TY - JOUR AU - Civerolo, E. L. PY - 1984 DA - 1984// TI - Bacterial canker disease of citrus [Xanthomonas campestris] JO - Journal of the Rio Grande Valley Horticultural Society VL - 37 ID - Civerolo1984 ER - TY - JOUR AU - Brunings, A. M. AU - Gabriel, D. W. PY - 2003 DA - 2003// TI - Xanthomonas citri: breaking the surface JO - Mol Plant Pathol VL - 4 UR - https://doi.org/10.1046/j.1364-3703.2003.00163.x DO - 10.1046/j.1364-3703.2003.00163.x ID - Brunings2003 ER - TY - JOUR AU - Graham, J. H. AU - Gottwald, T. R. AU - Cubero, J. AU - Achor, D. S. PY - 2004 DA - 2004// TI - Xanthomonas axonopodis pv. Citri: factors affecting successful eradication of citrus canker JO - Mol Plant Pathol VL - 5 UR - https://doi.org/10.1046/j.1364-3703.2004.00197.x DO - 10.1046/j.1364-3703.2004.00197.x ID - Graham2004 ER - TY - JOUR AU - Lee, H. A. PY - 1918 DA - 1918// TI - Further data on the susceptibility of rutaceous plants to citrus-canker JO - J Agric Res VL - 15 ID - Lee1918 ER - TY - JOUR AU - Bitancourt, A. A. PY - 1957 DA - 1957// TI - O Cancro Cítrico JO - Biológico VL - 23 ID - Bitancourt1957 ER - TY - STD TI - Schubert TS, Miller JW: Bacterial citrus canker. Fla Department Agric \& Consumer Services, Division of Plant Industry 1996. ID - ref6 ER - TY - JOUR AU - Raychaudhuri, S. P. AU - Verma, J. P. AU - Nariani, T. K. AU - Sen, B. PY - 1972 DA - 1972// TI - The history of plant pathology in India JO - Annu Rev Phytopathol VL - 10 UR - https://doi.org/10.1146/annurev.py.10.090172.000321 DO - 10.1146/annurev.py.10.090172.000321 ID - Raychaudhuri1972 ER - TY - STD TI - Malavolta VA Jr, Yamashiro T, Nogueira EMC, Feichtenberger E. Distribuição do tipo C de Xanthomonas campestris pv. citri no Estado de São Paulo. Summa Phytopathol. 1984;10(11). ID - ref8 ER - TY - JOUR AU - Silva, A. C. AU - Ferro, J. A. AU - Reinach, F. C. AU - Farah, C. S. AU - Furlan, L. R. AU - Quaggio, R. B. AU - Monteiro-Vitorello, C. B. AU - Sluys, M. A. AU - Almeida, N. F. AU - Alves, L. M. PY - 2002 DA - 2002// TI - Comparison of the genomes of two Xanthomonas pathogens with differing host specificities JO - Nature VL - 417 UR - https://doi.org/10.1038/417459a DO - 10.1038/417459a ID - Silva2002 ER - TY - JOUR AU - Verniere, C. AU - Hartung, J. S. AU - Pruvost, O. P. AU - Civerolo, E. L. AU - Alvarez, A. M. AU - Maestri, P. AU - Luisetti, J. PY - 1998 DA - 1998// TI - Characterization of phenotypically distinct strains of Xanthomonas axonopodis pv. Citri from Southwest Asia JO - Eur J Plant Pathol VL - 104 UR - https://doi.org/10.1023/A:1008676508688 DO - 10.1023/A:1008676508688 ID - Verniere1998 ER - TY - JOUR AU - Derso, E. AU - Vernière, C. AU - Pruvost, O. P. PY - 2009 DA - 2009// TI - First Report of Xanthomonas citri pv. citri-A* Causing Citrus Canker on Lime in Ethiopia JO - Plant Dis VL - 93 UR - https://doi.org/10.1094/PDIS-93-2-0203B DO - 10.1094/PDIS-93-2-0203B ID - Derso2009 ER - TY - JOUR AU - Sun, X. A. AU - Stall, R. E. AU - Jones, J. B. AU - Cubero, J. AU - Gottwald, T. R. AU - Graham, J. H. AU - Dixon, W. N. AU - Schubert, T. S. AU - Chaloux, P. H. AU - Stromberg, V. K. PY - 2004 DA - 2004// TI - Detection and characterization of a new strain of citrus canker bacteria from key Mexican lime and Alemow in South Florida JO - Plant Dis VL - 88 UR - https://doi.org/10.1094/PDIS.2004.88.11.1179 DO - 10.1094/PDIS.2004.88.11.1179 ID - Sun2004 ER - TY - JOUR AU - Zhang, Y. AU - Jalan, N. AU - Zhou, X. AU - Goss, E. AU - Jones, J. B. AU - Setubal, J. C. AU - Deng, X. AU - Wang, N. PY - 2015 DA - 2015// TI - Positive selection is the main driving force for evolution of citrus canker-causing Xanthomonas JO - ISME J VL - 9 UR - https://doi.org/10.1038/ismej.2015.15 DO - 10.1038/ismej.2015.15 ID - Zhang2015 ER - TY - JOUR AU - Gordon, J. L. AU - Lefeuvre, P. AU - Escalon, A. AU - Barbe, V. AU - Cruveiller, S. AU - Gagnevin, L. AU - Pruvost, O. PY - 2015 DA - 2015// TI - Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges JO - BMC Genomics VL - 16 UR - https://doi.org/10.1186/s12864-015-2310-x DO - 10.1186/s12864-015-2310-x ID - Gordon2015 ER - TY - JOUR