Dating whole-genome duplication reveals the evolutionary retardation of Angiopteris

doi:10.17520/biods.2020484

Abstract

Abstract:

Aim: Whole-genome duplication (WGD) plays a positive role in speciation in vascular plants and is considered to be an important mechanism for species adaptation to the extreme environments. Dating whole-genome duplication events in different species is essential for understanding the adaptive evolution of organisms. However, the role that these mechanisms play in vascular plants, especially ferns, is still poorly understood.

Method: Based on the synonymous substitution rates (Ks) and absolute dating of the WGD event, this study used three different transcriptome sequences of Angiopteris fokiensis to analyze the contribution of polyploidy to the evolution of plants, and the silent substitution rate. Gene annotation and functional enrichment were carried out to elucidate the biological processes, molecular function, and cellular component for the genes retained after the WGD.

Results: We found that there was at least one WGD event in A. fokiensis at 159-165 Mya, and most duplicated genes were often related to nutrient metabolism, signal transduction, adaptive regulation and anatomical structure development. The silent substitution rate of A. fokiensis is 1.66 × 10^‒9 synonymous substitutions per site per year. Based on the above results, we speculate that the WGD event was associated with gymnosperms flourishing and the emergence of core angiosperms, or the Toarcian extinction event. The retention of particular genes after the WGD may have promoted genetic and morphological innovation in Angiopteris, thus helping it adapt to the drastic changes in environmental conditions. At present, A. fokiensisis the slowest evolving group of land plants except gymnosperms, which may relate to the long generation time, large genome and stable living habitat.

Conclusion: In this study, we analyzed the whole-genome duplication history and the patterns of retention of duplicated genes in A. fokiensis, suggesting that WGD events are of great influence in promoting the adaptation to extreme environmental changes of plants with slower evolutionary rates. These results provide more inspiration for understanding the adaptive evolution of other land plants.

Key words: polyploidization, adaptive evolution, evolution rate, ferns, transcriptome

Ting Wang, Zengqiang Xia, Jiangping Shu, Jiao Zhang, Meina Wang, Jianbing Chen, Kanglin Wang, Jianying Xiang, Yuehong Yan. Dating whole-genome duplication reveals the evolutionary retardation of Angiopteris[J]. Biodiv Sci, 2021, 29(6): 722-734.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2020484

https://www.biodiversity-science.net/EN/Y2021/V29/I6/722

Figures/Tables 7

References 90

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物种 Species	NCBI登录号 NCBI no.	转录本Transcript	N50 (bp)	鸟嘌呤/胞嘧啶 GC (%)	编码序列数 No. of coding sequence	BUSCO (%)	文献 References
福建莲座蕨 Angiopteris fokiensis	SRR2103714	46,702	1,720	44.95	34,286	89.6	Shen et al, 2018
福建莲座蕨 Angiopteris fokiensis	SRR5499396	62,608	2,021	44.29	39,010	95.1	You et al, 2017
福建莲座蕨 Angiopteris fokiensis	SRR6920615	62,119	2,021	44.29	39,043	95.4	Huang et al, 2020
披散木贼 Equisetum diffusum	SRR2103706	55,430	1,537	44.93	39,399	91.4	Shen et al, 2018
桂皮紫萁 Osmundastrum cinnamomeum	SRR6727971	28,229	1,922	46.43	22,868	84.4	Wolf et al, 2018
紫萁 Osmunda japonica	SRR2103721	42,649	2,005	46.22	31,414	92.8	Huang et al, 2020
细叶双扇蕨 Dipteris lobbiana	SRR6920640	148,711	1,085	46.09	94,834	78.4	Huang et al, 2020
芒萁 Dicranopteris pedata	SRR5490811	62,818	1,954	45.78	40,874	97.5	You et al, 2017
假芒萁 Sticherus truncatus	SRR6920643	74,801	1,557	44.30	50,507	88.2	Huang et al, 2020

