Recombination and darwinian selection as drivers of genetic diversity and evolution of sweet potato leaf curl viruses in Tanzania

Clark, 2012, Sweetpotato viruses: 15 years of progress on understanding and managing complex diseases, Plant Dis., 96, 168, 10.1094/PDIS-07-11-0550 Mbanzibwa, 2014, Small RNA deep Sequencing-based detection and further evidence of DNA viruses infecting sweet potato plants in Tanzania, Ann. Appl. Biol., 165, 329, 10.1111/aab.12136 Bramwel, 2020, Storage root yield of sweetpotato as influenced by Sweetpotato leaf curl virus and its interaction with Sweetpotato feathery mottle virus and Sweetpotato chlorotic stunt virus in Kenya, Plant Dis., 104, 1477, 10.1094/PDIS-06-19-1196-RE Albuquerque, 2012, Genetic diversity and recombination analysis of sweepoviruses from Brazil, Virol. J., 9, 241, 10.1186/1743-422X-9-241 Zhang, 2011, Genetic diversity of sweet potato begomoviruses in the United States and identification of a natural recombinant between Sweet potato leaf curl virus and Sweet potato leaf curl Georgia virus, Arch. Virol., 156, 955, 10.1007/s00705-011-0930-2 Liu, 2017, Diversity of sweepoviruses infecting sweet potato in China, Plant Dis., 101, 2098, 10.1094/PDIS-04-17-0524-RE Seal, 2006, Factors influencing Begomovirus evolution and their increasing global significance: Implications for sustainable control, Crit. Rev. Plant Sci., 25, 23, 10.1080/07352680500365257 Pérez-Losada, 2015, Recombination in viruses: mechanisms, methods of study, and evolutionary consequences, Infect. Genet. Evol., 30, 296, 10.1016/j.meegid.2014.12.022 Sztuba-Solińska, 2011, RNA-RNA recombination in plant virus replication and evolution, Annu. Rev. Phytopathol., 49, 415, 10.1146/annurev-phyto-072910-095351 Lefeuvre, 2015, Recombination as a motor of host switches and virus emergence: geminiviruses as case studies, Curr. Opin. Virol., 10, 14, 10.1016/j.coviro.2014.12.005 Deng, 1997, Elongation properties of vaccinia virus RNA polymerase: pausing, slippage, 3′ end addition, and termination site choice, Biochemistry, 36, 15892, 10.1021/bi972037a Monci, 2002, A natural recombinant between the geminiviruses tomato yellow leaf curl Sardinia virus and tomato yellow leaf curl virus exhibits a novel pathogenic phenotype and is becoming prevalent in Spanish population, Virology, 303, 317, 10.1006/viro.2002.1633 Avedi, 2021, Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya, Virol. J., 18, 2, 10.1186/s12985-020-01466-z Briddon, 1996, Analysis of the nucleotide sequence of the treehopper-transmitted geminivirus, tomato pseudo-curly top virus, suggests a recombinant origin, Virology, 219, 387, 10.1006/viro.1996.0264 Mbanzibwa, 2011, Evolution of cassava brown streak disease associated viruses, J. Gen. Virol., 92, 974, 10.1099/vir.0.026922-0 García-Arenal, 2003, An analysis of the durability of the resistance to plant viruses, Phytopathol, 93, 941, 10.1094/PHYTO.2003.93.8.941 Zhang, 2020, The genetic structure and recombination analyses of sweet potato leaf curl virus (SPLCV) population in China, J. Plant Dis. Prot., 127, 741, 10.1007/s41348-020-00348-4 Lotrakul, 2000 Brown, 2015, Revision of Begomovirus taxonomy based on pairwise sequence comparisons, Arch. Virol., 160, 1593, 10.1007/s00705-015-2398-y Kumar, 2018, Mega X: molecular evolutionary genetics analysis across computing Platforms, Mol. Biol. Evol., 35, 1547, 10.1093/molbev/msy096 Tamura, 1993, Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees, Mol. Biol. Evol., 10, 512 Anisimova, 2003, Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites, Genetics, 164, 1229, 10.1093/genetics/164.3.1229 Librado, 2009, DnaSP v5: software for comprehensive analysis of DNA polymorphism data, Bioinformatics, 25, 1451, 10.1093/bioinformatics/btp187 Hall, 1999, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp. Ser., 41, 95 Martin, 2005, The evolutionary value of recombination is constrained by genome modularity, PLoS Genet., 1, 10.1371/journal.pgen.0010051 Padidam, 1999, Possible emergence of new geminiviruses by frequent recombination, Virology, 265, 