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

doi:10.17520/biods.2019236

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

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 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 发布日期:2020-01-17
通讯作者: 严岳鸿
基金资助:
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 Wang^1,^2#,Rui Zhang^1#,Jiao Zhang¹,Hui Shen¹,Xiling Dai²,Yuehong Yan^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 Published:2020-01-17
Contact: Yan Yuehong

摘要/Abstract

摘要：

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

Abstract

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

汪浩, 张锐, 张娇, 沈慧, 戴锡玲, 严岳鸿 (2019) 转录组测序揭示翼盖蕨(Didymochlaena trancatula)的全基因组复制历史. 生物多样性, 27, 1221-1227. DOI: 10.17520/biods.2019236.

Hao Wang, Rui Zhang, Jiao Zhang, Hui Shen, Xiling Dai, Yuehong Yan (2019) De novo transcriptome assembly reveals the whole genome duplication events of Didymochlaena trancatula. Biodiversity Science, 27, 1221-1227. DOI: 10.17520/biods.2019236.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2019236

https://www.biodiversity-science.net/CN/Y2019/V27/I11/1221

图/表 5

表1 翼盖蕨转录组de novo组装结果统计

Table 1 Summary of de novo assembly for Didymochlaena trancatula transcriptome

	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

Fig. 1 Morphology and Ks frequency distribution of Didymochlaena trancatula

表2 基于混合模型拟合的翼盖蕨的Ks结果

Table 2 Ks results of Didymochlaena trancatula based on mixture modeling

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

Fig. 2 Enriched GO terms of retained duplicates after whole genome duplication events in Didymochlaena trancatula

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。

Fig. 3 WGDs occurrence in ferns from previous reports. Circle represents WGDs. The solid line denotes the age of WGD at (about 90 Mya) Didymochlaena trancatula and Equisetum giganteum, the dash line indicates the age of WGD both detected in Didymochlaena trancatula and Ceretopteris thalictroides (about 50 Mya).

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

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

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