Genetic Variability and Host Adaption of Cymbidium Mosaic Virus

doi:10.16420/j.issn.0513-353x.2023-0170

Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (1): 203-212.doi: 10.16420/j.issn.0513-353x.2023-0170

• Plant Protection • Previous Articles Next Articles

Genetic Variability and Host Adaption of Cymbidium Mosaic Virus

GUAN Xiayu¹^,², CHEN Xihong³, GUO Jing³, LÜ Haoyang¹, LIANG Chenyuan¹, GAO Fangluan¹^,^*()

¹ Key Lab for Biopesticide and Chemical Biology，Ministry of Education，Fujian Agriculture and Forestry University，Fuzhou 350002，China
² School of Horticulture，Fujian Agriculture and Forestry University，Fuzhou 350002，China
³ Fujian Key Laboratory of Inspection and Quarantine Technology Research， Technology Center of Fuzhou Customs District，Fuzhou 350001，China

Received:2023-05-11 Revised:2023-08-30 Online:2024-01-25 Published:2024-01-16
Contact: * （E-mail：raindy@fafu.edu.cn）

Abstract

Abstract:

Cymbidium mosaic virus（CymMV）is a highly destructive plant pathogen that inflicts significant losses on orchid production. This study investigates the genetic variability and adaptive evolution of CymMV. The coat protein（CP）gene of 16 CymMV isolates from Dendrobium nobile was sequenced and analyzed alongside published CP sequences of 52 CymMV isolates from various host plants in China. Analysis reveals a substantial genetic diversity within the CP gene，with an overall nucleotide diversity of 0.039 and a haplotype diversity of 0.992. AMOVA tests demonstrate that the molecular variation among individuals accounts for 71.72% of the total variation of CymMV. Population structure analysis classifies CymMV into two distinct clusters. Cluster 1 exclusively consists of CymMV isolates from Cymbidium ensifolium，while Cluster 2 encompasses CymMV isolates from multiple host species，yet isolates from the same host species tend to form subclusters. Furthermore，a robust association between the phylogeny and host species of CymMV is revealed through phylogeny-trait association analysis. Overall，the findings of this study indicate that the genetic variation of CymMV is specific to its host species，suggesting that its evolution is primarily driven by selection pressures imposed by its hosts.

Key words: Cymbidium mosaic virus, coat protein gene, genetic diversity, discriminant analysis of principal components, adaptive evolution

GUAN Xiayu, CHEN Xihong, GUO Jing, LÜ Haoyang, LIANG Chenyuan, GAO Fangluan. Genetic Variability and Host Adaption of Cymbidium Mosaic Virus[J]. Acta Horticulturae Sinica, 2024, 51(1): 203-212.