AU - Bui Thi Ngoc, L. AU - Vernière, C. AU - Jouen, E. AU - Ah-You, N. AU - Lefeuvre, P. AU - Chiroleu, F. AU - Gagnevin, L. AU - Pruvost, O. PY - 2010 DA - 2010// TI - Amplified fragment length polymorphism and multilocus sequence analysis-based genotypic relatedness among pathogenic variants of Xanthomonas citri pv. Citri and Xanthomonas campestris pv. Bilvae JO - Int J Syst Evol Microbiol VL - 60 UR - https://doi.org/10.1099/ijs.0.009514-0 DO - 10.1099/ijs.0.009514-0 ID - Bui Thi Ngoc2010 ER - TY - JOUR AU - Pruvost, O. AU - Magne, M. AU - Boyer, K. AU - Leduc, A. AU - Tourterel, C. AU - Drevet, C. AU - Ravigne, V. AU - Gagnevin, L. AU - Guerin, F. AU - Chiroleu, F. PY - 2014 DA - 2014// TI - A MLVA genotyping scheme for global surveillance of the citrus pathogen Xanthomonas citri pv. citri suggests a worldwide geographical expansion of a single genetic lineage JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0098129 DO - 10.1371/journal.pone.0098129 ID - Pruvost2014 ER - TY - JOUR AU - Nixon, K. C. AU - Carpenter, J. M. PY - 1993 DA - 1993// TI - On Outgroups JO - Cladistics VL - 9 UR - https://doi.org/10.1111/j.1096-0031.1993.tb00234.x DO - 10.1111/j.1096-0031.1993.tb00234.x ID - Nixon1993 ER - TY - JOUR AU - Smith, A. B. PY - 1994 DA - 1994// TI - Rooting molecular trees: problems and strategies JO - Biol J Linn Soc VL - 51 UR - https://doi.org/10.1111/j.1095-8312.1994.tb00962.x DO - 10.1111/j.1095-8312.1994.tb00962.x ID - Smith1994 ER - TY - JOUR AU - Lyons-Weiler, J. AU - Hoelzer, G. A. AU - Tausch, R. J. PY - 1998 DA - 1998// TI - Optimal outgroup analysis JO - Biol J Linn Soc VL - 64 UR - https://doi.org/10.1111/j.1095-8312.1998.tb00346.x DO - 10.1111/j.1095-8312.1998.tb00346.x ID - Lyons-Weiler1998 ER - TY - JOUR AU - Bergsten, J. PY - 2005 DA - 2005// TI - A review of long-branch attraction JO - Cladistics VL - 21 UR - https://doi.org/10.1111/j.1096-0031.2005.00059.x DO - 10.1111/j.1096-0031.2005.00059.x ID - Bergsten2005 ER - TY - JOUR AU - Bansal, K. AU - Midha, S. AU - Kumar, S. AU - Patil, P. B. PY - 2017 DA - 2017// TI - Ecological and evolutionary insights into Xanthomonas citri pathovar diversity JO - Appl Env Microbiol VL - 83 UR - https://doi.org/10.1128/AEM.02993-16 DO - 10.1128/AEM.02993-16 ID - Bansal2017 ER - TY - JOUR AU - Parkinson, N. AU - Cowie, C. AU - Heeney, J. AU - Stead, D. PY - 2009 DA - 2009// TI - Phylogenetic structure of Xanthomonas determined by comparison of gyrB sequences JO - Int J Syst Evol Microbiol VL - 59 UR - https://doi.org/10.1099/ijs.0.65825-0 DO - 10.1099/ijs.0.65825-0 ID - Parkinson2009 ER - TY - JOUR AU - Darrasse, A. AU - Bolot, S. AU - Serres-Giardi, L. AU - Charbit, E. AU - Boureau, T. AU - Fisher-Le Saux, M. AU - Briand, M. AU - Arlat, M. AU - Gagnevin, L. AU - Koebnik, R. PY - 2013 DA - 2013// TI - High-quality draft genome sequences of Xanthomonas axonopodis pv. Glycines strains CFBP 2526 and CFBP 7119 JO - Genome Announc VL - 1 UR - https://doi.org/10.1128/genomeA.01036-13 DO - 10.1128/genomeA.01036-13 ID - Darrasse2013 ER - TY - JOUR AU - Cunnac, S. AU - Bolot, S. AU - Serna, N. F. AU - Ortiz, E. AU - Szurek, B. AU - Noël, L. D. AU - Arlat, M. AU - Jacques, M. -. A. AU - Gagnevin, L. AU - Carrere, S. PY - 2013 DA - 2013// TI - High-quality draft genome sequences of two Xanthomonas citri pv. Malvacearum strains JO - Genome Announc VL - 1 UR - https://doi.org/10.1128/genomeA.00674-13 DO - 10.1128/genomeA.00674-13 ID - Cunnac2013 ER - TY - CHAP AU - Midha, S. AU - Ranjan, M. AU - Sharma, V. AU - Pinnaka, A. K. AU - Patil, P. B. PY - 2012 DA - 2012// TI - Genome sequence of Xanthomonas citri pv. mangiferaeindicae strain LMG 941 BT - Am Soc Microbiol ID - Midha2012 ER - TY - STD TI - Gochez AM, Huguet-Tapia JC, Minsavage GV, Shantaraj D, Jalan N, Strauß A, Lahaye T, Wang N, Canteros BI, Jones JB: Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains. BMC genomics 2018, 19(1):16. ID - ref26 ER - TY - JOUR AU - Jalan, N. AU - Kumar, D. AU - Yu, F. AU - Jones, J. B. AU - Graham, J. H. AU - Wang, N. PY - 2013 DA - 2013// TI - Complete genome sequence of Xanthomonas