Whole-genome Duplication Reshaped Adaptive Evolution in A Relict Plant Species, Cyclocarya paliurus.

IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Genomics, Proteomics & Bioinformatics Pub Date : 2023-06-01 Epub Date: 2023-02-11 DOI:10.1016/j.gpb.2023.02.001
Yinquan Qu, Xulan Shang, Ziyan Zeng, Yanhao Yu, Guoliang Bian, Wenling Wang, Li Liu, Li Tian, Shengcheng Zhang, Qian Wang, Dejin Xie, Xuequn Chen, Zhenyang Liao, Yibin Wang, Jian Qin, Wanxia Yang, Caowen Sun, Xiangxiang Fu, Xingtan Zhang, Shengzuo Fang
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Abstract

Cyclocarya paliurus is a relict plant species that survived the last glacial period and shows a population expansion recently. Its leaves have been traditionally used to treat obesity and diabetes with the well-known active ingredient cyclocaric acid B. Here, we presented three C. paliurus genomes from two diploids with different flower morphs and one haplotype-resolved tetraploid assembly. Comparative genomic analysis revealed two rounds of recent whole-genome duplication events and identified 691 genes with dosage effects that likely contribute to adaptive evolution through enhanced photosynthesis and increased accumulation of triterpenoids. Resequencing analysis of 45 C. paliurus individuals uncovered two bottlenecks, consistent with the known events of environmental changes, and many selectively swept genes involved in critical biological functions, including plant defense and secondary metabolite biosynthesis. We also proposed the biosynthesis pathway of cyclocaric acid B based on multi-omics data and identified key genes, in particular gibberellin-related genes, associated with the heterodichogamy in C. paliurus species. Our study sheds light on evolutionary history of C. paliurus and provides genomic resources to study the medicinal herbs.

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青钱柳属植物的全基因组复制重塑适应性进化。
青钱柳是最后一次冰川期幸存下来的一种残余植物,最近种群数量有所增加。传统上,它的叶子被众所周知的活性成分环卡酸B用于治疗肥胖和糖尿病。在这里,我们展示了来自两个具有不同花形态的二倍体和一个单倍型解析的四倍体组合的三个青柳基因组。比较基因组分析揭示了最近两轮全基因组复制事件,并鉴定了691个具有剂量效应的基因,这些基因可能通过增强光合作用和增加三萜类化合物的积累来促进适应性进化。对45个青柳个体的重新测序分析发现了两个瓶颈,这与已知的环境变化事件一致,并且许多选择性地扫描了参与关键生物功能的基因,包括植物防御和次生代谢产物生物合成。基于多组学数据,我们还提出了环卡酸B的生物合成途径,并鉴定了与青柳异源二价体相关的关键基因,特别是赤霉素相关基因。我们的研究揭示了青柳的进化史,并为研究中草药提供了基因组资源。
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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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