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12, 2022;20 (6): 1106-1118.

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

Yinqing Yang, Kang Zhang, Ya Xiao, Lingkui Zhang, Yile Huang, Xing Li, Shumin Chen, Yansong Peng, Shuhua Yang, Yongbo Liu, Feng Cheng
Author Information
  1. Yinqing Yang: 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. Kang Zhang: 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.
  3. Ya Xiao: 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.
  4. Lingkui Zhang: 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.
  5. Yile Huang: 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.
  6. Xing Li: 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.
  7. Shumin Chen: 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.
  8. Yansong Peng: Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China.
  9. Shuhua Yang: 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. Electronic address: yangshuhua@caas.cn.
  10. Yongbo Liu: State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China. Electronic address: liuyb@craes.org.cn.
  11. Feng Cheng: 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. Electronic address: chengfeng@caas.cn.
PMID: 35643190 DOI: 10.1016/j.gpb.2022.05.003

Abstract

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.

Keywords

Divergence Genome assembly Genome evolution Resequencing Rubus corchorifolius

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MeSH Term

Rubus
China
Sequence Analysis, DNA
Genomics
Linkage Disequilibrium
Journal Article

Links to CNCB-NGDC Resources

BioProject: PRJCA004000 (Large-scale time-series RNA-seq data for Chinese cabbage)
GSA: CRA003829 (Large-scale time-series RNA-seq data for Chinese cabbage)
GWH: GWHBDNY00000000 (Rubus corchorifolius)

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