Scientia Agricultura Sinica ›› 2026, Vol. 59 ›› Issue (3): 543-555.doi: 10.3864/j.issn.0578-1752.2026.03.006

• PLANT PROTECTION • Previous Articles     Next Articles

The Phylogeographic History of Pepper Mild Mottle Virus

NING RuoYun1(), YIN YuQi1(), SHEN JianGuo2(), ZHANG ShuLing3, GONG MeiFang1, GAO FangLuan1()   

  1. 1 Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002
    2 Technology Center of Fuzhou Customs District, Fuzhou 350001
    3 Department of Horticulture and Garden, Fujian Vocational College of Agriculture, Fuzhou 350007
  • Received:2025-10-07 Accepted:2025-10-30 Online:2026-02-01 Published:2026-01-31
  • Contact: SHEN JianGuo, GAO FangLuan

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Abstract:

【Objective】Pepper mild mottle virus (PMMoV) belongs to the species Tobamovirus capsicai in the genus Tobamovirus (family Virgaviridae), has emerged as an important pathogen, significantly impacting pepper yield and quality. The objectives of this study are to investigate its phylogeographic history and evolutionary dynamics, and to lay the foundation for accurate monitoring and scientific prevention and control. 【Method】A specific primer pair flanking the PMMoV coat protein (CP) gene was designed. The CP gene sequences of 28 randomly selected PMMoV isolates from Fujian Province were subsequently amplified and cloned. In addition to the newly obtained sequences, all publicly available CP sequences from GenBank with known collection timestamps and geographical origins were assembled into a final dataset of 255 sequences. After confirming a sufficient temporal signal via a date-randomized test (DRT), a structured coalescent-based Bayesian phylodynamic framework (MultiTypeTree) was employed to reconstruct the evolutionary history and spatial dissemination of the virus. 【Result】A target fragment with the expected size was obtained from all 28 PMMoV-positive samples selected in this study. Their CP sequences share >98% nucleotide identity with known PMMoV isolates. The DRT showed no overlap in the 95% confidence intervals of substitution rates between the real and randomized datasets, confirming a reliable temporal signal for Bayesian molecular dating. Phylogenetic analysis estimated a mean substitution rate of 9.24×10-4 substitutions/site/year (95% CI: 6.20×10-4-1.01×10-3 substitutions/site/year) for the PMMoV CP, which is comparable to rates observed in animal RNA viruses, indicating its rapid evolutionary dynamics. The time to the most recent common ancestor (tMRCA) was dated to 1941 (95% CI: 1921-1957). The root of the maximum clade credibility (MCC) tree was placed in Europe, identifying this region as the most probable origin of contemporary global PMMoV isolates. Temporal migration analysis revealed multiple dispersal routes from Europe to other regions, underscoring its role as a central hub in the virus’s global dissemination. In addition to cross-regional transmission, frequent local spread of PMMoV was observed within regions. Bayesian skyline plot (BSP) analysis further revealed distinct historical population dynamics: the South American population underwent a significant expansion before stabilizing, whereas those in most other regions remained relatively stable over the long term. 【Conclusion】Europe served as the most likely source and a critical dissemination hub for the global spread of PMMoV. This study provides a foundation for understanding the molecular epidemiology of PMMoV and informs the development of future disease management strategies.

Key words: pepper mild mottle virus (PMMoV), Bayesian phylogeography, temporal signal, temporal migration pattern, structured coalescent, MultiTypeTree

Table 1

Information of PMMoV isolates sequenced in this study"