citri subsp. citri strain AW12879, a restricted-host-range citrus canker-causing bacterium JO - Genome Announc VL - 1 UR - https://doi.org/10.1128/genomeA.00235-13 DO - 10.1128/genomeA.00235-13 ID - Jalan2013 ER - TY - JOUR AU - Richard, D. AU - Tribot, N. AU - Boyer, C. AU - Terville, M. AU - Boyer, K. AU - Javegny, S. AU - Roux-Cuvelier, M. AU - Pruvost, O. AU - Moreau, A. AU - Chabirand, A. AU - Vernière, C. PY - 2017 DA - 2017// TI - First Report of Copper-resistant Xanthomonas citri pv. citri Pathotype A Causing Asiatic Citrus Canker in Réunion, France JO - Plant Disease VL - 101 UR - https://doi.org/10.1094/PDIS-09-16-1387-PDN DO - 10.1094/PDIS-09-16-1387-PDN ID - Richard2017 ER - TY - JOUR AU - Jalali, A. AU - Alavi, S. M. AU - Sangtarash, M. H. PY - 2017 DA - 2017// TI - Comparative genomic analysis of wide and narrow host range strains of Xanthomonas citri subsp. citri, showing differences in the genetic content of their pathogenicity and virulence factors JO - Australas Plant Pathol VL - 46 UR - https://doi.org/10.1007/s13313-016-0462-z DO - 10.1007/s13313-016-0462-z ID - Jalali2017 ER - TY - STD TI - Jalali A, Alavi SM, Sangtarash MH: Genomic characterization and phylogenetic analysis of a narrow host-range Iranian strain of Xanthmonas citri sub. citri, NIGEB-88. 2018. ID - ref30 ER - TY - JOUR AU - Bodnar, A. M. AU - Santillana, G. AU - Mavrodieva, V. AU - Liu, Z. AU - Nakhla, M. AU - Gabriel, D. W. PY - 2017 DA - 2017// TI - Complete genome sequences of three Xanthomonas citri strains from Texas JO - Genome Announc VL - 5 ID - Bodnar2017 ER - TY - JOUR AU - Mhedbi-Hajri, N. AU - Hajri, A. AU - Boureau, T. AU - Darrasse, A. AU - Durand, K. AU - Brin, C. AU - Fischer-Le Saux, M. AU - Manceau, C. AU - Poussier, S. AU - Pruvost, O. P. PY - 2013 DA - 2013// TI - Evolutionary history of the plant pathogenic bacterium Xanthomonas axonopodis JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0058474 DO - 10.1371/journal.pone.0058474 ID - Mhedbi-Hajri2013 ER - TY - JOUR AU - Laia, M. L. AU - Moreira, L. M. AU - Dezajacomo, J. AU - Brigati, J. B. AU - Ferreira, C. B. AU - Ferro, M. I. AU - Silva, A. C. AU - Ferro, J. A. AU - Oliveira, J. C. PY - 2009 DA - 2009// TI - New genes of Xanthomonas citri subsp citri involved in pathogenesis and adaptation revealed by a transposon-based mutant library JO - BMC Microbiol VL - 9 UR - https://doi.org/10.1186/1471-2180-9-12 DO - 10.1186/1471-2180-9-12 ID - Laia2009 ER - TY - JOUR AU - Li, J. AU - Wang, N. PY - 2012 DA - 2012// TI - The gpsX gene encoding a glycosyltransferase is important for polysaccharide production and required for full virulence in Xanthomonas citri subsp. citri JO - BMC Microbiol VL - 12 UR - https://doi.org/10.1186/1471-2180-12-31 DO - 10.1186/1471-2180-12-31 ID - Li2012 ER - TY - JOUR AU - Yan, Q. AU - Wang, N. PY - 2012 DA - 2012// TI - High-throughput screening and analysis of genes of Xanthomonas citri subsp. citri involved in citrus canker symptom development JO - Mol Plant-Microbe Interact VL - 25 UR - https://doi.org/10.1094/MPMI-05-11-0121 DO - 10.1094/MPMI-05-11-0121 ID - Yan2012 ER - TY - JOUR AU - Zhou, X. AU - Hu, X. AU - Li, J. AU - Wang, N. PY - 2015 DA - 2015// TI - A novel periplasmic protein, VrpA, contributes to efficient protein secretion by the type III secretion system in Xanthomonas spp JO - Mol Plant-Microbe Interact VL - 28 UR - https://doi.org/10.1094/MPMI-10-14-0309-R DO - 10.1094/MPMI-10-14-0309-R ID - Zhou2015 ER - TY - JOUR AU - Ferreira, C. B. AU - Moreira, L. M. AU - Brigati, J. B. AU - Lima, L. L. D. AU - Ferro, J. A. AU - Ferro, M. I. T. AU - Oliveira, J. C. F. PY - 2017 DA - 2017// TI - Identification of new genes related to virulence of Xanthomonas axonopodis pv. Citri during citrus host interactions JO - Advances in Microbiology VL - 7 UR - https://doi.org/10.4236/aim.2017.71003 DO - 10.4236/aim.2017.71003 ID - Ferreira2017 ER - TY - STD TI - Vieira FCF, Gonçalves AM, Mendoza EFR, Ferreira RM, Costa MLM, Balbuena TS, Sebinelli HG, Ciancaglini P, Pizauro JM Jr, Ferro JA. A Xanthomonas citri subsp citri hypothetical protein related