山眉(Rubus corchorifolius)基因组组装和种群重测序揭示其地理分化

IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY
Yinqing Yang , Kang Zhang , Ya Xiao , Lingkui Zhang , Yile Huang , Xing Li , Shumin Chen , Yansong Peng , Shuhua Yang , Yongbo Liu , Feng Cheng
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引用次数: 3

摘要

山莓(Rubus corchorifolius)在中国广泛分布,其果实具有很高的营养价值和药用价值。在此,我们报道了山梅高质量的染色体尺度基因组组装,其基因组大小为215.69 Mb,基因26,696个。蔷薇科种间基因组比较结果显示,山梅与富盆子亲缘关系最近,其次是黑莓,且环境适应相关基因在山梅基因组中扩增。对中国云南、湖南、江西、四川4个地区的101份山眉标本进行重测序,结果表明,山眉的湖南种群具有最高的多样性,代表了更多的祖先种群。此外,基于核苷酸多样性、连锁不平衡和历史有效群体大小分析,云南种群经历了强选择。此外,在黄酮类生物合成途径和植物激素信号转导途径中,来自表现出强烈分化的候选基因组区域的基因显著富集,表明山梅对当地环境的适应具有遗传基础。山梅高质量的基因组组装和多样性数据集为育种应用和阐明树属物种的基因组进化和生态适应提供了宝贵的资源。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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

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

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

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

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.

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来源期刊
Genomics, Proteomics & Bioinformatics
Genomics, Proteomics & Bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry
CiteScore
14.30
自引率
4.20%
发文量
844
审稿时长
61 days
期刊介绍: Genomics, Proteomics and Bioinformatics (GPB) is the official journal of the Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China. It aims to disseminate new developments in the field of omics and bioinformatics, publish high-quality discoveries quickly, and promote open access and online publication. GPB welcomes submissions in all areas of life science, biology, and biomedicine, with a focus on large data acquisition, analysis, and curation. Manuscripts covering omics and related bioinformatics topics are particularly encouraged. GPB is indexed/abstracted by PubMed/MEDLINE, PubMed Central, Scopus, BIOSIS Previews, Chemical Abstracts, CSCD, among others.
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