Whole-Genome Duplication Reshaped Adaptive Evolution in a Relict Plant Species, Cyclocarya Paliurus

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.

Genomic insights into biased allele loss and increased gene numbers after genome duplication in autotetraploid Cyclocarya paliurus

“…The unique chromosome number was considered to be the distinctness of Cyclocarya from its sister genus Pterocarya [ 19 ]. However, Zheng et al [ 21 ] and Qu et al [ 22 ] recently found that C. paliurus includes autotetraploid individuals with 64 chromosomes. Therefore, the autotetraploid individuals may previously have been wrongly regarded as diploids with a unique aneuploid chromosome number.…”

“…Therefore, the autotetraploid individuals may previously have been wrongly regarded as diploids with a unique aneuploid chromosome number. Considering that the sister genera Pterocarya and Juglans are diploid with 2 n = 2 x = 32, it is highly possible that C. paliurus is a naturally diploid–autotetraploid species [ 22 ], providing a powerful basis for investigating autotetraploid origins and genome evolution.…”

Effects on the Synthesis and Accumulation of Triterpenes in Leaves of Cyclocarya paliurus under MeJA Treatment

“…Cyclocarya paliurus is the only species in the family Juglandaceae and has medicinal, healthcare, material, and ornamental values. It is also called "Qing-qian-liu" or "Yaoqian-shu" because its fruit cluster is seen as a string of old Chinese copper coins [1][2][3]. Various bioactive constituents are found in the leaves of C. paliurus, including flavonoids, triterpenes, polysaccharides, and steroids, which have been shown to have pharmaceutical bioactivities [4][5][6].…”

Metabolomics and transcriptomics analyses provide new insights into the nutritional quality during the endosperm development of different ploidy rice

“…While exploring the improvement of rice yield, the nutritional quality and stress resistance of rice must also be increased. In nature, polyploids are extensively present ( Van de Peer et al., 2017 ; Qu et al., 2023 ). Most angiosperms, most eukaryotes, and crops such as rice have all undergone polyploidization during the course of evolution ( Xiong et al., 2022 ; He et al., 2023 ).…”