to virulence contains a non-functional HD domain and is implicated in flagellar motility. Genet Mol Res. 2017:16(3). ID - ref38 ER - TY - JOUR AU - Larsson, A. PY - 2014 DA - 2014// TI - AliView: a fast and lightweight alignment viewer and editor for large datasets JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu531 DO - 10.1093/bioinformatics/btu531 ID - Larsson2014 ER - TY - JOUR AU - Darling, A. E. AU - Mau, B. AU - Perna, N. T. PY - 2010 DA - 2010// TI - progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0011147 DO - 10.1371/journal.pone.0011147 ID - Darling2010 ER - TY - JOUR AU - Müller, K. PY - 2005 DA - 2005// TI - SeqState - primer design and sequence statistics for phylogenetic DNA data sets JO - Appl Bioinform VL - 4 UR - https://doi.org/10.2165/00822942-200504010-00008 DO - 10.2165/00822942-200504010-00008 ID - Müller2005 ER - TY - JOUR AU - Nguyen, L. T. AU - Schmidt, H. A. AU - Haeseler, A. AU - Minh, B. Q. PY - 2015 DA - 2015// TI - IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies JO - Mol Biol Evol VL - 32 UR - https://doi.org/10.1093/molbev/msu300 DO - 10.1093/molbev/msu300 ID - Nguyen2015 ER - TY - JOUR AU - Jombart, T. AU - Devillard, S. AU - Balloux, F. PY - 2010 DA - 2010// TI - Discriminant analysis of principal components: a new method for the analysis of genetically structured populations JO - BMC Genet VL - 11 UR - https://doi.org/10.1186/1471-2156-11-94 DO - 10.1186/1471-2156-11-94 ID - Jombart2010 ER - TY - JOUR AU - Didelot, X. AU - Wilson, D. J. PY - 2015 DA - 2015// TI - ClonalFrameML: efficient inference of recombination in whole bacterial genomes JO - PLoS Comput Biol VL - 11 UR - https://doi.org/10.1371/journal.pcbi.1004041 DO - 10.1371/journal.pcbi.1004041 ID - Didelot2015 ER - TY - JOUR AU - Ronquist, F. AU - Huelsenbeck, J. P. PY - 2003 DA - 2003// TI - MrBayes 3: Bayesian phylogenetic inference under mixed models JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg180 DO - 10.1093/bioinformatics/btg180 ID - Ronquist2003 ER - TY - JOUR AU - Revell, L. J. PY - 2012 DA - 2012// TI - Phytools: an R package for phylogenetic comparative biology (and other things) JO - Methods Ecol Evol VL - 3 UR - https://doi.org/10.1111/j.2041-210X.2011.00169.x DO - 10.1111/j.2041-210X.2011.00169.x ID - Revell2012 ER - TY - STD TI - Volz EM, SDW F. Scalable relaxed clock phylogenetic dating. Virus Evol. 2017:3(2). ID - ref47 ER - TY - JOUR AU - Rambaut, A. AU - Lam, T. T. AU - Max Carvalho, L. AU - Pybus, O. G. PY - 2016 DA - 2016// TI - Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) JO - Virus Evol VL - 2 UR - https://doi.org/10.1093/ve/vew007 DO - 10.1093/ve/vew007 ID - Rambaut2016 ER - TY - JOUR AU - Suchard, M. A. AU - Lemey, P. AU - Baele, G. AU - Ayres, D. L. AU - Drummond, A. J. AU - Rambaut, A. PY - 2018 DA - 2018// TI - Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 JO - Virus Evol VL - 4 UR - https://doi.org/10.1093/ve/vey016 DO - 10.1093/ve/vey016 ID - Suchard2018 ER - TY - STD TI - Raftery AE, Newton MA, Satagopan JM, Krivitsky PN: Estimating the integrated likelihood via posterior simulation using the harmonic mean identity. In: Bayesian Statistics 8. Edited by Bernardo JM, Bayarri MJ, Berger JO, Dawid AP, Heckerman D, Smith AFM, West M: Oxford University Press; 2007: 1–45. ID - ref50 ER - TY - JOUR AU - Corander, J. AU - Waldmann, P. AU - Marttinen, P. AU - Sillanpaa, M. J. PY - 2004 DA - 2004// TI - BAPS 2: enhanced possibilities for the analysis of genetic population structure JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth250 DO - 10.1093/bioinformatics/bth250 ID - Corander2004 ER - TY - JOUR AU - Vos, M. AU - Didelot, X. PY - 2009 DA - 2009// TI - A comparison of homologous recombination rates in bacteria and archaea JO - ISME J VL - 3 UR - https://doi.org/10.1038/ismej.2008.93 DO - 10.1038/ismej.2008.93 ID - Vos2009 ER - TY - JOUR AU - Goss, E. M. AU - Kreitman, M. AU - Bergelson, J. PY - 2005 DA - 2005// TI - Genetic diversity, recombination and cryptic clades in Pseudomonas viridiflava infecting natural populations of Arabidopsis thaliana JO - Genetics VL - 169 UR - https://doi.org/10.1534/genetics.104.031351 DO - 10.1534/genetics.104.031351 ID - Goss2005 ER - TY - JOUR AU - Sarkar, S. F. AU - Guttman, D. S. PY - 2004 DA - 2004// TI - Evolution of the core genome of pseudomonas syringae, a highly clonal, endemic plant pathogen JO - Appl Environ Microbiol VL - 70 UR - https://doi.org/10.1128/AEM.70.4.1999-2012.2004 DO - 10.1128/AEM.70.4.1999-2012.2004 ID - Sarkar2004 ER - TY - JOUR AU - Huang, C. L. AU - Pu, P. H. AU - Huang, H. J. AU - Sung, H. M. AU - Liaw, H. J. AU - Chen, Y. M. AU - Chen, C. M. AU - Huang, M. B. AU - Osada, N. AU - Gojobori, T. PY - 2015 DA - 2015// TI - Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts JO - BMC Genomics VL - 16 UR - https://doi.org/10.1186/s12864-015-1369-8 DO - 10.1186/s12864-015-1369-8 ID - Huang2015 ER - TY - JOUR AU - Srinivasan, M. C. AU - Patel, M. K. PY - 1957 DA - 1957// TI - Two new Phytopathogenic bacteria on verbenacious hosts JO - Curr Sci VL - 26 ID - Srinivasan1957 ER - TY - JOUR AU - Schenk, J. J. AU - Hufford, L. PY - 2010 DA - 2010// TI - Effects of substitution models on divergence time estimates: simulations and an empirical study of model uncertainty using Cornales JO - Syst Bot VL - 35 UR - https://doi.org/10.1600/036364410792495809 DO - 10.1600/036364410792495809 ID - Schenk2010 ER - TY - BOOK AU - Burnham, K. P. AU - Anderson, D. R. PY - 2002 DA - 2002// TI - Mode selection and inference: a practical information-theoretical approach PB - Springer-Verlag CY - New York ID - Burnham2002 ER - TY - STD TI - Duchene S, Holt KE, Weill FX, Le Hello S, Hawkey J, Edwards DJ, Fourment M, Holmes EC. Genome-scale rates of evolutionary change in bacteria. Microb Genomics. 2016;2(11). ID - ref59 ER - TY - JOUR AU - Drummond, A. J. AU - Rambaut, A. AU - Shapiro, B. AU - Pybus, O. G. PY - 2005 DA - 2005// TI - Bayesian coalescent inference of past population dynamics from molecular sequences JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi103 DO - 10.1093/molbev/msi103 ID - Drummond2005 ER - TY - JOUR AU - Ritchie, A. M. AU - Lo, N. AU - Ho, S. Y. W. PY - 2016 DA - 2016// TI - Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker JO - Org Divers Evol VL - 16 UR - https://doi.org/10.1007/s13127-016-0275-5 DO - 10.1007/s13127-016-0275-5 ID - Ritchie2016 ER - TY - JOUR AU - Drummond, A. l. e. x. e. i. J. AU - Rambaut, A. n. d. r. e. w. PY - 2007 DA - 2007// TI - BEAST: Bayesian evolutionary analysis by sampling trees JO - BMC Evolutionary Biology VL - 7 UR - https://doi.org/10.1186/1471-2148-7-214 DO - 10.1186/1471-2148-7-214 ID - Drummond2007 ER - TY - JOUR AU - Rademaker, J. L. AU - Hoste, B. AU - Louws, F. J. AU - Kersters, K. AU - Swings, J. AU - Vauterin, L. AU - Vauterin, P. AU - Bruijn, F. J. PY - 2000 DA - 2000// TI - Comparison of AFLP and rep-PCR genomic fingerprinting with DNA-DNA homology studies: Xanthomonas as a model system JO - Int J Syst Evol Microbiol VL - 50 UR - https://doi.org/10.1099/00207713-50-2-665 DO - 10.1099/00207713-50-2-665 ID - Rademaker2000 ER - TY - JOUR AU - Lapierre, M. AU - Blin, C. AU - Lambert, A. AU - Achaz, G. AU - Rocha, E. P. PY - 2016 DA - 2016// TI - The impact of selection, gene conversion, and biased sampling on the assessment of microbial demography JO - Mol Biol Evol VL - 33 UR - https://doi.org/10.1093/molbev/msw048 DO - 10.1093/molbev/msw048 ID - Lapierre2016 ER - TY - JOUR AU - Clark, P. U. AU - Dyke, A. S. AU - Shakun, J. D. AU - Carlson, A. E. AU - Clark, J. AU - Wohlfarth, B. AU - Mitrovica, J. X. AU - Hostetler, S. W. AU - McCabe, A. M. PY - 2009 DA - 2009// TI - The last glacial maximum JO - Science VL - 325 UR - https://doi.org/10.1126/science.1172873 DO - 10.1126/science.1172873 ID - Clark2009 ER - TY - CHAP AU - Fuller, D. Q. AU - Castillo, C. AU - Kingwell-Banham, E. AU - Qin, L. AU - Weisskopf, A. ED - Fiorentino, G. ED - Zech-Matterne, V. PY - 2018 DA - 2018// TI - Charred pummelo peel, historical linguistics and other tree crops: Approaches to framing the historical context of early Citrus cultivation in East, South and Southeast Asia BT - AGRUMED: Archaeology and history of citrus fruit in the mediterranean PB - Publications du Centre Jean Bérard CY - Naples ID - Fuller2018 ER - TY - JOUR AU - Carbonell-Caballero, J. AU - Alonso, R. AU - Ibanez, V. AU - Terol, J. AU - Talon, M. AU - Dopazo, J. PY - 2015 DA - 2015// TI - A phylogenetic analysis of 34 chloroplast genomes elucidates the relationships between wild and domestic species within the genus citrus JO - Mol Biol Evol VL - 32 UR - https://doi.org/10.1093/molbev/msv082 DO - 10.1093/molbev/msv082 ID - Carbonell-Caballero2015 ER - TY - JOUR AU - Wu, G. A. AU - Terol, J. AU - Ibanez, V. AU - Lopez-Garcia, A. AU - Perez-Roman, E. AU - Borreda, C. AU - Domingo, C. AU - Tadeo, F. R. AU - Carbonell-Caballero, J. AU - Alonso, R. PY - 2018 DA - 2018// TI - Genomics of the origin and evolution of citrus JO - Nature VL - 554 UR - https://doi.org/10.1038/nature25447 DO - 10.1038/nature25447 ID - Wu2018 ER - TY - JOUR AU - Bock, C. H. AU - Cook, A. Z. AU - Parker, P. E. AU - Gottwald, T. R. AU - Graham, J. H. PY - 2012 DA - 2012// TI - Short-distance dispersal of splashed bacteria of Xanthomonas citri subsp. citri from canker-infected grapefruit tree canopies in turbulent wind JO - Plant Pathol VL - 61 UR - https://doi.org/10.1111/j.1365-3059.2011.02588.x DO - 10.1111/j.1365-3059.2011.02588.x ID - Bock2012 ER - TY - JOUR AU - Barak, J. D. AU - Vancheva, T. AU - Lefeuvre, P. AU - Jones, J. B. AU - Timilsina, S. AU - Minsavage, G. V. AU - Vallad, G. E. AU - Koebnik, R. PY - 2016 DA - 2016// TI - Whole-genome sequences of Xanthomonas euvesicatoria strains clarify taxonomy and reveal a stepwise erosion of type 3 effectors JO - Front Plant Sci VL - 7 UR - https://doi.org/10.3389/fpls.2016.01805 DO - 10.3389/fpls.2016.01805 ID - Barak2016 ER - TY - JOUR AU - Furutani, A. AU - Takaoka, M. AU - Sanada, H. AU - Noguchi, Y. AU - Oku, T. AU - Tsuno, K. AU - Ochiai, H. AU - Tsuge, S. PY - 2009 DA - 2009// TI - Identification of novel type III secretion effectors in Xanthomonas oryzae pv. Oryzae JO - Mol Plant-Microbe Interact VL - 22 UR - https://doi.org/10.1094/MPMI-22-1-0096 DO - 10.1094/MPMI-22-1-0096 ID - Furutani2009 ER - TY - JOUR AU - Rybak, M. AU - Minsavage, G. V. AU - Stall, R. E. AU - Jones, J. B. PY - 2009 DA - 2009// TI - Identification of Xanthomonas citri ssp. citri host specificity genes in a heterologous expression host JO - Mol Plant Pathol VL - 10 UR - https://doi.org/10.1111/j.1364-3703.2008.00528.x DO - 10.1111/j.1364-3703.2008.00528.x ID - Rybak2009 ER - TY - JOUR AU - Bankevich, A. AU - Nurk, S. AU - Antipov, D. AU - Gurevich, A. A. AU - Dvorkin, M. AU - Kulikov, A. S. AU - Lesin, V. M. AU - Nikolenko, S. I. AU - Pham, S. AU - Prjibelski, A. D. PY - 2012 DA - 2012// TI - SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing JO - J Comput Biol VL - 19 UR - https://doi.org/10.1089/cmb.2012.0021 DO - 10.1089/cmb.2012.0021 ID - Bankevich2012 ER - TY - JOUR AU - Antipov, D. AU - Hartwick, N. AU - Shen, M. AU - Raiko, M. AU - Lapidus, A. AU - Pevzner, P. A. PY - 2016 DA - 2016// TI - plasmidSPAdes: assembling plasmids from whole genome sequencing data JO - Bioinformatics VL - 32 ID - Antipov2016 ER - TY - JOUR AU - Tanizawa, Y. AU - Fujisawa, T. AU - Nakamura, Y. PY - 2018 DA - 2018// TI - DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication JO - Bioinformatics VL - 34 UR - https://doi.org/10.1093/bioinformatics/btx713 DO - 10.1093/bioinformatics/btx713 ID - Tanizawa2018 ER - TY - JOUR AU - Tatusova, T. AU - DiCuccio, M. AU - Badretdin, A. AU - Chetvernin, V. AU - Nawrocki, E. P. AU - Zaslavsky, L. AU - Lomsadze, A. AU - Pruitt, K. D. AU - Borodovsky, M. AU - Ostell, J. PY - 2016 DA - 2016// TI - NCBI prokaryotic genome annotation pipeline JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkw569 DO - 10.1093/nar/gkw569 ID - Tatusova2016 ER - TY - JOUR AU - Contreras-Moreira, B. AU - Vinuesa, P. PY - 2013 DA - 2013// TI - GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis JO - Appl Environ Microbiol VL - 79 UR - https://doi.org/10.1128/AEM.02411-13 DO - 10.1128/AEM.02411-13 ID - Contreras-Moreira2013 