Genetic Variability and Evidence of a New Subgroup in Watermelon Mosaic Virus Isolates
Abstract
:1. Introduction
2. Results
2.1. Genetic Diversity of WMV in the U.S.
2.2. Phylogenetic Analysis of the CP Gene
2.3. Amino Acid Sequence Comparison
2.4. Selection Pressure in the CP Gene
2.5. Genetic Differentiation and Gene Flow Analysis of WMV Isolates
2.6. Co-Evolution Analysis of CP Gene Sequences
2.7. Phylogenetic Analysis of the Complete Genome WMV Isolates
2.8. Recombination Events within the CP Gene
3. Discussion
4. Materials and Methods
4.1. Sources of WMV Isolates
4.2. RNA Extraction, Amplification, and Sequencing
4.3. Consensus Sequences and Phylogenetic Analysis of the CP Gene
4.4. Selection Pressure Analysis
4.5. Genetic Differentiating and Gene Flow Analysis
4.6. Co-Evolution Analysis of CP Amino Acids
4.7. Phylogenetic Analysis of the Complete Genome Sequences
4.8. Detection of Recombination Events
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Khanal, V.; Wells, H.; Ali, A. High Prevalence of Three Potyviruses Infecting Cucurbits in Oklahoma and Phylogenetic Analysis of Cucurbit Aphid-Borne Yellows Virus Isolated from Pumpkins. Pathogens 2021, 10, 53. [Google Scholar] [CrossRef]
- Purcifull, D.; Hiebert, E.; Edwardson, J. Watermelon Mosaic Virus 2. Descriptions of Plant Viruses. 1984. no. 293. Available online: https://www.dpvweb.net/dpv/showdpv/?dpvno=293 (accessed on 30 August 2021).
- Grafton-Cardwell, E.E.; Perring, T.M.; Smith, R.F.; Valencia, J.; Farrar, C.A. Occurrence of mosaic viruses in melons in the central valley of California. Plant Dis. 1996, 80, 1092–1097. [Google Scholar] [CrossRef] [Green Version]
- Lecoq, H.; Desbiez, C. Watermelon mosaic virus and Zucchini yellow mosaic virus. In Encyclopedia of Virology, 3rd ed.; Mahy, B.W.J., van Regenmortel, M.H.V., Eds.; Academic Press: Waltham, MA, USA, 2008; pp. 433–440. [Google Scholar]
- Ali, A. Epidemiology and evolution of poytviruses infecting cucurbits. In Applied Plant Virology; Awasthi, L.P., Ed.; Academic Press: Cambridge, MA, USA, 2020; pp. 405–417. [Google Scholar]
- Riechmann, J.I.; Lain, S.; Garcia, J.A. Highlights and prospects of Potyvirus molecular biology. J. Gen. Virol. 1992, 73, 1–16. [Google Scholar] [CrossRef]
- Sharifi, M.; Massumi, H.; Heydarnejad, J.; Pour, A.H.; Shaabanian, M.; Rahimian, H. Analysis of the biological and molecular variability of Watermelon mosaic virus isolates from Iran. Virus Genes 2008, 37, 304–313. [Google Scholar] [CrossRef] [PubMed]
- Frenkel, M.J.; Ward, C.W.; Shukla, D.D. The use of 3 non-codig nucleotide sequences in the taxonomy of potyviruses: Application to Watermelon mosaic virus 2 and Soybean mosaic virus-N. J. Gen. Virol. 1989, 70, 2775–2783. [Google Scholar] [CrossRef] [PubMed]
- Desbiez, C.; Lecoq, H. The nucleotide sequence of Watermelon mosaic virus (WMV, Potyvirus) reveals interspecific recombination between two related potyviruses in the 5 part of the genome. Arch Virol. 2004, 149, 1619–1632. [Google Scholar] [CrossRef] [PubMed]
- Ali, A.; Natsuaki, T.; Okuda, S. The complete nucleotide sequence of a Pakistani isolate of Watermelon mosaic virus provides further insight into the taxonomic status in the Bean common mosaic virus subgroup. Virus Genes 2006, 32, 307–311. [Google Scholar] [CrossRef] [PubMed]