218, 10.1006/viro.1999.0056 Smith, 1992, Analyzing the mosaic structure of genes, J. Mol. Evol., 34, 126, 10.1007/BF00182389 Posada, 2001, Evaluation of methods for detecting recombination from DNA sequences: computer simulations, Proc. Natl. Acad. Sci. U.S.A., 98, 13757, 10.1073/pnas.241370698 Boni, 2007, An exact nonparametric method for inferring mosaic structure in sequence triplets, Genetics, 176, 1035, 10.1534/genetics.106.068874 Gibbs, 2000, Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences, Bioinformatics, 16, 573, 10.1093/bioinformatics/16.7.573 Yang, 2007, PAML4: phylogenetic analysis by maximum likelihood, Mol. Biol. Evol., 24, 1586, 10.1093/molbev/msm088 Wong, 2004, Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites, Genetics, 168, 1041, 10.1534/genetics.104.031153 Yang, 2005, Bayes Empirical Bayes inference of amino acid sites under positive selection, Mol. Biol. Evol., 22, 1107, 10.1093/molbev/msi097 Wasswa, 2011, First identification of a sweet potato begomovirus (sweepovirus) in Uganda: characterization, detection and distribution, Plant Pathol., 60, 1030, 10.1111/j.1365-3059.2011.02464.x Mohammed, 2017, First Report of Sweet potato leaf curl virus infecting sweet potato in Sudan, Plant Dis., 101, 849, 10.1094/PDIS-12-16-1705-PDN Esterhuizen, 2012, Genetic identification of two sweetpotato-infecting begomoviruses in South Africa, Arch. Virol., 157, 2241, 10.1007/s00705-012-1398-4 2020 Fauquet, 2005, Revising the way we conceive and name viruses below the species level: a review of geminivirus taxonomy calls for new standardized isolate descriptors, Arch. Virol., 150, 2151, 10.1007/s00705-005-0583-0 Walker, 2020, Changes to virus taxonomy and the Statutes ratified by the International Committee on taxonomy of viruses, Arch. Virol., 165, 2737, 10.1007/s00705-020-04752-x Lefeuvre, 2007, Begomovirus 'melting pot' in the south-west Indian Ocean islands: molecular diversity and evolution through recombination, J. Gen. Virol., 88, 3458, 10.1099/vir.0.83252-0 Froissart, 2005, Recombination every day: abundant recombination in a virus during a single multi-cellular host infection, PLoS Biol., 3, e89, 10.1371/journal.pbio.0030089 Ling, 2011, Experimental host range and natural reservoir of sweet potato leaf curl virus in the United States, Crop Prot, 30, 1055, 10.1016/j.cropro.2011.03.009 García-Arenal, 2001, Variability and genetic structure of plant virus populations, Annu. Rev. Phytopathol., 39, 157, 10.1146/annurev.phyto.39.1.157 Briddon, 1990, Geminivirus coat protein gene replacement alters insect specificity, Virology, 177, 85, 10.1016/0042-6822(90)90462-Z Farooq, 2021, Molecular phylogenetics and evolutionary analysis of a highly recombinant begomovirus, Cotton leaf curl Multan virus, and associated satellites, Virus Evol, 7, 1, 10.1093/ve/veab054 Harrison, 2002, Begomovirus coat protein: Serology, variation and functions, Physiol. Mol. Plant Pathol., 60, 257, 10.1006/pmpp.2002.0404 Mondal, 2019, Genome wide molecular evolution analysis of begomoviruses reveals unique diversification pattern in coat protein gene of Old World and New World viruses, Virus Dis, 30, 74, 10.1007/s13337-019-00524-7 Duffy, 2009, Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses, J. Gen. Virol., 90, 1539, 10.1099/vir.0.009266-0 Deom, 2021, Positive selection and intrinsic disorder are associated with multifunctional C4 (AC4) proteins and geminivirus diversification, Sci. Rep., 11, 10.1038/s41598-021-90557-0 Luna, 2012, Functional analysis of gene-silencing suppressors from tomato yellow leaf curl disease viruses, Mol. Plant Microbe Interact., 25, 1294, 10.1094/MPMI-04-12-0094-R Mwaipopo, 2021, Next-generation sequencing-based detection of common bean viruses in wild plants from Tanzania and their mechanical transmission to common bean plants, Plant Dis., 105, 2541, 10.1094/PDIS-07-20-1420-RE Geetanjali, 2013, Natural association of two different betasatellites with Sweet potato leaf curl virus in wild morning glory (Ipomoea purpurea) in India, Virus Gene., 47, 184, 10.1007/s11262-013-0901-7