Genome Assembly and Population Resequencing Reveal the Geographical Divergence of Shanmei(Rubus corchorifolius)  

作　　者：Yinqing Yang Kang Zhang Ya Xiao Lingkui Zhang Yile Huang Xing Li Shumin Chen Yansong Peng Shuhua Yang Yongbo Liu Feng Cheng 

机构地区：[1]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 [2]Biotechnology Research Center,Xiangxi Academy of Agricultural Sciences,Jishou 416000,China [3]Lushan Botanical Garden,Chinese Academy of Sciences,Jiujiang 332900,China [4]State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment,Chinese Research Academy of Environmental Sciences,Beijing 100012,China

出　　处：《Genomics, Proteomics & Bioinformatics》2022年第6期1106-1118,共13页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by the grants from the Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China (Grant No. 2019HJ2096001006);the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences;the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, China

摘　　要：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 highquality 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.

关 键 词：Rubus corchorifolius Genome assembly RESEQUENCING DIVERGENCE Genome evolution 

分 类 号：Q948[生物学—植物学]