Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses.

Autor: Patané JSL; Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.; Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil., Martins J Jr; Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil., Rangel LT; Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil., Belasque J; Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba, SP, Brazil., Digiampietri LA; Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, SP, Brazil., Facincani AP; Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil., Ferreira RM; Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil., Jaciani FJ; Departamento de Pesquisa e Desenvolvimento, Fundo de Defesa da Citricultura (Fundecitrus), Araraquara, SP, Brazil., Zhang Y; Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL, USA., Varani AM; Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil., Almeida NF; Faculdade de Computação, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil., Wang N; Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL, USA., Ferro JA; Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil., Moreira LM; Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil., Setubal JC; Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil. setubal@iq.usp.br.; Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA. setubal@iq.usp.br.
Jazyk: angličtina
Zdroj: BMC genomics [BMC Genomics] 2019 Sep 09; Vol. 20 (1), pp. 700. Date of Electronic Publication: 2019 Sep 09.
DOI: 10.1186/s12864-019-6007-4
Abstrakt: Background: Xanthomonas citri subsp. citri pathotypes cause bacterial citrus canker, being responsible for severe agricultural losses worldwide. The A pathotype has a broad host spectrum, while A* and A w are more restricted both in hosts and in geography. Two previous phylogenomic studies led to contrasting well-supported clades for sequenced genomes of these pathotypes. No extensive biogeographical or divergence dating analytic approaches have been so far applied to available genomes.
Results: Based on a larger sampling of genomes than in previous studies (including six new genomes sequenced by our group, adding to a total of 95 genomes), phylogenomic analyses resulted in different resolutions, though overall indicating that A + A W is the most likely true clade. Our results suggest the high degree of recombination at some branches and the fast diversification of lineages are probable causes for this phylogenetic blurring effect. One of the genomes analyzed, X. campestris pv. durantae, was shown to be an A* strain; this strain has been reported to infect a plant of the family Verbenaceae, though there are no reports of any X. citri subsp. citri pathotypes infecting any plant outside the Citrus genus. Host reconstruction indicated the pathotype ancestor likely had plant hosts in the family Fabaceae, implying an ancient jump to the current Rutaceae hosts. Extensive dating analyses indicated that the origin of X. citri subsp. citri occurred more recently than the main phylogenetic splits of Citrus plants, suggesting dispersion rather than host-directed vicariance as the main driver of geographic expansion. An analysis of 120 pathogenic-related genes revealed pathotype-associated patterns of presence/absence.
Conclusions: Our results provide novel insights into the evolutionary history of X. citri subsp. citri as well as a sound phylogenetic foundation for future evolutionary and genomic studies of its pathotypes.
Databáze: MEDLINE
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