- Ali, A.; Abdalla, O.; Bruton, B.; Fish, W.; Sikora, E.; Zhang, S.; Taylor, M. Occurrence of viruses infecting watermelon, other cucurbits, and weeds in the parts of southern United States. Plant Health Prog. 2012, 13, 9. [Google Scholar] [CrossRef] [Green Version]
- Luis-Arteaga, M.; Alvarez, J.M.; Alonso-Prados, J.L.; Bernal, J.J.; Garcia-Arenal, F.; Lavina, A.; Batlle, A.; Moriones, E. Occurrence, distribution, and relative incidence of mosaic viruses infecting field-grown melon in Spain. Plant Dis. 1998, 82, 979–982. [Google Scholar] [CrossRef] [Green Version]
- Shoeibi, S.; Masumi, M.; Nasrollanezhad, D.; Heydari, S.; Izadpanah, K.; Ahmadikhah, S. Sequencing of six Iranian isolates of Watermelon mosaic virus and phylogenetic comparison of Iranian isolates with other isolates of the world. Iran J. Plant Path. 2009, 45, 34–37. [Google Scholar]
- Yakoubi, S.; Lecoq, H.; Desbiez, C. Algerian watermelon mosaic virus (AWMV): A new Potyvirus species in the PRSV cluster. Virus Genes 2008, 37, 103–109. [Google Scholar] [CrossRef]
- Webb, R.E.; Scott, H.A. Isolation and identification of watermelon mosaic viruses 1 and 2. Phytopathology 1965, 55, 895–900. [Google Scholar]
- Chala, V.H.; Harrison, C.W.; Halliwell, R.S. Identification of two distinct strains of Watermelon mosaic virus 2 affecting cucurbits in Texas. Plant Dis. 1987, 71, 750–752. [Google Scholar] [CrossRef]
- Davis, R.E.; Mizuki, M.K. Detection of cucurbit viruses in New Jersey. Plant Dis. 1987, 71, 40–44. [Google Scholar] [CrossRef]
- Jossey, S.; Babadoost, M. Occurrence and distribution of pumpkin and squash viruses in Illinois. Plant Dis. 2008, 92, 61–68. [Google Scholar] [CrossRef] [PubMed]
- Ali, A.; Mohammad, O.; Khattab, A. Distribution of viruses infecting cucurbit crops and isolation of potential new virus-like sequences from weeds on Oklahoma. Plant Dis. 2012, 96, 242–248. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Desbiez, C.; Joannon, B.; Wipf-Scheibel, C.; Chandeysson, C.; Lecoq, H. Emergence of new strains of Watermelon mosaic virus in south-eastern France: Evidence for limited spread but rapid local population shift. Virus Res. 2009, 14, 201–228. [Google Scholar] [CrossRef]
- Desbiez, C.; Costa, C.; Wipf-Scheibel, C.; Girard, M.; Lecoq, H. Serological and molecular variability of Watermelon mosaic virus (genus Potyvirus). Arch Virol. 2007, 152, 775–781. [Google Scholar] [CrossRef]
- Lecoq, H.; Fabre, F.; Joannon, B.; Wipf-Scheiberl, C.; Chandeysson, C.; Schoeny, A.; Desbiez, C. Search for factors involved in the rapid shift of Watermelon mosaic virus (WMV) populations in South-eastern France. Virus Res. 2011, 159, 115–123. [Google Scholar] [CrossRef] [Green Version]
- Glasa, M.; Bananej, K.; Predajna, L.; Vahdat, A. Genetic diversity of Watermelon mosaic virus is Slovakia and Iran shows distinct pattern. Plant Dis. 2011, 95, 38–42. [Google Scholar] [CrossRef] [Green Version]
- Wang, D.; Li, G.; Shan, S.D. Occurrence of viruses infecting melon in Xinjiang of China and molecular characterization of Watermelon mosaic virus isolates. Eur. J. Plant Pathol. 2017, 147, 919–931. [Google Scholar] [CrossRef]
- Quemada, H.; Sieu, L.C.; Siemieniak, D.R.; Gonsalves, D.; Slightom, J.L. Watermelon mosaic virus II and Zucchini yellow mosaic virus: Cloning of 3-terminal regions, nucleotide sequences and phylogenetic comparisons. J. Gen. Virol. 1990, 71, 203–210. [Google Scholar] [CrossRef]