Figures/Tables 10

References 30

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寄主 Host	采样省份 Location	分离物 Isolate	GenBank 登录号 Accession No.	寄主 Host	采样省份 Location	分离物 Isolate	GenBank 登录号 Accession No.
国兰 Cymbidium sinense	福建Fujian	CHN-FJZZ12	DQ067878	蝴蝶兰 Phalaenopsis aphrodite	河南Henan	CHN-HNZZ02	KU873001
		CHN-FJZZ13	DQ067879	蕙兰C. faberi	西藏Tibet	C-LZ02	KP137368
	湖北Hubei	CHN-HBWH21	DQ067880			C-LZ06	KP137369
		CHN-HBWH22	DQ067881			C-LZ14	KP137370
	浙江Zhejiang	CHN-ZJHZ52	DQ067882			C-LZ18	KP137371
		CHN-ZJHZ61	DQ067883			C-LZ21	KP137372
		CHN-ZJHZ62	DQ067884	石斛兰 Dendrobium nobile	中国台湾 Taiwan，China	CyMV-1 ^*	OQ615774
		CHN-ZJHZ63	DQ067885			CyMV-2 ^*	OQ615782
		CHN-ZJHZ67	DQ067886			CyMV-3 ^*	OQ615783
		CHN-ZJHZ69	DQ067887			CyMV-4 ^*	OQ615784
		CHN-ZJHZ612	DQ067888			CyMV-5 ^*	OQ615785
蝴蝶兰 Phalaenopsis aphrodite	浙江Zhejiang	CyMV-hangzhou	AM398153			CyMV-6 ^*	OQ615786
		CrMV-HZ	DQ915439			CyMV-7 ^*	OQ615787
	福建Fujian	xm	GQ507023			CyMV-8 ^*	OQ615788
	江苏Jiangsu	CrMV-NJ-1	JQ860108			CyMV-9 ^*	OQ615789
	广东Guangdong	FS2	KF853247			CyMV-10 ^*	OQ615775
		FS3	KF853248			CyMV-11 ^*	OQ615776
		FS4	KF853249			CyMV-12 ^*	OQ615777
		FS5	KF853250			CyMV-13^*	OQ615778
		GZ1	KF853251			CyMV-14 ^*	OQ615779
		CH	KF853252			CyMV-15 ^*	OQ615780
		GZ2	KF853253			CyMV-16 ^*	OQ615781
		GZ3	KF853254		广东Guangdong	ZHD1	EU672821
		FS6	KF853255	建兰 C. ensifolium	浙江Zhejiang	ZJXTHC1	GU295167
		ZH1	KF853256		四川Sichuan	SCJJC7	GU295168
		ZH2	KF853257			SCDXZC4	GU295172
		FS7	KF853258		广东 Guangdong	GZKTLC6	GU295170
		FS8	KF853259			GDDHLC5	GU295173
		FS9	KF853260		北京 Beijing	BJKTLC3	GU295169
		FS10	KF853261		云南 Yunnan	KMMLC2	GU295171
		SZ1	KF853262	墨兰 C. haematodes	广东 Guangdong	gd2	AY360409
		SZ2	KF853263			gd3	AY360410
		SZ3	KF853264		中国台湾 Taiwan，China	CrMV-CS	AY429021
		SZ4	KF853265			Taiwan，China	AY571289

寄主 Host	采样省份 Location	分离物 Isolate	GenBank 登录号 Accession No.	寄主 Host	采样省份 Location	分离物 Isolate	GenBank 登录号 Accession No.
国兰 Cymbidium sinense	福建Fujian	CHN-FJZZ12	DQ067878	蝴蝶兰 Phalaenopsis aphrodite	河南Henan	CHN-HNZZ02	KU873001
		CHN-FJZZ13	DQ067879	蕙兰C. faberi	西藏Tibet	C-LZ02	KP137368
	湖北Hubei	CHN-HBWH21	DQ067880			C-LZ06	KP137369
		CHN-HBWH22	DQ067881			C-LZ14	KP137370
	浙江Zhejiang	CHN-ZJHZ52	DQ067882			C-LZ18	KP137371
		CHN-ZJHZ61	DQ067883			C-LZ21	KP137372
		CHN-ZJHZ62	DQ067884	石斛兰 Dendrobium nobile	中国台湾 Taiwan，China	CyMV-1 ^*	OQ615774
		CHN-ZJHZ63	DQ067885			CyMV-2 ^*	OQ615782
		CHN-ZJHZ67	DQ067886			CyMV-3 ^*	OQ615783
		CHN-ZJHZ69	DQ067887			CyMV-4 ^*	OQ615784
		CHN-ZJHZ612	DQ067888			CyMV-5 ^*	OQ615785
蝴蝶兰 Phalaenopsis aphrodite	浙江Zhejiang	CyMV-hangzhou	AM398153			CyMV-6 ^*	OQ615786
		CrMV-HZ	DQ915439			CyMV-7 ^*	OQ615787
	福建Fujian	xm	GQ507023			CyMV-8 ^*	OQ615788
	江苏Jiangsu	CrMV-NJ-1	JQ860108			CyMV-9 ^*	OQ615789
	广东Guangdong	FS2	KF853247			CyMV-10 ^*	OQ615775
		FS3	KF853248			CyMV-11 ^*	OQ615776
		FS4	KF853249			CyMV-12 ^*	OQ615777
		FS5	KF853250			CyMV-13^*	OQ615778
		GZ1	KF853251			CyMV-14 ^*	OQ615779
		CH	KF853252			CyMV-15 ^*	OQ615780
		GZ2	KF853253			CyMV-16 ^*	OQ615781
		GZ3	KF853254		广东Guangdong	ZHD1	EU672821
		FS6	KF853255	建兰 C. ensifolium	浙江Zhejiang	ZJXTHC1	GU295167
		ZH1	KF853256		四川Sichuan	SCJJC7	GU295168
		ZH2	KF853257			SCDXZC4	GU295172
		FS7	KF853258		广东 Guangdong	GZKTLC6	GU295170
		FS8	KF853259			GDDHLC5	GU295173
		FS9	KF853260		北京 Beijing	BJKTLC3	GU295169
		FS10	KF853261		云南 Yunnan	KMMLC2	GU295171
		SZ1	KF853262	墨兰 C. haematodes	广东 Guangdong	gd2	AY360409
		SZ2	KF853263			gd3	AY360410
		SZ3	KF853264		中国台湾 Taiwan，China	CrMV-CS	AY429021
		SZ4	KF853265			Taiwan，China	AY571289

