基于转录组数据揭示4种兜兰的全基因组复制历史
收稿日期: 2021-06-22
录用日期: 2021-11-24
网络出版日期: 2021-11-24
基金资助
中央林业改革发展资金(粤财资环[2019]5号)
Revealing the New Whole-genome Duplication Event of Four Paphiopedilum Species Based on Transcriptome Data
Received date: 2021-06-22
Accepted date: 2021-11-24
Online published: 2021-11-24
多倍化或全基因组复制(WGD)是物种多样性发生的重要驱动力。目前, 在蕨类、菊科以及豆科等类群丰富的植物中已多次报道全基因组复制事件, 而兰科(Orchidaceae)全基因组复制事件报道极少, 与其丰富的物种多样性存在矛盾, 推测与前期样本量小但类群跨度大的研究策略有关。选取染色体数目变异丰富且多样性较高的兜兰属(Paphiopedilum)为兰科植物代表类群, 基于共享数据库中4种兜兰的转录组数据, 采用同义替换率(Ks)、系统发生基因组学以及相对定年的方法分析兜兰属植物是否发生过全基因组复制事件。结果表明, 在4种兜兰中均检测到3次全基因组复制事件, 分别发生在110.17-119.77 Mya (WGD1)、60.95-74.19 Mya (WGD2)和38.19-45.85 Mya (WGD3)。其中, WGD3为新检测到的全基因组复制事件, 推测其发生在杓兰亚科(Cypripedioideae)与姐妹类群分化后, 兜兰属与姐妹类群分化之前。此外, 3次全基因组复制事件发生后优先保留的基因拷贝在功能上多与当时的环境胁迫响应相关, 推测全基因组复制提高了兜兰属植物祖先对当时极端环境变化的适应性。
王蒙, 王婷, 夏增强, 李廷章, 金效华, 严岳鸿, 陈建兵 . 基于转录组数据揭示4种兜兰的全基因组复制历史[J]. 植物学报, 2021 , 56(6) : 699 -714 . DOI: 10.11983/CBB21100
Polyploidization or whole-genome duplication (WGD) is a major driving force in species diversification. Repeated WGD has been found in species-rich groups or families such as ferns, Asteraceae or Fabaceae. However, there is a paradox between the abundant species diversity of Orchidaceae and the rarely discovered WGD events. We hypothesized that it could be due to the early research strategy of a small sample size of species belonging to not closely related groups. Paphiopedilum has a rich variation on chromosome number and morphology. Here, we select it as the representative group of orchids, and use the synonymous substitution rate (Ks), phylogenomic and relative dating methods to detect whether WGD events have been occurred in P. armeniacum, P. concolor, P. hirsutissimum or P. malipoense based on the shared transcriptome data. The result shows that three WGDs are detected in all four species of Paphiopedilum, which occurred in 110.17-119.77 Mya (WGD1), 60.95-74.19 Mya (WGD2), and 38.19-45.85 Mya (WGD3), respectively. WGD3 is a newly detected whole-genome duplication event in orchids and speculated to occur after the differentiation of Cypripedioideae and its sister groups, but before the differentiation of Paphiopedilum and its sister groups. In addition, the retained duplicated genes of three WGDs are functionally related with the environmental stress response at that time. It is speculated that WGD has improved the adaptability of the ancestors of Paphiopedilum to extreme environmental changes.
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