- Gal-On, A.; Antignus, Y.; Rosner, A.; Raccah, B. A zucchini yellow mosaic virus coat protein gene mutation restores aphid transmissibility but has no effect on multiplication. J. Gen. Virol. 1992, 73, 2183–2187. [Google Scholar] [CrossRef] [PubMed]
- Kehoe, M.A.; Coults, B.A.; Buirchell, B.J.; Jones, R.A.C. Split Personality of a Potyvirus: To Specialize or Not to Specialize? PLoS ONE 2014, 9, e105770. [Google Scholar] [CrossRef] [PubMed]
- Wylie, S.J.; Jones, R.A.C. Role of recombination in the evolution of host specialization within Bean yellow mosaic virus. Phytopathology 2009, 99, 512–518. [Google Scholar] [CrossRef] [Green Version]
- Lecoq, H.; Wisler, G.; Pitrat, M. Cucurbit viruses: The classics and the emerging. In Cucurbitacea, Evaluation and Enhancement of Cucurbit Germplasm; McCreight, J.D., Ed.; Alexandria ASHS: Alexandria, LA, USA, 1998; pp. 126–142. [Google Scholar]
- Ali, A.; Li, H.; Schneider, W.L.; Sherman, D.J.; Gray, S.; Smith, D.; Roossinck, M.J. Analysis of genetic bottlenecks during horizontal transmission of Cucumber mosaic virus. J. Virol. 2006, 80, 8345–8350. [Google Scholar] [CrossRef] [Green Version]
- Garcia-Arenal, F.; Fraile, A.; Malpica, J.M. Variation and evolution of plant virus populations. Int. Microbiol. 2003, 6, 225–232. [Google Scholar] [CrossRef]
- Nigam, D.; LaTourrette, K.; Souza, P.F.N.; Garcia-Ruiz, H. Genome- Wide Variation in Potyviruses. Front. Plant Sci. 2019, 10, 1439. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Roossinck, M.J.; Ali, A. Mechanisms of plant virus evolution and identification of geneticbottlenecks: Impact on disease management. In Biotechnology and Plant Disease Management; Punja, Z.K., DeBoer, S., Sanfacon, H., Eds.; CAB International: Wallingford, UK, 2007; pp. 109–124. [Google Scholar]
- Chare, E.R.; Holmes, E.C. A phylogenetic survey of recombination frequency in plant RNAviruses. Arch. Virol. 2006, 151, 933–946. [Google Scholar] [CrossRef] [PubMed]
- Sztuba-Solińska, J.; Urbanowicz, A.; Figlerowicz, M.; Bujarski, J.J. RNA-RNA recombination in plant virus replication and evolution. Ann. Rev. Phytopathol. 2011, 49, 415–443. [Google Scholar] [CrossRef]
- Abdalla, O.A.; Ali, A. Genetic diversity in the 3’-terminal region of Papaya ringspot virus (PRSV-W) isolates from watermelon in Oklahoma. Arch. Virol. 2011, 157, 405–412. [Google Scholar] [CrossRef]
- Larkin, M.A.; Blackshields, G.; Brown, N.P.; Chenna, R.; McGettigan, P.A.; McWilliam, H. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23, 2947–2948. [Google Scholar] [CrossRef] [Green Version]
- Hall, T. BioEdit: A user friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 1999, 41, 95–98. [Google Scholar]
- Tamura, K.; Nei, M.; Kumar, S. Prospects of inferring very large phylogenies by using the neighbor-joining method. Pro. Natl. Acad. Sci. USA 2004, 101, 11030–11035. [Google Scholar] [CrossRef] [Green Version]
- Kumar, S.; Stecher, G.; Tamura, K. MEGA7, Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 2015, 33, 1870–1874. [Google Scholar] [CrossRef] [Green Version]
- Rambaut, A. FigTree 1.3.1. Institute of Evolutionary Biology, University of Edinburgh: Edinburgh, UK, 2010. Available online: http://tree.bio.ed.ac.uk/software/figtree (accessed on 30 August 2021).
