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Plant Science Today (PST)

Research Articles

Vol. 13 No. sp5 (2026): Recent Advances in Agriculture

Evolution and selection patterns in begomoviruses infecting Phaseolus vulgaris L.

DOI
https://doi.org/10.14719/pst.13691
Submitted
15 January 2026
Published
04-08-2026

Abstract

Begomoviruses affect Phaseolus vulgaris L. that considerably decrease yield in many bean growing areas. Their evolutionary dynamics, genetic diversity and selection patterns were investigated in this study. Complete genome sequences of begomovirus isolates from different parts of the world were retrieved from GenBank. The MEGA11 was employed to align the sequences and to select the best nucleotide substitution models. Phylogenetic clustering appeared broadly consistent with geographical origin in maximum-likelihood phylogenetic trees. Transition/transversion analysis indicated relatively higher substitution rates in AV1 and AC4 as compared with other genomic regions, most likely due to vector influence and host–virus interactions. Analysis was carried out using RDP4.1 revealed that recombination is one of
the major factors for diversification of these viruses. Neutrality tests using DnaSP v6.12 indicated that purifying selection is a predominant force driving the evolution of these viruses. High nucleotide diversity was observed in both DNA-B and betasatellites. The role of geographical distribution, mutation, recombination and selection has been analysed and discussed in the present study. In addition, the observed genetic variability among isolates highlights the adaptive potential of begomoviruses under diverse environmental and host conditions. The findings provide valuable insights into the evolutionary mechanisms shaping Begomovirus populations and contribute to a better understanding of their emergence and spread. Such information may be useful for developing effective disease management strategies and supporting breeding programs aimed at improving resistance in common bean cultivars.

