title: Positive selection is the main driving force for evolution of citrus canker-causing Xanthomonas.
abstract: Understanding the evolutionary history and potential of bacterial pathogens is critical to prevent the emergence of new infectious bacterial diseases. Xanthomonas axonopodis subsp. citri (Xac) (synonym X. citri subsp. citri), which causes citrus canker, is one of the hardest-fought plant bacterial pathogens in US history. Here, we sequenced 21 Xac strains (14 XacA, 3 XacA* and 4 XacA(w)) with different host ranges from North America and Asia and conducted comparative genomic and evolutionary analyses. Our analyses suggest that acquisition of beneficial genes and loss of detrimental genes most likely allowed XacA to infect a broader range of hosts as compared with XacA(w) and XacA*. Recombination was found to have occurred frequently on the relative ancient branches, but rarely on the young branches of the clonal genealogy. The ratio of recombination/mutation ρ/θ was 0.0790±0.0005, implying that the Xac population was clonal in structure. Positive selection has affected 14% (395 out of 2822) of core genes of the citrus canker-causing Xanthomonas. The genes affected are enriched in 'carbohydrate transport and metabolism' and 'DNA replication, recombination and repair' genes (P<0.05). Many genes related to virulence, especially genes involved in the type III secretion system and effectors, are affected by positive selection, further highlighting the contribution of positive selection to the evolution of citrus canker-causing Xanthomonas. Our results suggest that both metabolism and virulence genes provide advantages to endow XacA with higher virulence and a wider host range. Our analysis advances our understanding of the genomic basis of specialization by positive selection in bacterial evolution.
authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL, USA.
authors: Yunzeng
authors: Y
authors: Zhang
authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL, USA.
authors: Neha
authors: N
authors: Jalan
authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL, USA.
authors: Xiaofeng
authors: X
authors: Zhou
authors: Department of Plant Pathology, University of Florida, Gainesville, FL, USA.
authors: Erica
authors: E
authors: Goss
authors: Department of Plant Pathology, University of Florida, Gainesville, FL, USA.
authors: Jeffrey B
authors: JB
authors: Jones
authors: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
authors: João C
authors: JC
authors: Setubal
authors: Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, China.
authors: Xiaoling
authors: X
authors: Deng
authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL, USA.
authors: Nian
authors: N
authors: Wang
mesh_terms: D005075:Biological Evolution; D002957:Citrus / Q000382:microbiology*; D004269:DNA, Bacterial / Q000032:analysis; D016680:Genome, Bacterial; D023281:Genomics; D058507:Host Specificity / Q000235:genetics; D010935:Plant Diseases / Q000382:microbiology*; D012641:Selection, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D014774:Virulence / Q000235:genetics; D053532:Xanthomonas axonopodis / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity
chemical_list: D004269:DNA, Bacterial