- Korber, B. HIV Signature and Sequence Variation Analysis. In Computational Analysis of HIV Molecular Sequences; Rodrigo, A.G., Learn, G.H., Eds.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 2000; pp. 55–72. [Google Scholar]
- Kosakovsky, P.S.L.; Frost, S.D.W. Datamonkey: Rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 2005, 21, 2531–2533. [Google Scholar]
- Nei, M.; Gojobori, T. Simple methods for estimating the number of synonymous and non-synonymous nucleotide substitutions. Mol. Biol. Evol. 1986, 3, 418–426. [Google Scholar]
- Rozas, J.; Ferrer-Mata, A.; Sanchez-Delbarrio, J.S.; Guirao-Rico, S.; Librado, P.; Ramos-Onsins, S.; Sanchez-Garcia, A. DnaSP 6, D Sequence Polymorphism Analysis of Large Datasets. Mol. Biol. Evol. 2017, 34, 3299–3302. [Google Scholar] [CrossRef] [PubMed]
- Fuglsang, A. Estimating the Effective Number of Codons: The Wright way of Determining Codon Homozygosity Leads to Superior Estimates. Genetics 2006, 172, 1301–1307. [Google Scholar] [CrossRef]
- Poon, A.F.; Lewis, F.I.; Frost, S.D.W.; Pond, S.L. Spidermonkey: Rapid Detection of Co-Evolving Sites Using Bayesian Graphical Models. Bioinformatics 2008, 24, 1949–1950. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Rajbanshi, N.; Ali, A. First complete genome sequence of a Watermelon mosaic virus isolated from watermelon in the United States. Genome Announc. 2016, 4, e00299-16. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Muhire, B.M.; Varsani, A.; Martin, D.P. SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS ONE 2014, 9, e108277. [Google Scholar] [CrossRef] [PubMed]
- Martin, D.P.; Murrell, B.; Golden, M.; Khoosal, A.; Muhire, B. RDP4, Detection and analysis of recombination patterns in virus genomes. Virus Evol. 2015, 1, vev003. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Lole, K.S.; Bollinger, R.C.; Paranjape, R.S.; Garkari, D.; Kulkarni, S.S.; Novak, N.G.; Ingersoll, R.; Sheppard, H.W.; Ray, S.C. Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination. J. Virol. 1999, 73, 152–160. [Google Scholar] [CrossRef] [Green Version]
- Desbiez, C.; Lecoq, H. Evidence for multiple interspecific recombination in natural population of Watermelon mosaic virus (WMV, Potyvirus). Arch. Virol. 2008, 153, 1749–1754. [Google Scholar] [CrossRef]
- Desbiez, C.; Joannon, B.; Wipf-Scheibel, C.; Chandeysson, C.; Lecoq, H. Recombination in natural populations of watermelon mosaic virus: New agronomic threat or damp squib? J. Gen. Virol. 2011, 92, 1939–1948. [Google Scholar] [CrossRef]
- Moreno, M.; Malpice, J.M.; Diaz-Pendon, J.A.; Moriones, E.; Fraile, A.; Garcia-Arenal, F. Variability and genetic structure of the population of Watermelon mosaic virus infecting melon in Spain. Virology 2004, 318, 451–460. [Google Scholar] [CrossRef] [Green Version]
