生物多样性 ›› 2019, Vol. 27 ›› Issue (11): 1221-1227.doi: 10.17520/biods.2019236

• 研究报告 • 上一篇    下一篇

转录组测序揭示翼盖蕨(Didymochlaena trancatula)的全基因组复制历史

汪浩1, 2#, 张锐1#, 张娇1, 沈慧1, 戴锡玲2, 严岳鸿1, *()   

  1. 1 上海辰山植物园, 中国科学院上海辰山植物科学研究中心, 上海 201602
    2 上海师范大学生命科学学院, 上海 200234
  • 收稿日期:2019-07-25 接受日期:2019-12-17 出版日期:2019-11-20
  • 通讯作者: 严岳鸿 E-mail:yan.yh@126.com
  • 基金项目:
    中国科学院战略性先导科技专项A类(XDA19050404);上海市绿化和市容管理局科学技术项目(G152420)

De novo transcriptome assembly reveals the whole genome duplication events of Didymochlaena trancatula

Hao Wang1, 2#, Rui Zhang1#, Jiao Zhang1, Hui Shen1, Xiling Dai2, Yuehong Yan1, *()   

  1. 1 Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602
    2 College of Life Sciences, Shanghai Normal University, Shanghai 200234
  • Received:2019-07-25 Accepted:2019-12-17 Online:2019-11-20
  • Contact: Yan Yuehong E-mail:yan.yh@126.com

全基因组复制在动植物中普遍存在, 被认为是促进物种进化的重要动力之一。作为蕨类植物的单种科物种, 翼盖蕨(Didymochlaena trancatula)是真水龙骨类I的基部类群, 在蕨类中具有独特的演化地位。本研究基于高通量测序, 通过同义替换率(Ks)分析、相对定年分析揭示翼盖蕨的全基因组复制发生情况。Ks分析表明, 翼盖蕨至少经历了两次全基因组复制事件, 其中一次发生于59-62 million years ago (Mya), 另一次发生于90-94 Mya, 这两次全基因组复制事件分别和白垩纪第三纪的Cretaceous-Tertiary (C-T)大灭绝事件以及翼盖蕨的物种分化时间相吻合。进一步对两次全基因组复制保留的基因进行功能注释和富集分析, 结果显示与转录及代谢调控相关的基因优势被保留。翼盖蕨的全基因组复制事件可能促进了该物种的分化及其对极端环境的适应性。

关键词: 全基因组复制, 蕨类植物, 白垩纪大灭绝事件, 进化生物学, 同义替换率

Whole genome duplication is an important driving force to speciation and evolution. Moreover, most existing plants and animals have experienced whole genome duplication in their evolutionary history. As the basal group of the Eupolypods I, Didymochlaena trancatula is the single fern species of Didymochlaenaceae. We performed transcriptome sequencing to detect whole genome duplication (WGD) events by analyzing age distributions built from synonymous substitution rates (Ks). We found that D. trancatula has experienced at least two WGDs during its evolutionary history. We dated the two WGDs at 59-62 million years ago (Mya) and 90-94 Mya, corresponding to Cretaceous-Tertiary (C-T) extinction event and the divergence time of D. trancatula, respectively. Annotation and functional enrichment analysis showed most duplicated genes that were retained are related to environmental regulation, further emphasizing the role that WGDs may play in the adaptive evolution of D. trancatula.

Key words: whole genome duplication, fern, the Cretaceous-Tertiary extinction event, evolutionary biology, Ks

表1

翼盖蕨转录组de novo组装结果统计"

转录本
Transcript
单基因簇 Unigene
序列数目 Sequence number 77,709 58,871
平均长度 Mean length (bp) 986 836
最大长度 Max. length (bp) 17,374 17,374
最小长度 Min. length (bp) 201 201
N50 1,734 1,546

图1

翼盖蕨的形态及其Ks分布图"

表2

基于混合模型拟合的翼盖蕨的Ks结果"

加倍数目
No. of duplications
组件数目
No. of components
贝叶斯信息标准
Bayesian information criterion
中值
Median
方差
Variance
比例
Proportion
1,951 7 5,012.931 0.1211 0.0002 0.0953
1,951 7 5,012.931 0.1796 0.0015 0.0897
1,951 7 5,012.931 0.3518 0.0134 0.0584
1,951 7 5,012.931 1.3359 0.1921 0.3296
1,951 7 5,012.931 2.0329 0.1872 0.2107
1,951 7 5,012.931 3.2182 0.5590 0.1958
1,951 7 5,012.931 4.7933 0.0105 0.0205

图2

翼盖蕨全基因组复制保留基因的功能富集"

图3

蕨类中已报道的WGDs发生概况。圆圈代表WGD, 实线代表翼盖蕨和巨木贼中(约90 Mya)发生WGD的时间; 虚线代表翼盖蕨和水蕨中(约50 Mya)发生WGD的时间。"

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