Revealing the New Whole-genome Duplication Event of Four Paphiopedilum Species Based on Transcriptome Data

doi:10.11983/CBB21100

Abstract

Abstract: 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 (K_s), 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.

Key words: polyploidization, Ochidaceae, Cypripedioideae, adaptive evolution, synonymous substitution rate

Meng Wang, Ting Wang, Zengqiang Xia, Tingzhang Li, Xiaohua Jin, Yuehong Yan, Jianbing Chen. Revealing the New Whole-genome Duplication Event of Four Paphiopedilum Species Based on Transcriptome Data[J]. Chinese Bulletin of Botany, 2021, 56(6): 699-714.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB21100

https://www.chinbullbotany.com/EN/Y2021/V56/I6/699

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References 82

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	Paphiopedilum concolor	P. hirsutissimum	P. malipoense	P. armeniacum
Accession number	SRR1405683	SRR1405685	SRR5722160	SRR9842184
Tissues	Leaf	Leaf	Stem	Seed
Bases (Gb)	3.6	3	14.1	8
Number of transcripts	156581	76006	239105	164515
Average length of transcript (bp)	907.1	1162.3	884.5	993.2
N50 of transcript (bp)	1486	1971	1627	1856
Number of unigenes	116919	62565	201606	139203
Average length of unigene (bp)	863.3	1071.1	815.6	906.4
N50 of unigene (bp)	1438	1829	1480	1704
Source of raw data	Li et al., 2014	Li et al., 2014	Zhang et al., 2017	Fang et al., 2020

	Paphiopedilum concolor	P. hirsutissimum	P. malipoense	P. armeniacum
Accession number	SRR1405683	SRR1405685	SRR5722160	SRR9842184
Tissues	Leaf	Leaf	Stem	Seed
Bases (Gb)	3.6	3	14.1	8
Number of transcripts	156581	76006	239105	164515
Average length of transcript (bp)	907.1	1162.3	884.5	993.2
N50 of transcript (bp)	1486	1971	1627	1856
Number of unigenes	116919	62565	201606	139203
Average length of unigene (bp)	863.3	1071.1	815.6	906.4
N50 of unigene (bp)	1438	1829	1480	1704
Source of raw data	Li et al., 2014	Li et al., 2014	Zhang et al., 2017	Fang et al., 2020

	Paphiopedilum concolor	P. hirsutissimum	P. malipoense	P. armeniacum
Number of protein coding sequences	56439	33207	79854	58575
Average length of protein coding sequence (bp)	936.1	994.9	829.1	914.7
N50 of protein coding sequence (bp)	1209	1308	1089	1215
Number of CDS identified as transcription factor	1950	1181	2586	2014
Number of transcription factor families	66	67	67	68

	Paphiopedilum concolor	P. hirsutissimum	P. malipoense	P. armeniacum
Number of protein coding sequences	56439	33207	79854	58575
Average length of protein coding sequence (bp)	936.1	994.9	829.1	914.7
N50 of protein coding sequence (bp)	1209	1308	1089	1215
Number of CDS identified as transcription factor	1950	1181	2586	2014
Number of transcription factor families	66	67	67	68

Species	No. of components	No. of duplicates	BIC	Variance	Mean (K_s)	Proportion
Paphiopedilum concolor	9	207	-4673.731	0.0000	0.1077	0.0527
	9	385	-4673.731	0.0002	0.1314	0.1048
	9	416	-4673.731	0.0007	0.1740	0.1194
	9	311	-4673.731	0.0026	0.2517	0.0964
	9	522	-4673.731	0.0175	0.5161	0.1544
	9	642	-4673.731	0.0241	0.8236	0.1741
	9	567	-4673.731	0.1557	1.5043	0.1594
	9	300	-4673.731	0.5765	2.4529	0.1148
	9	90	-4673.731	0.1277	4.3036	0.0240
P. hirsutissimum	7	196	-4604.688	0.0001	0.1146	0.0632
	7	277	-4604.688	0.0005	0.1504	0.0991
	7	290	-4604.688	0.0026	0.2292	0.1109
	7	558	-4604.688	0.0282	0.5407	0.2162
	7	508	-4604.688	0.0260	0.8544	0.1693
	7	585	-4604.688	0.2594	1.5894	0.2351
	7	236	-4604.688	0.8550	3.0527	0.1062
Species	No. of components	No. of duplicates	BIC	Variance	Mean (K_s)	Proportion
P. malipoense	9	377	-14027.68	0.0000	0.1081	0.0399
	9	751	-14027.68	0.0003	0.1362	0.0890
	9	820	-14027.68	0.0016	0.2006	0.1005
	9	579	-14027.68	0.0067	0.3290	0.0768
	9	1611	-14027.68	0.0287	0.6196	0.1983
	9	1464	-14027.68	0.0447	1.0026	0.1778
	9	1634	-14027.68	0.1002	1.6186	0.1952
	9	683	-14027.68	0.5901	2.6205	0.1105
	9	105	-14027.68	0.0568	4.5773	0.0121
P. armeniacum	9	206	-8261.607	0.0000	0.1063	0.0359
	9	472	-8261.607	0.0002	0.1296	0.0870
	9	478	-8261.607	0.0008	0.1744	0.0950
	9	400	-8261.607	0.0039	0.2729	0.0849
	9	1089	-8261.607	0.0213	0.5664	0.2105
	9	778	-8261.607	0.0287	0.8825	0.1457
	9	999	-8261.607	0.1443	1.4888	0.1980
	9	455	-8261.607	0.5375	2.4393	0.1195
	9	120	-8261.607	0.1481	4.3256	0.0234