- Wang, C.; Bau, H.; Yeh, S. Comparison of the nuclear inclusion b protein and coat protein genes of five Papaya ringspot virus strains distinct in geographic origin and pathogenicity. Phytopathology 1994, 84, 1205–1210. [Google Scholar] [CrossRef]
- Salvaudon, L.; De Moraes, C.M.; Mescher, M.C. Outcomes of co-infection by two potyviruses: Implications for the evolution of manipulative strategies. Proc. R. Soc. B 2013, 280, 20122959. [Google Scholar] [CrossRef] [Green Version]
- Romay, G.; Lecoq, H.; Desbiez, C. First report of watermelon mosaic virus naturally infecting Cucumis anguria. Plant Dis. 2013, 97, 1515. [Google Scholar] [CrossRef]
- Finetti-Sialer, M.M.; Mascia, T.; Cillo, F.; Vovlas, C.; Gallitelli, D. Biological and molecular characterization of a recombinant isolate of Watermelon mosaic virus associated with a watermelon necrotic disease in Italy. Eur. J. Plant Pathol. 2012, 132, 317–322. [Google Scholar] [CrossRef]
No | Name of State | Name of Isolate | Host | Year Collected | Accession Number |
---|---|---|---|---|---|
1 | Alabama | AL-1 | Watermelon | 2010 | MG021270 |
2 | Arkansas | AR-1 | Pumpkin | 2010 | MG021275 |
3 | AR-2 | Watermelon | 2010 | MG021276 | |
4 | AR-3 | Pumpkin | 2010 | MG021277 | |
5 | AR-4 | Cantaloupe | 2010 | MG021278 | |
6 | AR-5 | Watermelon | 2010 | MG021279 | |
7 | AR-6 | Watermelon | 2010 | MG021280 | |
8 | AR-7 | Watermelon | 2010 | MG021281 | |
9 | Florida | FL-1 | Squash | 2011 | MG021262 |
10 | FL-2 | Pumpkin | 2011 | MG021263 | |
11 | FL-3 | Cucumber | 2011 | MG021264 | |
12 | FL-4 | Watermelon | 2011 | MG021265 | |
13 | Georgia | GA-1 | Watermelon | 2010 | MG021271 |
14 | GA-2 | Watermelon | 2010 | MG021272 | |
15 | Kentucky | KY-1 | Watermelon | 2010 | MG021273 |
16 | Louisiana | LA-1 | Watermelon | 2010 | MG021274 |
17 | Mississippi | MS-1 | Cantaloupe | 2007 | MG021266 |
18 | MS-2 | Squash | 2007 | MG021267 | |
19 | MS-3 | Squash | 2008 | MG021268 | |
20 | MS-4 | Watermelon | 2010 | MG021269 | |
21 | Oklahoma | OK-1 | Squash | 2008 | MG021247 |
22 | OK-2 | Watermelon | 2010 | MG021248 | |
23 | OK-3 | Watermelon | 2009 | MG021249 | |
24 | OK-4 | Watermelon | 2009 | MG021250 | |
25 | OK-5 | Watermelon | 2009 | MG021251 | |
26 | OK-6 | Cantaloupe | 2009 | MG021252 | |
27 | OK-7 | Watermelon | 2010 | MG021253 | |
28 | OK-8 | Watermelon | 2010 | MG021254 | |
29 | OK-9 | Watermelon | 2010 | MG021255 | |
30 | OK-10 | Watermelon | 2010 | MG021256 | |
31 | OK-11 | Palmer amaranth | 2010 | MG021257 | |
32 | OK-12 | Pumpkin | 2010 | MG021258 | |
