Garlic common latent virus (GarCLV, Carlavirus), in co-infection, often worsens the severity of other Allium viruses on the garlic (Allium sativum Linnaeus). The nucleotide (nt) and amino acid (aa) sequences of the TGB and CP genes were analysed to get the first deep insight into the genomic variations and population structure of GarCLV. Global recombinant-free isolates were clustered into three clades in both the nt-based phylogenetic trees of TGB and CP. The clade 3 isolates shared low similarity percentages among themselves, as well as to the clade 1 and 2 isolates. Most major aa changes in the CP were observed on its 5' and 3' ends. Clade 2 obtained the lowest S, η, k, and π values for both the TGB and CP, which indicated low variations among its isolates. Both TGB and CP have undergone a negative selection, with CP being under stronger negative pressure than TGB. Neutrality tests estimated the non-significant negative values to all clades for TGB and CP, except Tajima's D for clade 2 of the TGB. The results of the Ks*, Kst*, Z*, and Snn tests suggested that all three phylogroups were divergent to each other for both TGB and CP. The high Fst on all the clade comparisons for both TGB and CP showed a large gene flow among three clades.
Chodorska M., Paduch-Cichal E., Kalinowska E., Szyndel M.S. (2014): First report of Onion yellow dwarf virus, Garlic common latent virus and Shallot latent virus on garlic in Poland. Plant Disease, 98: 858. doi: 10.1094/PDIS-11-13-1160-PDN https://doi.org/10.1094/PDIS-11-13-1160-PDN
Fajardo T.V.M., Nishijima M., Buso J.A., Torres A.C., Ávila A.C., Resende R.O. (2001): Garlic viral complex: Identification of Potyviruses and Carlavirus in central Brazil. Fitopatologia Brasileira, 26: 619–626. https://doi.org/10.1590/S0100-41582001000300007
Fu Y.X., Li W.H. (1993): Statistical tests of neutrality of mutations. Genetics, 133: 693–709. https://doi.org/10.1093/genetics/133.3.693
Gao F., Lin W., Shen J., Liao F. (2016): Genetic diversity and molecular evolution of Arabis mosaic virus based on the CP gene sequence. Archives of Virology, 161: 1047–1051. https://doi.org/10.1007/s00705-015-2729-z
Ge B., He Z., Zhang Z., Wang H., Li S. (2014): Genetic variation in Potato virus M isolates infecting pepino (Solanum muricatum) in China. Archives of Virology, 159: 3197–3210. https://doi.org/10.1007/s00705-014-2180-6
Hall B.G. (2013): Building phylogenetic trees from molecular data with MEGA. Molecular Biology and Evolution, 30: 1229–1235. https://doi.org/10.1093/molbev/mst012
Hall T.A. (1999): BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41: 95–98.
Hudson R.R. (2000): A new statistic for detecting genetic differentiation. Genetics, 155: 2011–2014. https://doi.org/10.1093/genetics/155.4.2011
Hudson R.R., Boos D.D., Kaplan N.L. (1992): A statistical test for detecting geographic subdivision. Molecular Biology and Evolution, 9: 138–151.
King A.M.Q., Adams M.J., Carstens E.B., Lefkowitz E.J. (2011): Virus taxonomy. In: Ninth Report of the International Committee on Taxonomy of Viruses. San Diego, Elsevier: 1221–1234.
Lot H., Chovelon V., Souche S., Delecolle B. (1998): Effects of Onion yellow dwarf and Leek yellow stripe viruses on symptomatology and yield loss of three French garlic cultivars. Plant Disease, 82: 1381–1385. https://doi.org/10.1094/PDIS.1922.214.171.1241
Martin D.P., Murrell B., Golden M., Khoosal A., Muhire B. (2015): RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evolution, 1: 1–5. https://doi.org/10.1093/ve/vev003
Muhire B.M., Varsani A., Martin D.P. (2014): SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS ONE, 9: e108277. doi: 10.1371/journal.pone.0108277 https://doi.org/10.1371/journal.pone.0108277
Parrano L., Afunian M., Pagliaccia D., Douhan G., Vidalakis G. (2012): Characterization of viruses associated with garlic plants propagated from different reproductive tissues from Italy and other geographic regions.Phytopathologia Mediterranea, 51: 549–565.
Pramesh D., Baranwal V.K. (2013): Molecular characterization of coat protein gene of Garlic common latent virus isolates from India: An evidence for distinct phylogeny and recombination. Virus Genes, 47: 189–193. https://doi.org/10.1007/s11262-013-0909-z
Rozas J., Ferrer-Mata A., Sánchez-DelBarrio J.C., Guirao-Rico S., Librado P., Ramos-Onsins S.E., Sánchez-Gracia A. (2017): DnaSP 6: DNA sequence Ppolymorphism analysis of large data sets. Molecular Biology and Evolution, 34: 3299–3302. https://doi.org/10.1093/molbev/msx248
Santosa A.I., Ertunc F. (2020): Identification, molecular detection and phylogenetic analysis of four viruses infecting Allium cepa in Ankara province, Turkey. Journal of Plant Diseases and Protection, 127: 561–569. https://doi.org/10.1007/s41348-020-00347-5
Shahraeen N., Lesemann D.E., Ghotbi T. (2008): Survey for viruses infecting onion, garlic and leek crops in Iran. Bulletin OEPP/EPPO Bulletin, 38: 131–135. https://doi.org/10.1111/j.1365-2338.2008.01198.x
Tajima F. (1989): Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123: 585–595. https://doi.org/10.1093/genetics/123.3.585
Tamura K. (1992): Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Molecular Biology and Evolution 9: 678–687.
Torrico A.K., Celli M.G., Conci L.R., Conci V.C. (2015): Incidence of Garlic common latent virus in Argentina, and phylogenetic and recombination analyses of isolates. Pesquisa Agropecuária Brasileira, 50: 363–373. https://doi.org/10.1590/S0100-204X2015000500003
Tsompana M., Abad J., Purugganan M., Moyer J. (2005): The molecular population genetics of the Tomato spotted wilt virus (TSWV) genome. Molecular Ecology, 14: 53–66. https://doi.org/10.1111/j.1365-294X.2004.02392.x
Tsuneyoshi T., Matsumi T., Deng T.C., Sako I., Sumi S. (1998): Differentiation of Allium carlaviruses isolated from different parts of the world based on the viral coat protein sequence. Archives of Virology, 143: 1093–1107. https://doi.org/10.1007/s007050050358
Wylie S.J., Luo H., Li H., Jones M.G.K. (2012): Multiple polyadenylated RNA viruses detected in pooled cultivated and wild plant samples. Archives of Virology, 157: 271–284. https://doi.org/10.1007/s00705-011-1166-x
Yadav V., Majumder S. (2019): The first complete genome sequence of Garlic common latent virus occurring in India. VirusDisease, 30: 311–314. https://doi.org/10.1007/s13337-018-0505-x