Phylogenetic analysis of a Bean yellow mosaic virus isolate from Iran and selecting the phylogenetic marker by comparing the individual genes and complete genome trees of BYMV isolates

Bos, 1970, The identification of three new viruses isolated from Wisteria and Pisum in The Netherlands, and the problem of variation within the potato virus Y group, Neth. J. Plant Pathol., 76, 8, 10.1007/BF01976763 Edwardson, 2018 Mohammad, 2004, A revised medium for rapid growth and bioassay with tissue cultures, Physiol. Plantarum, 15, 257 Chen, 2001, A universal PCR primer to detect members of the Potyviridae and its use to examine the taxonomic status of several members of the family, Arch. Virol., 146, 757, 10.1007/s007050170144 Ha, 2008, Design and application of two novel degenerate primer pairs for the detection and complete genomic characterization of potyviruses, Arch. Virol., 153, 25, 10.1007/s00705-007-1053-7 Rybicki, 1992, Coat protein phylogeny and systematics of potyviruses, Potyvirus Taxonomy, 139, 10.1007/978-3-7091-6920-9_13 Wada, 2000, Comparison of pathogenicity and nucleotide sequences of 3′ terminal regions of Bean yellow mosaic virus isolates from Gladiolus, J. Gen. Plant Pathol., 66, 345, 10.1007/PL00012976 Wylie, 2008, Phylogenetic analysis of Bean yellow mosaic virus isolates from four continents: relationship between the seven groups found and their hosts and origins, Plant Dis., 92, 1596, 10.1094/PDIS-92-12-1596 Kumar, 2009, Identification and characterization of Bean yellow mosaic virus infecting Freesia, J. Plant Biochem. Biotechnol., 18, 253, 10.1007/BF03263331 Parrella, 2009, Identification of a new pathotype of Bean yellow mosaic virus (BYMV) infecting blue passion flower and some evolutionary characteristics of BYMV, Arch. Virol., 154, 1689, 10.1007/s00705-009-0485-7 Wylie, 2012, Multiple polyadenylated RNA viruses detected in pooled cultivated and wild plant samples, Arch. Virol., 157, 271, 10.1007/s00705-011-1166-x Sharma, 2015, Current status of potyvirus in India, Arch. Phytopathol. Plant Protect., 47, 906, 10.1080/03235408.2013.825963 Zakubanskiy, 2017, Molecular characterization of viruses infecting canna in Russia, Eur. J. Plant Pathol., 149, 923, 10.1007/s10658-017-1241-6 Selvaraj, 2009, Variability of Bean yellow mosaic virus isolates in the Czech Republic, Acta Virol., 53, 277, 10.4149/av_2009_04_277 Kehoe, 2014, Plant virology and next generation sequencing: experiences with a Potyvirus, PloS One, 9, 10.1371/journal.pone.0104580 Kaur, 2018, Sequence analysis of six full-length Bean yellow mosaic virus genomes reveals phylogenetic diversity in India strains suggesting subdivision of phylogenetic group-IV, Arch. Virol., 163, 235, 10.1007/s00705-017-3609-5 Herniou, 2001, Use of whole genome sequence data to infer baculovirus phylogeny, J. Virol., 75, 8117, 10.1128/JVI.75.17.8117-8126.2001 Magiorkinis, 2004, Phylogenetic analysis of the full-length SARS-CoV sequences: evidence for phylogenetic discordance in three genomic regions, J. Med. Virol., 74, 369, 10.1002/jmv.20187 Olvera, 2007, Molecular evolution of porcine circovirus type 2 genomes: phylogeny and clonality, Virology, 357, 175, 10.1016/j.virol.2006.07.047 Anderson, 2012, 3 Mengual-Chuliá, 2016, Assessing parallel gene histories in viral genomes, BMC Evol. Biol., 16, 32, 10.1186/s12862-016-0605-4 Wiens, 2005, Missing data and the design of phylogenetic analyses, J. Biomed. Inf., 39, 34, 10.1016/j.jbi.2005.04.001 Wang, 2013, Calculation of evolutionary correlation between individual genes and full-length genome: a method useful for choosing phylogenetic markers for molecular epidemiology, PloS One, 8 Planet, 2006, Tree disagreement: measuring and testing incongruence in phylogenies, J. Biomed. Inf., 39, 86, 10.1016/j.jbi.2005.08.008 Kuhner, 2015, Practical performance of tree comparison metrics, Syst. Biol., 64, 205, 10.1093/sysbio/syu085 Shimodaira, 2002, An approximately unbiased test of phylogenetic tree selection, Syst. Biol., 51, 492, 10.1080/10635150290069913 Felsenstein, 1985, Confidence limits on phylogenies: an approach using the bootstrap, Evolution, 39, 783, 10.2307/2408678 Linhart, 1988, A test whether two AIC's differ significantly, S. Afr. Stat. J., 22, 153 Kishino, 1989, Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data and the branching order in Hominoidea, J. Mol. Evol., 29, 170, 10.1007/BF02100115 Vuong, 1989, Likelihood ratio tests for model selection and non-nested