33 | OK-13 | Watermelon | 2010 | MG021259 | |
34 | OK-14 | Watermelon | 2010 | MG021260 | |
35 | OK-15 | Pumpkin | 2010 | MG021261 | |
36 | Texas | TX-1 | Watermelon | 2010 | MG021282 |
37 | TX-2 | Cucumber | 2010 | MG021283 | |
38 | TX-3 | Watermelon | 2010 | MG021284 | |
39 | TX-4 | Watermelon | 2010 | MG021285 | |
40 | TX-5 | Watermelon | 2010 | MG021286 | |
41 | TX-6 | Watermelon | 2010 | MG021287 | |
42 | TX-7 | Watermelon | 2010 | MG021288 | |
43 | TX-8 | Watermelon | 2010 | MG021289 | |
44 | TX-9 | Watermelon | 2010 | MG021290 | |
45 | TX-10 | Watermelon | 2010 | MG021291 | |
46 | TX-11 | Watermelon | 2010 | MG021292 | |
47 | TX-12 | Watermelon | 2010 | MG021293 | |
48 | TX-13 | Watermelon | 2010 | MG021294 | |
49 | TX-14 | Watermelon | 2010 | MG021295 | |
50 | TX-15 | Watermelon | 2010 | MG021296 | |
51 | TX-16 | Watermelon | 2010 | MG021297 | |
52 | TX-17 | Watermelon | 2010 | MG021298 | |
53 | TX-18 | Watermelon | 2010 | MG021299 | |
54 | TX-19 | Watermelon | 2010 | MG0212300 | |
55 | TX-20 | Watermelon | 2010 | MG0212301 | |
56 | TX-21 | Watermelon | 2010 | MG0212302 | |
57 | TX-22 | Watermelon | 2010 | MG0212303 |
Subgroups within G3 (EM Isolates) | No. of Isolates a | ENC b | No. of Nnegatively c Selected Codons | dNSd | Variance (dNS) | Standard Deviation (dNS) | dSe | Variance (dNS) | Standard Deviation (dNS) | dNS/dS | ||
---|---|---|---|---|---|---|---|---|---|---|---|---|
SLAC | FEL | REL | ||||||||||
EM1 | 17 | 50.092 | 2 | 29 | 55 | 0.0129 | 0.0000 | 0.0022 | 0.0639 | 0.0000 | 0.0098 | 0.2019 |
EM2 | 31 | 51.828 | 9 | 25 | 1 | 0.0148 | 0.0000 | 0.0024 | 0.0479 | 0.0001 | 0.0077 | 0.3089 |
EM5 | 9 | 50.573 | 2 | 17 | 31 | 0.0188 | 0.0001 | 0.0037 | 0.0906 | 0.0002 | 0.0154 | 0.2075 |
States | Fst | Nm | Ks | Kst | p-Value | Ks* | Kst* | p-Value | Z* | p-Value | Snn | p-Value |
---|---|---|---|---|---|---|---|---|---|---|---|---|
AR vs. FL | 0.439 | 0.32 | 30.54 | 0.246 | 0.008 ** | 3.06 | 0.112 | 0.007 ** | 2.66 | 0.006 ** | 0.95 | 0.008 ** |
AR vs. MS | 0.083 | 2.73 | 43.03 | 0.043 | 0.180 ns | 3.54 | 0.021 | 0.095 ns | 2.88 | 0.051 ns | 0.95 | 0.007 ** |
AR vs. OK | 0.004 | 65.87 | 48.56 | 0.001 | 0.364 ns | 3.68 | 0.000 | 0.036 ns | 4.44 | 0.293 ns | 0.772 | 0.013 * |
AR vs. TX | 0.061 | 3.84 | 44.73 | 0.024 | 0.100 ns | 3.52 | 0.013 | 0.082 ns | 4.94 | 0.051 ns | 0.84 | 0.004 ** |
AR vs. OS a | 0.019 | 12.93 | 46.84 | 0.010 | 0.025 ns | 3.66 | -0.000 | 0.280 ns | 3.19 | 0.319 ns | 0.83 | 0.028 * |
Fl vs. MS | 0.620 | 0.15 | 22.0 | 0.483 | 0.024 * | 2.42 | 0.279 | 0.024 * | 8.62 | 0.024 * | 1.00 | 0.024 * |
FL vs. OK | 0.470 | 0.28 | 40.58 | 0.174 | 0.001 ** | 3.40 | 0.079 | 0.0010 ** | 3.86 | 0.0010 ** | 1.00 | 0.002 ** |
