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Evolutionary Contribution of Duplicated Genes to Genome Evolution i... |
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by Ming-Rui Li, Ning Ding, Tianyuan Lu, Jing Zhao, Zhen-Hui Wang, Peng... |
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Genes duplicated by whole genome duplication (WGD) and |
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small-scale |
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duplication (SSD) have played important roles in adaptive |
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evolution of |
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all flowering plants. However, it still remains |
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underinvestigated how |
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the distinct models of duplication events and their |
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contending |
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evolutionary patterns have shaped the genome and |
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epigenomes of extant |
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plant species. In this study, we investigated the |
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contribution of the |
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WGD- and SSD-derived duplicate genes to the genome |
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evolution of one |
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diploid and three closely related allotetraploid Panax |
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species |
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based on genome, methylome, and proteome data sets. Our |
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genome-wide |
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comparative analyses revealed that although the ginseng |
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species complex |
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was recently diverged, they have evolved distinct overall |
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patterns of |
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nucleotide variation, cytosine methylation, and protein- |
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level |
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expression. In particular, genetic and epigenetic |
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asymmetries observed |
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in the recent WGD-derived genes are largely consistent |
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across the |
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ginseng species complex. In addition, our results |
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revealed that gene |
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duplicates generated by ancient WGD and SSD mechanisms |
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exhibited |
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distinct evolutionary patterns. We found the ancient WGD- |
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derived genes |
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(i.e., ancient collinear gene) are genetically more |
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conserved and |
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hypomethylated at the cytosine sites. In contrast, some |
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of the |
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SSD-derived genes (i.e., dispersal duplicated gene) |
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showed |
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hypermethylation and high variance in nucleotide |
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variation pattern. |
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Functional enrichment analyses of the duplicated genes |
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indicated that |
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adaptation-related traits (i.e., photosynthesis) created |
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during the |
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distant ancient WGDs are further strengthened by both the |
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more recent |
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WGD and SSD. Together, our findings suggest that |
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different types of |
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duplicated genes may have played distinct but relaying |
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evolutionary |
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roles in the polyploidization and speciation processes in |
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the ginseng |
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species complex. |
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Date Published: 2022-02-01 17:36:09 |
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Identifier: evab051 |
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Item Size: 14640886 |
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Language: eng |
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Media Type: texts |
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# Topics |
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gene duplication model |
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polyploidy |
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DNA methylation |
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gene expression |
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Panax |
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