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schaffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - JOUR AU - Li, L. AU - Stoeckert, C. J. AU - Roos, D. S. PY - 2003 DA - 2003// TI - OrthoMCL: identification of ortholog groups for eukaryotic genomes JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1224503 DO - 10.1101/gr.1224503 ID - Li2003 ER - TY - JOUR AU - Comas, I. ñ. a. k. i. AU - Moya, A. n. d. r. é. s. AU - González-Candelas, F. e. r. n. a. n. d. o. PY - 2007 DA - 2007// TI - Phylogenetic signal and functional categories in Proteobacteria genomes JO - BMC Evolutionary Biology VL - 7 UR - https://doi.org/10.1186/1471-2148-7-S1-S7 DO - 10.1186/1471-2148-7-S1-S7 ID - Comas2007 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with high accuracy and high throughput JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - JOUR AU - Kück, P. AU - Meusemann, K. PY - 2010 DA - 2010// TI - FASconCAT: convenient handling of data matrices JO - Mol Phylogenet Evol VL - 56 UR - https://doi.org/10.1016/j.ympev.2010.04.024 DO - 10.1016/j.ympev.2010.04.024 ID - Kück2010 ER - TY - JOUR AU - Felsenstein, J. PY - 1984 DA - 1984// TI - Distance methods for inferring phylogenies: a justification JO - Evolution VL - 38 UR - https://doi.org/10.1111/j.1558-5646.1984.tb00255.x DO - 10.1111/j.1558-5646.1984.tb00255.x ID - Felsenstein1984 ER - TY - JOUR AU - Xia, X. AU - Xie, Z. PY - 2001 DA - 2001// TI - DAMBE: software package for data analysis in molecular biology and evolution JO - J Hered VL - 92 UR - https://doi.org/10.1093/jhered/92.4.371 DO - 10.1093/jhered/92.4.371 ID - Xia2001 ER - TY - JOUR AU - Philippe, H. AU - Brinkmann, H. AU - Lavrov, D. V. AU - Littlewood, D. T. AU - Manuel, M. AU - Worheide, G. AU - Baurain, D. PY - 2011 DA - 2011// TI - Resolving difficult phylogenetic questions: why more sequences are not enough JO - PLoS Biol VL - 9 UR - https://doi.org/10.1371/journal.pbio.1000602 DO - 10.1371/journal.pbio.1000602 ID - Philippe2011 ER - TY - JOUR AU - Hoang, D. T. AU - Chernomor, O. AU - Haeseler, A. AU - Minh, B. Q. AU - Vinh, L. S. PY - 2017 DA - 2017// TI - UFBoot2: improving the ultrafast bootstrap approximation JO - Mol Biol Evol VL - 35 UR - https://doi.org/10.1093/molbev/msx281 DO - 10.1093/molbev/msx281 ID - Hoang2017 ER - TY - JOUR AU - Hoang, D. T. AU - Vinh, L. S. AU - Flouri, T. AU - Stamatakis, A. AU - Haeseler, A. AU - Minh, B. Q. PY - 2018 DA - 2018// TI - MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation JO - BMC Evol Biol VL - 18 UR - https://doi.org/10.1186/s12862-018-1131-3 DO - 10.1186/s12862-018-1131-3 ID - Hoang2018 ER - TY - JOUR AU - Huson, D. H. AU - Bryant, D. PY - 2006 DA - 2006// TI - Application of phylogenetic networks in evolutionary studies JO - Mol Biol Evol VL - 23 UR - https://doi.org/10.1093/molbev/msj030 DO - 10.1093/molbev/msj030 ID - Huson2006 ER - TY - JOUR AU - Davidson, R. u. t. h. AU - Vachaspati, P. r. a. n. j. a. l. AU - Mirarab, S. i. a. v. a. s. h. AU - Warnow, T. a. n. d. y. PY - 2015 DA - 2015// TI - Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer JO - BMC Genomics VL - 16 UR - https://doi.org/10.1186/1471-2164-16-S10-S1 DO - 10.1186/1471-2164-16-S10-S1 ID - Davidson2015 ER - TY - JOUR AU - Zhang, C. AU - Rabiee, M. AU - Sayyari, E. AU - Mirarab, S. PY - 2018 DA - 2018// TI - ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees JO - BMC Bioinformatics VL - 19 UR - https://doi.org/10.1186/s12859-018-2129-y DO - 10.1186/s12859-018-2129-y ID - Zhang2018 ER - TY - JOUR AU - Gupta, R. S. PY - 2001 DA - 2001// TI - The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins JO - Int Microbiol VL - 4 UR - https://doi.org/10.1007/s10123-001-0037-9 DO - 10.1007/s10123-001-0037-9 ID - Gupta2001 ER - TY - JOUR AU - Lewis, P. O. PY - 2001 DA - 2001// TI - A likelihood approach to estimating phylogeny from discrete morphological character data JO - Syst Biol VL - 50 UR - https://doi.org/10.1080/106351501753462876 DO - 10.1080/106351501753462876 ID - Lewis2001 ER - TY - JOUR AU - Tria, F. D. K. AU - Landan, G. AU - Dagan, T. PY - 2017 DA - 2017// TI - Phylogenetic rooting using minimal ancestor deviation JO - Nature Ecol Evol VL - 1 UR - https://doi.org/10.1038/s41559-017-0193 DO - 10.1038/s41559-017-0193 ID - Tria2017 ER - TY - JOUR AU - Jombart, T. PY - 2008 DA - 2008// TI - Adegenet: a R package for the multivariate analysis of genetic markers JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn129 DO - 10.1093/bioinformatics/btn129 ID - Jombart2008 ER - TY - JOUR AU - Bruen, T. C. AU - Philippe, H. AU - Bryant, D. PY - 2006 DA - 2006// TI - A simple and robust statistical test for detecting the presence of recombination JO - Genetics VL - 172 UR - https://doi.org/10.1534/genetics.105.048975 DO - 10.1534/genetics.105.048975 ID - Bruen2006 ER - TY - STD TI - Bouckaert R, Vaughan TG, Barido-Sottani J, Duchene S, Fourment M, Gavryushkina A, Heled J, Jones G, Kuhnert D, De Maio N et al: BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. Plos Comput Biol 2019, 15(4):e1006650. ID - ref96 ER - TY - JOUR AU - Hasse, C. H. PY - 1915 DA - 1915// TI - Pseudomonas citri, the cause of citrus canker - a preliminary report JO - J Agric Res VL - 4 ID - Hasse1915 ER - TY - JOUR AU - Drake, J. W. PY - 1991 DA - 1991// TI - Spontaneous mutation JO - Annu Rev Genet VL - 25 UR - https://doi.org/10.1146/annurev.ge.25.120191.001013 DO - 10.1146/annurev.ge.25.120191.001013 ID - Drake1991 ER - TY - JOUR AU - Ochman, H. AU - Elwyn, S. AU - Moran, N. A. PY - 1999 DA - 1999// TI - Calibrating bacterial evolution JO - Proc Natl Acad Sci U S A VL - 96 UR - https://doi.org/10.1073/pnas.96.22.12638 DO - 10.1073/pnas.96.22.12638 ID - Ochman1999 ER - TY - JOUR AU - Kuo, C. H. AU - Ochman, H. PY - 2009 DA - 2009// TI - Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria JO - Biol Direct VL - 4 UR - https://doi.org/10.1186/1745-6150-4-35 DO - 10.1186/1745-6150-4-35 ID - Kuo2009 ER - TY - STD TI - Gibson B, Wilson DJ, Feil E, Eyre-Walker A. The distribution of bacterial doubling times in the wild. Proc Biol Sci. 2018:285(1880). ID - ref101 ER - TY - JOUR AU - Xie, W. AU - Lewis, P. O. AU - Fan, Y. AU - Kuo, L. AU - Chen, M. H. PY - 2011 DA - 2011// TI - Improving marginal likelihood estimation for Bayesian phylogenetic model selection JO - Syst Biol VL - 60 UR - https://doi.org/10.1093/sysbio/syq085 DO - 10.1093/sysbio/syq085 ID - Xie2011 ER - TY - JOUR AU - Baele, G. AU - Lemey, P. AU - Bedford, T. AU - Rambaut, A. AU - Suchard, M. A. AU - Alekseyenko, A. V. PY - 2012 DA - 2012// TI - Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty JO - Mol Biol Evol VL - 29 UR - https://doi.org/10.1093/molbev/mss084 DO - 10.1093/molbev/mss084 ID - Baele2012 ER - TY - JOUR AU - Baele, G. AU - Li, W. L. AU - Drummond, A. J. AU - Suchard, M. A. AU - Lemey, P. PY - 2013 DA - 2013// TI - Accurate model selection of relaxed molecular clocks in bayesian phylogenetics JO - Mol Biol Evol VL - 30 UR - https://doi.org/10.1093/molbev/mss243 DO - 10.1093/molbev/mss243 ID - Baele2013 ER - TY - STD TI - Zarza E, O'Hara RB, Kolb A, Pfenninger M. A prior-based approach for hypothesis comparison and its utility to discern among temporal scenarios of divergence. bioRxiv. 2018;302539. ID - ref105 ER - TY - JOUR AU - Rambaut, A. AU - Drummond, A. J. AU - Xie, D. AU - Baele, G. AU - Suchard, M. A. PY - 2018 DA - 2018// TI - Posterior summarization in Bayesian Phylogenetics using tracer 1.7 JO - Syst Biol VL - 67 UR - https://doi.org/10.1093/sysbio/syy032 DO - 10.1093/sysbio/syy032 ID - Rambaut2018 ER - TY - JOUR AU - Yu, Y. AU - Harris, A. J. AU - Blair, C. AU - He, X. PY - 2015 DA - 2015// TI - RASP (reconstruct ancestral state in phylogenies): a tool for historical biogeography JO - Mol Phylogenet Evol VL - 87 UR - https://doi.org/10.1016/j.ympev.2015.03.008 DO - 10.1016/j.ympev.2015.03.008 ID - Yu2015 ER - TY - JOUR AU - Camacho, C. AU - Coulouris, G. AU - Avagyan, V. AU - Ma, N. AU - Papadopoulos, J. AU - Bealer, K. AU - Madden, T. L. PY - 2009 DA - 2009// TI - BLAST+: architecture and applications JO - BMC Bioinformatics VL - 10 UR - https://doi.org/10.1186/1471-2105-10-421 DO - 10.1186/1471-2105-10-421 ID - Camacho2009 ER -