Genetic variation and molecular evolution of tomato yellow leaf curl China virus and its betasatellite DNA isolates in China

Yu, Jingwen; Xiong, Yan; Li, Yin; Zhao, Meisheng; Yang, Xiaolong; Wang, Yalu; Huang, Hongkun; Zhou, Changyong; Huang, Wenkun; Qing, Ling

doi:10.1186/s42483-025-00312-w

Table 4 Genetic parameters, neutrality test, and selection pressure on 57 Tomato yellow leaf curl China virus (TYLCCNV) isolates and 109 Tomato yellow leaf curl China virus betasatellite (TYLCCNB) subpopulations based on geographic origin

From: Genetic variation and molecular evolution of tomato yellow leaf curl China virus and its betasatellite DNA isolates in China

Genomic region^a	Population	N^b	Haplotype diversity	Nucleotide diversity	Tajima’s D^c	dN/dS^d
C1 (Rep)	All (n = 57)	54	0.998 ± 0.004	0.10369 ± 0.00959	− 0.40650 (ns)	0.42
	Yunan (n = 37)	36	0.998 ± 0.007	0.09762 ± 0.01258	− 0.55573 (ns)	0.42
	Sichuan (n = 15)	14	0.990 ± 0.028	0.12311 ± 0.01582	0.39777 (ns)	0.44
	Guangxi (n = 5)	5	1.000 ± 0.126	0.01971 ± 0.00305	− 0.38767 (ns)	0.44
C2 (TrAP)	All (n = 57)	49	0.993 ± 0.005	0.06435 ± 0.00392	− 1.38557 (ns)	0.37
	Yunan (n = 37)	32	0.991 ± 0.009	0.06336 ± 0.00420	− 0.97510 (ns)	0.37
	Sichuan (n = 15)	14	0.990 ± 0.028	0.04889 ± 0.01240	− 1.47299 (ns)	0.41
	Guangxi (n = 5)	5	1.000 ± 0.126	0.02519 ± 0.00373	− 0.25279 (ns)	0.28
C3 (Ren)	All (n = 57)	44	0.987 ± 0.007	0.05400 ± 0.00454	− 1.55238 (ns)	0.39
	Yunan (n = 37)	33	0.992 ± 0.009	0.07747 ± 0.00327	− 0.42140 (ns)	0.33
	Sichuan (n = 15)	13	0.971 ± 0.039	0.04846 ± 0.01419	− 1.33768 (ns)	0.27
	Guangxi (n = 5)	5	1.000 ± 0.126	0.02815 ± 0.00600	− 0.37214 (ns)	0.23
C4 (SD)	All (n = 57)	41	0.970 ± 0.014	0.12779 ± 0.01968	0.38725 (ns)	1.25
	Yunan (n = 37)	27	0.943 ± 0.032	0.11601 ± 0.02509	− 0.11698 (ns)	1.29
	Sichuan (n = 15)	11	0.952 ± 0.040	0.17128 ± 0.03323	1.29297 (ns)	1.29
	Guangxi (n = 5)	4	0.900 ± 0.161	0.01565 ± 0.00321	0.46060 (ns)	3.10
V1 (CP)	All (n = 57)	55	0.999 ± 0.004	0.09616 ± 0.00292	− 0.40929 (ns)	0.09
	Yunan (n = 37)	35	0.997 ± 0.007	0.09282 ± 0.00498	− 0.41862 (ns)	0.09
	Sichuan (n = 15)	15	1.000 ± 0.024	0.06206 ± 0.01684	− 0.88493 (ns)	0.09
	Guangxi (n = 5)	5	1.000 ± 0.126	0.03826 ± 0.00820	− 0.52106 (ns)	0.07
V2 (Pre-CP)	All (n = 57)	51	0.987 ± 0.010	0.10064 ± 0.00497	− 0.57899 (ns)	0.17
	Yunan (n = 37)	31	0.968 ± 0.022	0.09765 ± 0.00865	− 0.73616 (ns)	0.19
	Sichuan (n = 15)	15	1.000 ± 0.024	0.06526 ± 0.01677	− 0.69765 (ns)	0.15
	Guangxi (n = 5)	5	1.000 ± 0.126	0.03448 ± 0.00710	0.30976 (ns)	0.07
βC1	All (n = 109)	70	0.982 ± 0.005	0.11688 ± 0.00325	− 0.59699 (ns)	2.68
	Yunan (n = 92)	55	0.975 ± 0.007	0.11421 ± 0.00307	− 0.09960 (ns)	2.79
	Sichuan (n = 7)	7	1.000 ± 0.076	0.06736 ± 0.01154	− 0.00819 (ns)	0.20
	Guangxi (n = 10)	9	0.978 ± 0.054	0.08472 ± 0.02861	− 1.45465 (ns)	0.23
βV1	All (n = 109)	31	0.922 ± 0.012	0.12021 ± 0.23330	− 1.55761 (ns)	0.35
	Yunan (n = 92)	23	0.904 ± 0.016	0.10909 ± 0.11022	− 0.03154 (ns)	0.31
	Sichuan (n = 7)	7	1.000 ± 0.076	0.07423 ± 0.07003	0.34393 (ns)	0.36
	Guangxi (n = 10)	8	0.956 ± 0.076	0.09820 ± 0.14104	− 1.49921 (ns)	0.46

^aC1 = Replication-associated protein, C2 = Transcriptional activator protein, C3 = Replication enhancer protein, C4 = Disease symptom determinants, V1 = Coat protein, V2 = Pre-coat protein, βC1 = Movement protein, βV1 = Promotion of virulence during the infection
^bNumber of haplotypes
^cns = not significant (P > 0.05)
^dNonsynonymous/synonymous ratio (dN/dS) < 1 (negative selection), dN/dS = 1 (neutral evolution), and dN/dS > 1 (positive selection)

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Table 4 Genetic parameters, neutrality test, and selection pressure on 57 Tomato yellow leaf curl China virus (TYLCCNV) isolates and 109 Tomato yellow leaf curl China virus betasatellite (TYLCCNB) subpopulations based on geographic origin

Phytopathology Research