FL vs. TX | 0.569 | 0.19 | 38.45 | 0.186 | 0.001 ** | 3.31 | 0.076 | 0.000 *** | 4.52 | 0.0010 ** | 1.00 | 0.000 *** |
FL vs. OS | 0.270 | 0.68 | 29.42 | 0.158 | 0.028 * | 2.83 | 0.120 | 0.036 * | 2.29 | 0.028 * | 0.888 | 0.024 * |
MS vs. OK | 0.010 | 24.29 | 47.80 | 0.003 | 0.035 ns | 3.63 | 0.009 | 0.192 ns | 4.08 | 0.115 ns | 0.921 | 0.005 ** |
MS vs. TX | 0.026 | 9.07 | 43.73 | 0.007 | 0.307 ns | 3.46 | 0.012 | 0.125 ns | 4.69 | 0.040 * | 0.961 | 0.003 ** |
MS vs. OS | 0.128 | 1.69 | 44.68 | 0.074 | 0.130 ns | 3.51 | 0.033 | 0.157 ns | 2.48 | 0.112 ns | 0.833 | 0.044 * |
OK vs. TX | 0.027 | 8.88 | 46.81 | 0.014 | 0.162 ns | 3.56 | 0.019 | 0.022 * | 5.39 | 0.005 ** | 0.887 | 0.000 *** |
OK vs. OS | 0.024 | 10.06 | 49.86 | 0.009 | 0.315 ns | 3.68 | 0.006 | 0.278 ns | 4.21 | 0.181 ns | 0.850 | 0.014 * |
TX vs. OS | 0.122 | 1.79 | 45.41 | 0.043 | 0.097 ns | 3.51 | 0.024 | 0.041 * | 4.75 | 0.020 * | 0.944 | 0.000 *** |
Sub-Groups a | Event No. | Recomb. | Major Parent | Minor Parent | Recombination Sites | Detection Methods | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
EM1 Isolates | RDP | GENECON V | Bootscan | Maxchi | Chimaera | Sisscan | 3-Seq | |||||
1 | AR-3 | TX-13 | Unknown (Al-1) | 69–735 nt | - | - | - | 8.115 × 10−2 | - | - | 2.864 × 10−2 | |
2 | OK-2 | TX-13 | Unknown (Al-1) | 680–832 nt | - | - | - | 8.115 × 10−2 | - | - | 2.864 × 10−2 | |
3 b | OK-15 | OK-2 | Unknown(Al-1) | 298–810 nt | 1.243 × 10−4 | 4.828 × 10−3 | - | 6.683 × 10−8 | 2.881 × 10−5 | - | 9.765 × 10−9 | |
EM2 | None | |||||||||||
EM5 isolates | ||||||||||||
1 | OK-11 | MS-3 | OK-12 | 230–824 nt | 8.231 × 10−4 | 4.035 × 10−10 | 1.655 × 10−6 | |||||
2 | TX-7 | TX-5 | OK-12 | 627–743 nt | 3.198 × 10−2 | 1.201 × 10−4 | ||||||
3 b | MS-3 | TX-6 | Unknown (OK-12) | 155–724 nt | 7.921 × 10−3 | 1.214 × 10−1 | 4.096 × 10−2 | 4.814 × 10−3 | ||||
4 | OK-13 | OK-12 | TX-6 | 58–783 nt | 3.987 × 10−3 | 6.198 × 10−3 |
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Abdalla, O.A.; Ali, A. Genetic Variability and Evidence of a New Subgroup in Watermelon Mosaic Virus Isolates. Pathogens 2021, 10, 1245. https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10101245
Abdalla OA, Ali A. Genetic Variability and Evidence of a New Subgroup in Watermelon Mosaic Virus Isolates. Pathogens. 2021; 10(10):1245. https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10101245
Chicago/Turabian StyleAbdalla, Osama A., and Akhtar Ali. 2021. "Genetic Variability and Evidence of a New Subgroup in Watermelon Mosaic Virus Isolates" Pathogens 10, no. 10: 1245. https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10101245