物种 Species	NCBI登录号 NCBI no.	转录本Transcript	N50 (bp)	鸟嘌呤/胞嘧啶 GC (%)	编码序列数 No. of coding sequence	BUSCO (%)	文献 References
福建莲座蕨 Angiopteris fokiensis	SRR2103714	46,702	1,720	44.95	34,286	89.6	Shen et al, 2018
福建莲座蕨 Angiopteris fokiensis	SRR5499396	62,608	2,021	44.29	39,010	95.1	You et al, 2017
福建莲座蕨 Angiopteris fokiensis	SRR6920615	62,119	2,021	44.29	39,043	95.4	Huang et al, 2020
披散木贼 Equisetum diffusum	SRR2103706	55,430	1,537	44.93	39,399	91.4	Shen et al, 2018
桂皮紫萁 Osmundastrum cinnamomeum	SRR6727971	28,229	1,922	46.43	22,868	84.4	Wolf et al, 2018
紫萁 Osmunda japonica	SRR2103721	42,649	2,005	46.22	31,414	92.8	Huang et al, 2020
细叶双扇蕨 Dipteris lobbiana	SRR6920640	148,711	1,085	46.09	94,834	78.4	Huang et al, 2020
芒萁 Dicranopteris pedata	SRR5490811	62,818	1,954	45.78	40,874	97.5	You et al, 2017
假芒萁 Sticherus truncatus	SRR6920643	74,801	1,557	44.30	50,507	88.2	Huang et al, 2020

样本 Sample	采集地 Collection sites	加倍数目 No. of duplicates	组件数目 No. of components	贝叶斯信息标准 Bayesian information criterion	中值 Median (Ks)	方差 Variance	比例 Proportion
福建莲座蕨 Angiopteris fokiensis SRR2103714	上海 Shanghai	3,667	6	?6,824.9400	0.1310	0.0005	0.0763
		3,667	6	?6,824.9400	0.2147	0.0029	0.0577
		3,667	6	?6,824.9400	0.5814	0.0200	0.2697
		3,667	6	?6,824.9400	0.9172	0.0312	0.2529
		3,667	6	?6,824.9400	1.3513	0.1683	0.2040
		3,667	6	?6,824.9400	3.0112	0.8830	0.1393
福建莲座蕨 Angiopteris fokiensis SRR5499396	广东 Guangdong	4,238	7	?7,662.1730	0.1241	0.0003	0.0680
		4,238	7	?7,662.1730	0.2002	0.0023	0.0921
		4,238	7	?7,662.1730	0.5856	0.0191	0.2940
		4,238	7	?7,662.1730	0.9331	0.0198	0.1781
		4,238	7	?7,662.1730	1.1911	0.1116	0.1935
		4,238	7	?7,662.1730	2.3596	0.4994	0.1330
		4,238	7	?7,662.1730	4.1443	0.2343	0.0412
福建莲座蕨 Angiopteris fokiensis SRR6920615	广西 Guangxi	4,235	6	?7,662.1730	0.1259	0.0003	0.0753
		4,235	6	?7,662.1730	0.1996	0.0022	0.0834
		4,235	6	?7,662.1730	0.5489	0.0148	0.2082
		4,235	6	?7,662.1730	0.8841	0.0452	0.3284
		4,235	6	?7,662.1730	1.3642	0.1874	0.1606
		4,235	6	?7,662.1730	2.9677	0.9873	0.1441

样本 Sample	采集地 Collection sites	加倍数目 No. of duplicates	组件数目 No. of components	贝叶斯信息标准 Bayesian information criterion	中值 Median (Ks)	方差 Variance	比例 Proportion
福建莲座蕨 Angiopteris fokiensis SRR2103714	上海 Shanghai	3,667	6	?6,824.9400	0.1310	0.0005	0.0763
		3,667	6	?6,824.9400	0.2147	0.0029	0.0577
		3,667	6	?6,824.9400	0.5814	0.0200	0.2697
		3,667	6	?6,824.9400	0.9172	0.0312	0.2529
		3,667	6	?6,824.9400	1.3513	0.1683	0.2040
		3,667	6	?6,824.9400	3.0112	0.8830	0.1393
福建莲座蕨 Angiopteris fokiensis SRR5499396	广东 Guangdong	4,238	7	?7,662.1730	0.1241	0.0003	0.0680
		4,238	7	?7,662.1730	0.2002	0.0023	0.0921
		4,238	7	?7,662.1730	0.5856	0.0191	0.2940
		4,238	7	?7,662.1730	0.9331	0.0198	0.1781
		4,238	7	?7,662.1730	1.1911	0.1116	0.1935
		4,238	7	?7,662.1730	2.3596	0.4994	0.1330
		4,238	7	?7,662.1730	4.1443	0.2343	0.0412
福建莲座蕨 Angiopteris fokiensis SRR6920615	广西 Guangxi	4,235	6	?7,662.1730	0.1259	0.0003	0.0753
		4,235	6	?7,662.1730	0.1996	0.0022	0.0834
		4,235	6	?7,662.1730	0.5489	0.0148	0.2082
		4,235	6	?7,662.1730	0.8841	0.0452	0.3284
		4,235	6	?7,662.1730	1.3642	0.1874	0.1606
		4,235	6	?7,662.1730	2.9677	0.9873	0.1441