References

  1. 1. Gepts P. Crop domestication as a long-term selection experiment. In: Plant Breed Rev. 2003. p. 1–44. https://doi.org/10.1002/9780470650288.ch1
  2. 2. Blair MW, González LF, Kimani PM, Butare L. Genetic diversity, inter-gene pool introgression and nutritional quality of common beans (Phaseolus vulgaris L.) from Central Africa. Theor Appl Genet. 2010;121:237–48. https://doi.org/10.1007/s00122-010-1305-x
  3. 3. Broughton WJ, Hernández G, Blair M, Beebe S, Gepts P, Vanderleyden J. Beans (Phaseolus spp.)-model food legumes. Plant Soil. 2003;252:55–128. https://doi.org/10.1023/A:1024146710611
  4. 4. Winge T. Seed legislation in Europe and crop genetic diversity. In: Lichtfouse E, editor. Sustainable Agriculture Reviews. Vol. 15. Cham: Springer; 2015. p. 1–64. https://doi.org/10.1007/978-3-319-09132-7_1
  5. 5. Bhagat S, Kumar S, Dogra S. Identification of induced mutants for morpho-physiological and biochemical traits of rajmash (Phaseolus vulgaris). Indian J Agric Sci. 2023;93:1338–43. https://doi.org/10.56093/ijas.v93i12.135595
  6. 6. Chang-Sidorchuk L, González-Alvarez H, Martínez-Zubiaur Y. Begomoviruses infecting common beans (Phaseolus vulgaris L.) in production areas in Cuba. Span J Agric Res. 2018;16. https://doi.org/10.5424/sjar/2018162-11735
  7. 7. Lima ATM, Silva JCF, Silva FN, Castillo-Urquiza GP, Silva FF, Seah YM, et al. The diversification of begomovirus populations is predominantly driven by mutational dynamics. Virus Evol. 2017;3. https://doi.org/10.1093/ve/vex005
  8. 8. Duffy S, Holmes EC. Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus tomato yellow leaf curl virus. J Virol. 2008;82:957–65. https://doi.org/10.1128/JVI.01929-07
  9. 9. Saitou N, Imanishi T. Relative efficiencies of the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree. Mol Biol Evol. 1989;6(5):514–25. https://doi.org/10.1093/oxfordjournals.molbev.a040572
  10. 10. Kumar Chanchal D, Alok S, Kumar M, Kumar Bijauliya R, Rashi S, Gupta S. A brief review on Abelmoschus esculentus Linn. okra. Int J Pharm Sci Res. 2018;9:58–66.
  11. 11. Posada D, Crandall KA. Selecting the best-fit model of nucleotide substitution. Syst Biol. 2001;50:580–601. https://doi.org/10.1080/106351501750435121
  12. 12. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol. 2021;38:3022–7. https://doi.org/10.1093/molbev/msab120
  13. 13. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35:1547–9. https://doi.org/10.1093/molbev/msy096
  14. 14. Martin DP, Murrell B, Golden M, Khoosal A, Muhire B. RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evol. 2015;1. https://doi.org/10.1093/ve/vev003
  15. 15. Bland JM, Altman DG. Statistics notes: Multiple significance tests: The Bonferroni method. BMJ. 1995;310:170. https://doi.org/10.1136/bmj.310.6973.170
  16. 16. Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol. 2017;34:3299–302. https://doi.org/10.1093/molbev/msx248
  17. 17. Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics. 1983;105:437–60. https://doi.org/10.1093/genetics/105.2.437
  18. 18. Watterson GA. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 1975;7:256–76. https://doi.org/10.1016/0040-5809(75)90020-9
  19. 19. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123:585–95. https://doi.org/10.1093/genetics/123.3.585
  20. 20. Lefeuvre P, Lett JM, Reynaud B, Martin DP. Avoidance of protein fold disruption in natural virus recombinants. PLoS Pathog. 2007;3(11). https://doi.org/10.1371/journal.ppat.0030181
  21. 21. Brown JK, Zerbini FM, Navas-Castillo J, Moriones E, Ramos-Sobrinho R, Silva JCF, et al. Revision of Begomovirus taxonomy based on pairwise sequence comparisons. Arch Virol. 2015;160:1593–619.
  22. https://doi.org/10.1007/s00705-015-2398-y
  23. 22. Mondal D, Mandal S, Shil S, Sahana N, Pandit GK, Choudhury A. Genome wide molecular evolution analysis of begomoviruses reveals unique diversification pattern in coat protein gene of Old World and New World viruses. Virusdisease. 2019;30:74–83. https://doi.org/10.1007/s13337-019-00524-7
  24. 23. Fiallo-Olivé E, Navas-Castillo J. Begomoviruses: What is the secret(s) of their success? Trends Plant Sci. 2023;28:715–27. https://doi.org/10.1016/j.tplants.2023.01.012
  25. 24. Crespo-Bellido A, Hoyer JS, Dubey D, Jeannot RB, Duffy S. Interspecies recombination has driven the macroevolution of cassava mosaic begomoviruses. J Virol. 2021;95. https://doi.org/10.1128/JVI.00541-21
  26. 25. Naveed H, Islam W, Jafir M, Andoh V, Chen L, Chen K. A review of interactions between plants and whitefly-transmitted begomoviruses. Plants. 2023;12:3677. https://doi.org/10.3390/plants12213677
  27. 26. Breves SS, Silva FA, Euclydes NC, Saia TFF, Jean-Baptiste J, Andrade Neto ER, et al. Begomovirus-host interactions: Viral proteins orchestrating intra- and intercellular transport of viral DNA while suppressing host defense mechanisms. Viruses. 2023;15:1593. https://doi.org/10.3390/v15071593
  28. 27. Vinoth Kumar R, Singh D, Singh AK, Chakraborty S. Molecular diversity, recombination and population structure of alphasatellites associated with begomovirus disease complexes. Infect Genet Evol. 2017;49:39–47. https://doi.org/10.1016/j.meegid.2017.01.001
  29. 28. Nigam D. Genomic variation and diversification in begomovirus genome in implication to host and vector adaptation. Plants. 2021;10:1706. https://doi.org/10.3390/plants10081706
  30. 29. Chahat S, Akshu J, Rahul K, Yogesh K. Evolutionary dynamics and recombination patterns in begomoviruses infecting Abelmoschus esculentus: A phylogenetic and population structure analysis. Plant Sci Today. 2026;13. https://doi.org/10.14719/pst.11190

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