hypotheses, Econometrica.J.Econom. Soc., 307, 10.2307/1912557 Martin, 2011, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet. Journal, 17, 10, 10.14806/ej.17.1.200 Sedlazeck, 2013, NextGenMap: fast and accurate read mapping in highly polymorphic genomes, Bioinformatics, 29, 2790, 10.1093/bioinformatics/btt468 Knyazev, 2018, 264242 Katoh, 2013, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol., 30, 772, 10.1093/molbev/mst010 Maddison, 2015 Martin, 2015, RDP4: detection and analysis of recombination patterns in virus genomes, Virus Evolution, 1, 10.1093/ve/vev003 Nguyen, 2015, IQ-TREE, A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol. Biol. Evol., 32, 268, 10.1093/molbev/msu300 Ronquist, 2012, MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space, Syst. Biol., 61, 539, 10.1093/sysbio/sys029 Miller, 2010, Creating the CIPRES Science Gateway for inference of large phylogenetic trees, 1 Anisimova, 2011, Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes, Syst. Biol., 60, 685, 10.1093/sysbio/syr041 Minh, 2013, Ultrafast approximation for phylogenetic bootstrap, Mol. Biol. Evol., 30, 1188, 10.1093/molbev/mst024 Vaidya, 2011, SequenceMatrix: concatenation software for the fast assembly of multi‐gene datasets with character set and codon information, Cladistics, 27, 171, 10.1111/j.1096-0031.2010.00329.x Lanfear, 2016, PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses, Mol. Biol. Evol., 34, 772 Schliep, 2011, Phangorn: phylogenetic analysis in R, Bioinformatics, 27, 592, 10.1093/bioinformatics/btq706 Bogdanowicz, 2011, Matching split distance for unrooted binary phylogenetic trees, IEEE ACM Trans. Comput. Biol. Bioinf, 9, 150, 10.1109/TCBB.2011.48 Steel, 1993, Distributions of tree comparison metrics—some new results, Syst. Biol., 42, 126 Williams, 1971, On the comparison of two classifications of the same set of elements, Taxon, 20, 519, 10.2307/1218253 Cardona, 2013, Cophenetic metrics for phylogenetic trees, after Sokal and Rohlf, BMC Bioinf., 14, 3, 10.1186/1471-2105-14-3 Robinson, 1981, Comparison of phylogenetic trees, Math. Biosci., 53, 131, 10.1016/0025-5564(81)90043-2 Kuhner, 1994, A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates, Mol. Biol. Evol., 11, 459 Tavare, 1986, Some probabilistic and statistical problems in the analysis of DNA sequences, Lect. Math. Life Sci., 17, 57 Posada, 2003, Using MODELTEST and PAUP* to select a model of nucleotide substitution, Curr. Protoc.Bioinf., 10.1002/0471250953.bi0605s00 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 Kimura, 1980, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, J. Mol. Evol., 16, 111, 10.1007/BF01731581 Yang, 1994, Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods, J. Mol. Evol., 39, 306, 10.1007/BF00160154 Gu, 1995, Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites, Mol. Biol. Evol., 12, 546 Jia, 2014, The impact of modelling rate heterogeneity among sites on phylogenetic estimates of intraspecific evolutionary rates and timescales, PloS One, 9, 10.1371/journal.pone.0095722 Atteson, 1997, The performance of neighbor-joining algorithms of phylogeny reconstruction, 101 Xia, 2003, An index of substitution saturation and its application, Mol. Phylogenet. Evol., 26, 1, 10.1016/S1055-7903(02)00326-3 Degnan, 2009, Gene tree discordance, phylogenetic inference and the multispecies coalescent, Trends Ecol. Evol., 24, 332, 10.1016/j.tree.2009.01.009 Shapiro, 2006, Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences, Mol. Biol. Evol., 23, 7, 10.1093/molbev/msj021 Kaur, 2015, Characterization of a new isolate of Bean yellow mosaic virus Group-IV associated with mosaic disease of Gladiolus in India, Plant Pathol Microbiol, 6, 10 Gibbs, 2015, The 'emergence' of turnip mosaic virus was probably a 'gene-for-quasi-gene' event, Current Opinion in Virology, 10, 20, 10.1016/j.coviro.2014.12.004 Adams, 2005, Overview and analysis of the polyprotein cleavage sites in the family. Potyviridae, Mol. Plant Pathol., 6, 471, 10.1111/j.1364-3703.2005.00296.x Tomimur, 2003, The phylogeny of Turnip mosaic virus; comparisons of 38 genomic sequences reveal a Eurasian origin and a recent ‘emergence’in east Asia, Mol. Ecol., 12, 2099, 10.1046/j.1365-294X.2003.01881.x Schaad, 1996, Analysis of the VPg-Proteinase (NIa) encoded by tobacco potyvirus: effects of mutations on subcellular transport, proteolytic processing and genome amplification, J. Virol., 70, 7039, 10.1128/jvi.70.10.7039-7048.1996