Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China.
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China; Biotechnology Research Center, Xiangxi Academy of Agricultural Sciences, Jishou 416000, China.
Genomics Proteomics Bioinformatics. 2022 Dec;20(6):1106-1118. doi: 10.1016/j.gpb.2022.05.003. Epub 2022 May 25.
Rubus corchorifolius (Shanmei or mountain berry, 2n = 14) is widely distributed in China, and its fruits possess high nutritional and medicinal values. Here, we reported a high-quality chromosome-scale genome assembly of Shanmei, with contig size of 215.69 Mb and 26,696 genes. Genome comparison among Rosaceae species showed that Shanmei and Fupenzi (Rubus chingii Hu) were most closely related, followed by blackberry (Rubus occidentalis), and that environmental adaptation-related genes were expanded in the Shanmei genome. Further resequencing of 101 samples of Shanmei collected from four regions in the provinces of Yunnan, Hunan, Jiangxi, and Sichuan in China revealed that among these samples, the Hunan population of Shanmei possessed the highest diversity and represented the more ancestral population. Moreover, the Yunnan population underwent strong selection based on the nucleotide diversity, linkage disequilibrium, and historical effective population size analyses. Furthermore, genes from candidate genomic regions that showed strong divergence were significantly enriched in the flavonoid biosynthesis and plant hormone signal transduction pathways, indicating the genetic basis of adaptation of Shanmei to the local environment. The high-quality assembled genome and the variome dataset of Shanmei provide valuable resources for breeding applications and for elucidating the genome evolution and ecological adaptation of Rubus species.
山莓（Shanmei 或山莓，2n=14）广泛分布于中国，其果实具有较高的营养价值和药用价值。本研究报道了山莓高质量的染色体水平基因组组装，contig 大小为 215.69Mb，包含 26696 个基因。蔷薇科物种的基因组比较表明，山莓与伏盆（Rubus chingii Hu）亲缘关系最近，其次是黑莓（Rubus occidentalis），山莓基因组中与环境适应相关的基因得到了扩展。对来自中国云南、湖南、江西和四川四省四个地区的 101 份山莓样本进行重测序后发现，这些样本中，湖南山莓群体具有最高的多样性，代表了更原始的群体。此外，基于核苷酸多样性、连锁不平衡和历史有效种群大小分析，云南山莓群体经历了强烈的选择。此外，候选基因组区域中表现出强烈分化的基因在类黄酮生物合成和植物激素信号转导途径中显著富集，表明了山莓适应当地环境的遗传基础。高质量组装的基因组和山莓的变基因组数据集为山莓的育种应用和解析蔷薇属物种的基因组进化和生态适应提供了有价值的资源。
