Analyses of Seven New Genomes of Xanthomonas citri pv. aurantifolii Strains, Causative Agents of Citrus Canker B and C, Show a Reduced Repertoire of Pathogenicity-Related Genes

Natasha Peixoto Fonseca; José S L Patané; Alessandro M Varani; Érica Barbosa Felestrino; Washington Luiz Caneschi; Angélica Bianchini Sanchez; Isabella Ferreira Cordeiro; Camila Gracyelle de Carvalho Lemes; Renata de Almeida Barbosa Assis; Camila Carrião Machado Garcia; José Belasque Jr; Joaquim Martins Jr; Agda Paula Facincani; Rafael Marini Ferreira; Fabrício José Jaciani; Nalvo Franco de Almeida; Jesus Aparecido Ferro; Leandro Marcio Moreira; João C Setubal

doi:10.3389/fmicb.2019.02361

Analyses of Seven New Genomes of Xanthomonas citri pv. aurantifolii Strains, Causative Agents of Citrus Canker B and C, Show a Reduced Repertoire of Pathogenicity-Related Genes

Front Microbiol. 2019 Oct 11:10:2361. doi: 10.3389/fmicb.2019.02361. eCollection 2019.

Authors

Natasha Peixoto Fonseca¹, José S L Patané², Alessandro M Varani³, Érica Barbosa Felestrino¹, Washington Luiz Caneschi¹, Angélica Bianchini Sanchez¹, Isabella Ferreira Cordeiro¹, Camila Gracyelle de Carvalho Lemes¹, Renata de Almeida Barbosa Assis¹, Camila Carrião Machado Garcia¹, José Belasque Jr⁴, Joaquim Martins Jr⁵, Agda Paula Facincani³, Rafael Marini Ferreira³, Fabrício José Jaciani⁶, Nalvo Franco de Almeida⁷, Jesus Aparecido Ferro³, Leandro Marcio Moreira^{1

8}, João C Setubal⁵

Affiliations

¹ Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil.
² Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, Brazil.
³ Departamento de Tecnologia, Universidade Estadual Paulista, UNESP, Campus de Jaboticabal, Jaboticabal, Brazil.
⁴ Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, Brazil.
⁵ Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
⁶ Fundo de Defesa da Citricultura (FUNDECITRUS), São Paulo, Brazil.
⁷ Faculdade de Computação, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil.
⁸ Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil.

Abstract

Xanthomonas citri pv. aurantifolii pathotype B (XauB) and pathotype C (XauC) are the causative agents respectively of citrus canker B and C, diseases of citrus plants related to the better-known citrus canker A, caused by Xanthomonas citri pv. citri. The study of the genomes of strains of these related bacterial species has the potential to bring new understanding to the molecular basis of citrus canker as well as their evolutionary history. Up to now only one genome sequence of XauB and only one genome sequence of XauC have been available, both in draft status. Here we present two new genome sequences of XauB (both complete) and five new genome sequences of XauC (two complete). A phylogenomic analysis of these seven genome sequences along with 24 other related Xanthomonas genomes showed that there are two distinct and well-supported major clades, the XauB and XauC clade and the Xanthomonas citri pv. citri clade. An analysis of 62 Type III Secretion System effector genes showed that there are 42 effectors with variable presence/absence or pseudogene status among the 31 genomes analyzed. A comparative analysis of secretion-system and surface-structure genes showed that the XauB and XauC genomes lack several key genes in pathogenicity-related subsystems. These subsystems, the Types I and IV Secretion Systems, and the Type IV pilus, therefore emerge as important ones in helping explain the aggressiveness of the A type of citrus canker and the apparent dominance in the field of the corresponding strain over the B and C strains.

Keywords: Xanthomonas evolution; adaptation; effectors; genome sequencing; virulence.