分离物
Isolate		 采样地点
Location		 采样日期
Sampling date		 登录号
Accession number		 分离物
Isolate		 采样地点
Location		 采样日期
Sampling date		 登录号
Accession number
QZST001 泉州Quanzhou 2024-03-04 PQ807648 NPDH011 南平Nanping 2023 PQ807668
QZST002 泉州Quanzhou 2024-03-04 PQ807649 NPDH012 南平Nanping 2023 PQ807669
QZST003 泉州Quanzhou 2024-03-04 PQ807650 NPDH013 南平Nanping 2023 PQ807670
QZST004 泉州Quanzhou 2024-03-04 PQ807651 NPDH015 南平Nanping 2023 PQ807671
QZST005 泉州Quanzhou 2024-03-04 PQ807652 SMJL002 三明Sanming 2023-06 PQ807673
QZST008 泉州Quanzhou 2024-03-04 PQ807653 SMJL004 三明Sanming 2023-06 PQ807675
QZST011 泉州Quanzhou 2024-03-04 PQ807654 SMJL007 三明Sanming 2023-06 PQ807678
QZST012 泉州Quanzhou 2024-03-04 PQ807655 SMJL008 三明Sanming 2023-06 PQ807679
QZST015 泉州Quanzhou 2024-03-04 PQ807657 SMJL015 三明Sanming 2023-06 PQ807681
QZST036 泉州Quanzhou 2024-03-04 PQ807660 QZHL007 泉州Quanzhou 2022-11-28 PQ807686
NPDH003 南平Nanping 2023 PQ807662 FZSP002 福州Fuzhou 2023-03-02 PQ807688
NPDH004 南平Nanping 2023 PQ807663 FZSP005 福州Fuzhou 2023-03-02 PQ807690
NPDH009 南平Nanping 2023 PQ807666 FZSP006 福州Fuzhou 2023-03-02 PQ807691
NPDH010 南平Nanping 2023 PQ807667 FZSP011 福州Fuzhou 2023-03-02 PQ807692

Fig. 1

Diagram showing the temporal distribution of PMMoV isolates across different regions"

Fig. 2

RT-PCR amplification of CP from PMMoV"

Fig. 3

Assessment of temporal signal of PMMoV dataset"

Table 2

Marginal likelihoods of different combinations of molecular clock model and tree prior model"

分子钟模型Molecular clock model 树先验模型Tree prior model 对数边际似然值Marginal likelihoods
严格分子钟Strict clock 恒定大小Constant -3753.326
严格分子钟Strict clock 指数增长Exponential growth -3736.539
严格分子钟Strict clock 贝叶斯天际线Bayesian skyline -3634.739
严格分子钟Strict clock 多类型树MultiTypeTree -3489.759
不相关对数正态分布宽松分子钟Uncorrelated lognormal relaxed 恒定大小Constant -4261.053
不相关对数正态分布宽松分子钟Uncorrelated lognormal relaxed 指数增长Exponential growth -4335.131
不相关对数正态分布宽松分子钟Uncorrelated lognormal relaxed 贝叶斯天际线Bayesian skyline -4242.967
不相关对数正态分布宽松分子钟Uncorrelated lognormal relaxed 多类型树MultiTypeTree -3827.067

Table 3

Estimates of the substitution rate and time to the most common ancestor"

参数Parameter 数值Value
序列长度Sequence length (nt) 474
日期范围Date range (year) 1980-2024
样本大小Sample size 255
最近共祖时间tMRCA (year) 1941 (1921-1957)
替代速率
Substitution rate (subs/site/year)		 9.24×10-4 (6.20×10-4-1.01×10-3)

Fig. 4

The maximum clade credibility tree inferred from the CP sequences of PMMoV The tree topology is shown with branch lengths scaled to time. Only the posterior probabilities >0.90 are shown on the nodes. Branch colors represent the inferred location states. The inset panel displays the root state posterior probabilities for each region. The labels “Europe+India” and “Europe+China+North America” indicate uncertainty in the inferred geographic locations"

Fig. 5

Region-randomized test for the inferred origin of PMMoV The blue solid line indicates the posterior probability of the root state inferred from the real dataset. The orange and green dashed lines represent the maximum and minimum posterior probabilities of the root state, respectively, inferred from the region-randomized datasets"

Fig. 6

PMMoV migration dynamics across different regions over time The y-axis represents the number of migration events, and the x-axis represents the time scale"

Fig. 7

Demographic history of PMMoV populations The y-axis represents the effective population size (Ne) and the x-axis is measured in calendar years. The black line shows the median estimate of the population size, and the shading region shows the 95% credibility interval"

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