Comparative Genomics of <i>Xylella fastidiosa</i> Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems
<i>Xylella fastidiosa</i> causes diseases in many plant species. Originally confined to the Americas, infecting mainly grapevine, citrus, and coffee, <i>X. fastidiosa</i> has spread to several plant species in Europe causing devastating diseases. Many pathogenicity and virule...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-04-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/10/5/914 |
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| author | Guillermo Uceda-Campos Oseias R. Feitosa-Junior Caio R. N. Santiago Paulo M. Pierry Paulo A. Zaini Wesley O. de Santana Joaquim Martins-Junior Deibs Barbosa Luciano A. Digiampietri João C. Setubal Aline M. da Silva |
| author_facet | Guillermo Uceda-Campos Oseias R. Feitosa-Junior Caio R. N. Santiago Paulo M. Pierry Paulo A. Zaini Wesley O. de Santana Joaquim Martins-Junior Deibs Barbosa Luciano A. Digiampietri João C. Setubal Aline M. da Silva |
| author_sort | Guillermo Uceda-Campos |
| collection | DOAJ |
| description | <i>Xylella fastidiosa</i> causes diseases in many plant species. Originally confined to the Americas, infecting mainly grapevine, citrus, and coffee, <i>X. fastidiosa</i> has spread to several plant species in Europe causing devastating diseases. Many pathogenicity and virulence factors have been identified, which enable the various <i>X. fastidiosa</i> 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 <i>X. fastidiosa</i> 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 <i>X. fastidiosa</i> 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 <i>X. fastidiosa</i> mobile genetic elements and immunity systems. |
| first_indexed | 2024-03-10T03:23:10Z |
| format | Article |
| id | doaj.art-7852a69bf9884238b5363f53dcbe863c |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T03:23:10Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-7852a69bf9884238b5363f53dcbe863c2023-11-23T12:14:55ZengMDPI AGMicroorganisms2076-26072022-04-0110591410.3390/microorganisms10050914Comparative Genomics of <i>Xylella fastidiosa</i> Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity SystemsGuillermo Uceda-Campos0Oseias R. Feitosa-Junior1Caio R. N. Santiago2Paulo M. Pierry3Paulo A. Zaini4Wesley O. de Santana5Joaquim Martins-Junior6Deibs Barbosa7Luciano A. Digiampietri8João C. Setubal9Aline M. da Silva10Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, BrazilDepartamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, BrazilPrograma de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo 05508-090, BrazilDepartamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, BrazilDepartment of Plant Sciences, University of California, Davis, CA 95616, USADepartamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, BrazilDepartamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, BrazilDepartamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, BrazilEscola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo 03828-000, BrazilDepartamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, BrazilDepartamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, Brazil<i>Xylella fastidiosa</i> causes diseases in many plant species. Originally confined to the Americas, infecting mainly grapevine, citrus, and coffee, <i>X. fastidiosa</i> has spread to several plant species in Europe causing devastating diseases. Many pathogenicity and virulence factors have been identified, which enable the various <i>X. fastidiosa</i> 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 <i>X. fastidiosa</i> 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 <i>X. fastidiosa</i> 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 <i>X. fastidiosa</i> mobile genetic elements and immunity systems.https://www.mdpi.com/2076-2607/10/5/914phytopathogenvirulencepangenomeprophagephage-defenseXanthomonadaceae |
| spellingShingle | Guillermo Uceda-Campos Oseias R. Feitosa-Junior Caio R. N. Santiago Paulo M. Pierry Paulo A. Zaini Wesley O. de Santana Joaquim Martins-Junior Deibs Barbosa Luciano A. Digiampietri João C. Setubal Aline M. da Silva Comparative Genomics of <i>Xylella fastidiosa</i> Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems Microorganisms phytopathogen virulence pangenome prophage phage-defense Xanthomonadaceae |
| title | Comparative Genomics of <i>Xylella fastidiosa</i> Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems |
| title_full | Comparative Genomics of <i>Xylella fastidiosa</i> Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems |
| title_fullStr | Comparative Genomics of <i>Xylella fastidiosa</i> Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems |
| title_full_unstemmed | Comparative Genomics of <i>Xylella fastidiosa</i> Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems |
| title_short | Comparative Genomics of <i>Xylella fastidiosa</i> Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems |
| title_sort | comparative genomics of i xylella fastidiosa i explores candidate host specificity determinants and expands the known repertoire of mobile genetic elements and immunity systems |
| topic | phytopathogen virulence pangenome prophage phage-defense Xanthomonadaceae |
| url | https://www.mdpi.com/2076-2607/10/5/914 |
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