簇 Cluster	亚簇 Subcluster	样本量大小 Sample size	单倍型 Haplotypes	单倍型多样性H_d Haplotype diversity	核苷酸多样性P_i Nucleotide diversity
1		7	3	0.524 ± 0.209	0.002 ± 0.009
2		61	53	0.995 ± 0.004	0.040 ± 0.004
2	1	17	14	0.971 ± 0.032	0.041 ± 0.008
	2	11	9	0.961 ± 0.051	0.041 ± 0.012
	3	33	30	0.994 ± 0.009	0.036 ± 0.007
总计Total		68	56	0.992 ± 0.005	0.039 ± 0.004

簇 Cluster	亚簇 Subcluster	样本量大小 Sample size	单倍型 Haplotypes	单倍型多样性H_d Haplotype diversity	核苷酸多样性P_i Nucleotide diversity
1		7	3	0.524 ± 0.209	0.002 ± 0.009
2		61	53	0.995 ± 0.004	0.040 ± 0.004
2	1	17	14	0.971 ± 0.032	0.041 ± 0.008
	2	11	9	0.961 ± 0.051	0.041 ± 0.012
	3	33	30	0.994 ± 0.009	0.036 ± 0.007
总计Total		68	56	0.992 ± 0.005	0.039 ± 0.004

变异源 Source of variation	自由度 df	平方和 Sum of squares	变量组分 Variance components	变异比例 Percentage of variation	固定系数 Fixation index
簇间Among clusters	1	65.903	3.580	21.880	0.220 ^ns
簇内亚簇间Among sub-clusters within clusters	2	61.563	1.046	6.390	0.082^*
亚簇内Within sub-clusters	64	750.931	11.733	71.720	0.282^***
总计Total	67	878.397	16.359

Genetic Variability and Host Adaption of Cymbidium Mosaic Virus

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簇 Cluster	亚簇 Subcluster	Tajima's D	P值 P value	Fu's F_S	P 值 P value
1		-1.434	0.067	0.263	0.475^ns
2		-1.335	0.043^*	-19.765	0.000^***
2	1	0.483	0.729	0.029	0.517^ns
	2	-1.446	0.072	1.339	0.696^ns
	3	-1.309	0.042^*	-8.222	0.011^*

统计参数Statistic	寄主 Host	观测平均值（95% HPD） Observed mean（95% HPD）	零假设平均值（95% HPD） Null mean（95% HPD）	P 值 P value
AI		1.319（0.830 ~ 1.803）	5.775（5.005 ~ 6.531）	< 0.001^***
PS		20.472（19.000 ~ 21.000）	38.091（35.370 ~ 0.624）	< 0.001^***
MC	国兰Cymbidium sinense	4.064（3.000 ~ 5.000）	1.518（1.003 ~ 2.182）	0.010^**
	建兰C. ensifolium	6.981（6.000 ~ 7.000）	1.225（1.000 ~ 1.998）	0.010^**
	蕙兰C. faberi	2.049（2.000 ~ 3.000）	1.103（1.000 ~ 1.989）	0.030^*
	墨兰C. haematodes	1.008（1.000 ~ 2.000）	1.065（1.000 ~ 1.335）	1.000^ns
	蝴蝶兰Phalaenopsis	6.017（6.000 ~ 7.000）	2.414（1.686 ~ 3.375）	0.010^**
	石斛兰Dendrobium nobile	5.975（5.000 ~ 6.000）	1.887（1.079 ~ 2.982）	0.010^**

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