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

doi:10.17520/biods.2019236

Abstract

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

Hao Wang, Rui Zhang, Jiao Zhang, Hui Shen, Xiling Dai, Yuehong Yan. De novo transcriptome assembly reveals the whole genome duplication events of Didymochlaena trancatula[J]. Biodiv Sci, 2019, 27(11): 1221-1227.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2019236

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

Figures/Tables 5

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

Fig. 1 Morphology and Ks frequency distribution of Didymochlaena trancatula

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

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

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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