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

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

Genomics, Proteomics & Bioinformatics (Jun 2023)

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

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

Affiliations

Yinquan Qu: Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Xulan Shang: Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
Ziyan Zeng: Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Yanhao Yu: Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
Guoliang Bian: Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
Wenling Wang: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Li Liu: Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
Li Tian: Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
Shengcheng Zhang: Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Qian Wang: Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
Dejin Xie: Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Xuequn Chen: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Zhenyang Liao: Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Yibin Wang: Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Jian Qin: Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
Wanxia Yang: Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
Caowen Sun: Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
Xiangxiang Fu: Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China; Corresponding authors.
Xingtan Zhang: Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Corresponding authors.
Shengzuo Fang: Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China; Corresponding authors.

Journal volume & issue: Vol. 21, no. 3
pp. 455 – 469

Abstract

Read online

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.

Published in Genomics, Proteomics & Bioinformatics

ISSN: 1672-0229 (Print); 2210-3244 (Online)
Publisher: Oxford University Press
Country of publisher: United Kingdom
LCC subjects: Science: Biology (General); Medicine: Medicine (General): Computer applications to medicine. Medical informatics
Website: https://academic.oup.com/gpb

About the journal

Abstract

Keywords