Comparative Genomics of Xylella fastidiosa Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems

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Uceda-Campos, Guillermo ; Feitosa-Junior, Oseias R. ; Santiago, Caio R. N. ; Pierry, Paulo M. ; Zaini, Paulo A. ; de Santana, Wesley O. ; Martins, Joaquim ; Barbosa, Deibs ; Digiampietri, Luciano A. ; Setubal, Joao C. ; da Silva, Aline M.

• Document type: Journal article
• Source: MICROORGANISMS; v. 10, n. 5, p. 20-pg., 2022-05-01.

Abstract

Xylella fastidiosa causes diseases in many plant species. Originally confined to the Americas, infecting mainly grapevine, citrus, and coffee, X. fastidiosa has spread to several plant species in Europe causing devastating diseases. Many pathogenicity and virulence factors have been identified, which enable the various X. fastidiosa strains to successfully colonize the xylem tissue and cause disease in specific plant hosts, but the mechanisms by which this happens have not been fully elucidated. Here we present thorough comparative analyses of 94 whole-genome sequences of X. fastidiosa strains from diverse plant hosts and geographic regions. Core-genome phylogeny revealed clades with members sharing mostly a geographic region rather than a host plant of origin. Phylogenetic trees for 1605 orthologous CDSs were explored for potential candidates related to host specificity using a score of mapping metrics. However, no candidate host-specificity determinants were strongly supported using this approach. We also show that X. fastidiosa accessory genome is represented by an abundant and heterogeneous mobilome, including a diversity of prophage regions. Our findings provide a better understanding of the diversity of phylogenetically close genomes and expand the knowledge of X. fastidiosa mobile genetic elements and immunity systems. (AU)

• FAPESP's process: 11/09409-3 - Microfluidic technology to study phytopathogenic bacteria adhesion mechanisms
• Grantee: Paulo Adriano Zaini
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 08/11703-4 - Identification of genes potentially involved in adaptation, evolution and virulence of Xylella fastidiosa
• Grantee: Aline Maria da Silva
• Support Opportunities: Regular Research Grants
• FAPESP's process: 21/04062-7 - Distribution, diversity, and dynamics of the antiphage immune systems in prokaryotic genomes and metagenomes.
• Grantee: Guillermo Uceda Campos
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 09/13527-1 - Genome sequencing e comparative analysis of a Xylella fastidiosa strain.
• Grantee: Paulo Marques Pierry
• Support Opportunities: Scholarships in Brazil - Master
• FAPESP's process: 11/01217-8 - Characterization of Citrus sinensis response to Xylella fastidiosa infection and phylogenomics of its different strains.
• Grantee: Joaquim Martins Junior
• Support Opportunities: Scholarships in Brazil - Post-Doctoral