通过影响其附近基因的表达来指定性状。我们对与耐淹、种子破碎和植物结构相关的遗传变异进行了特征描述，并发现了一组共同的基因受到独立选择，这些基因推动了亚洲和非洲水稻的适应和驯化。这个超级泛基因组有助于确定与性状相关基因的谱系特异性单倍型，并深入了解塑造各种水稻基因组结构的进化事件。
