Phylogenetic and Population Analysis of Lettuce mosaic virus Isolates Based on the Coat Protein Gene

Lettuce mosaic virus (LMV) is one of the most important and destructive members of Potyviruses in the family Potyviridae that is transmitted by aphid and seed which cause economic damage and serious yield losses to different crops around the world. To explore phylogenetic relationships, population evolution, and the effect of selection forces on the complete coat protein (CP) gene of LMV isolates, 36 complete coat protein gene sequences retrieved from the GenBank database in several different countries in four continents: Central and East Asia (China, Taiwan, South Korea, and Turkey), Europe (France), Africa (Tunisia), and America (Chile and Brazil). The phylogenetic tree of LMV isolates was grouped into independent clades with the significance of FST values (>0.27). The ratio of dN/dS is calculated less than one and showed that the LMV-CP has been under negative selection. Statistical tests (Tajima’s D, Fu and Li’s D* and F*) were used to estimate non-significantly negative values for all clades and geographic populations except for the Brazilian population and Clade III in a phylogenetic group. The negatives values revealed that there is less polymorphism estimation. All geographic populations in four phylogroups of LMV seem to be at equilibrium because all neutrality test statistics were non-significant. The findings suggested that the dynamics of LMV molecular evolution may be dependent on mutation, recombination, and negative selection. No recombination events were observed in this part of the LMV genome. Therefore, this study provides the first time evolution and differentiation between populations of LMV isolates from around the world and suggested that they may be occurred by the transmission of the virus among lettuce plants by types of aphid species, migration in different geographical areas by infected seeds and plant material, and broad host range which seems that these events have played an important role in shaping the LMV population structure.

[1]  M. Hajizadeh,et al.  Global population genetic structure of Bean common mosaic virus , 2020 .

[2]  A. Gibbs,et al.  The Potyviruses: An Evolutionary Synthesis Is Emerging , 2020, Viruses.

[3]  Miroslav Glasa,et al.  The global phylogeny of Plum pox virus is emerging. , 2019, The Journal of general virology.

[4]  D. Koolivand,et al.  A New Distinct Clade for Iranian Tomato spotted wilt virus Isolates Based on the Polymerase, Nucleocapsid, and Non-structural Genes , 2018, The plant pathology journal.

[5]  Juan C. Sánchez-DelBarrio,et al.  DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. , 2017, Molecular biology and evolution.

[6]  S. Sharma,et al.  Incidence of Lettuce mosaic virus in lettuce and its detection by polyclonal antibodies produced against recombinant coat protein expressed in Escherichia coli. , 2016, Journal of virological methods.

[7]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[8]  Fangluan Gao,et al.  Genetic diversity and molecular evolution of arabis mosaic virus based on the CP gene sequence , 2016, Archives of Virology.

[9]  Arvind Varsani,et al.  SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation , 2014, PloS one.

[10]  Hyoun-Sub Lim,et al.  Characteristics of a Lettuce mosaic virus Isolate Infecting Lettuce in Korea , 2014, The plant pathology journal.

[11]  S. German-Retana,et al.  Adaptation of lettuce mosaic virus to Catharanthus roseus involves mutations in the central domain of the VPg. , 2014, Molecular plant-microbe interactions : MPMI.

[12]  J. Guerri,et al.  Genetic variability and evolutionary dynamics of viruses of the family Closteroviridae , 2013, Front. Microbiol..

[13]  U. Melcher,et al.  Population genetic analysis of grapevine fanleaf virus , 2012, Archives of Virology.

[14]  G. Mosahebi,et al.  Identification of some viruses causing mosaic on lettuce and characterization of Lettuce mosaic virus from Tehran Province in Iran , 2011 .

[15]  A. Gibbs,et al.  Potyviruses and the digital revolution. , 2010, Annual review of phytopathology.

[16]  S. German-Retana,et al.  Lettuce mosaic virus: from pathogen diversity to host interactors. , 2008, Molecular plant pathology.

[17]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[18]  A. Fereres,et al.  Estimation of vector propensity for Lettuce mosaic virus based on viral detection in single aphids , 2007 .

[19]  A. Fereres,et al.  Temporal and spatial spread of Lettuce mosaic virus in lettuce crops in central Spain: factors involved in Lettuce mosaic virus epidemics , 2007 .

[20]  S. German-Retana,et al.  Molecular mapping of the viral determinants of systemic wilting induced by a Lettuce mosaic virus (LMV) isolate in some lettuce cultivars. , 2005, Virus research.

[21]  M. Purugganan,et al.  The molecular population genetics of the Tomato spotted wilt virus (TSWV) genome , 2004, Molecular ecology.

[22]  A. Fraile,et al.  Variation and evolution of plant virus populations , 2003, International microbiology : the official journal of the Spanish Society for Microbiology.

[23]  S. German-Retana,et al.  The Eukaryotic Translation Initiation Factor 4E Controls Lettuce Susceptibility to the Potyvirus Lettuce mosaic virus1 , 2003, Plant Physiology.

[24]  T. Candresse,et al.  Molecular and Biological Characterization of Lettuce mosaic virus (LMV) Isolates Reveals a Distinct and Widespread Type of Resistance-Breaking Isolate: LMV-Most. , 2002, Phytopathology.

[25]  T. Candresse,et al.  ANALYSIS OF THE VARIABILITY OF TUNISIAN ISOLATES OF LETTUCE MOSAIC VIRUS USING BIOLOGICAL AND MOLECULAR PROPERTIES , 2001 .

[26]  R. Hudson,et al.  A new statistic for detecting genetic differentiation. , 2000, Genetics.

[27]  T. Candresse,et al.  Biological and molecular variability of lettuce mosaic virus isolates. , 1997, Phytopathology.

[28]  J. Riechmann,et al.  Highlights and prospects of potyvirus molecular biology. , 1992, The Journal of general virology.

[29]  M. Nei,et al.  DNA polymorphism detectable by restriction endonucleases. , 1981, Genetics.

[30]  R. P. Madden,et al.  characteristics of , 2007 .

[31]  I. C. Jagger.  A transmissible Mosaic Disease of Lettuce. , 1921 .