DNA Markers for Detection and Genotyping of <i>Xanthomonas euroxanthea</i>
<i>Xanthomonas euroxanthea</i> is a bacterial species encompassing both pathogenic and non-pathogenic strains and is frequently found colonizing the same host plants as <i>X. arboricola</i>. This presents the need to develop a detection and genotyping assay able to track thes...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-05-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/10/6/1078 |
| _version_ | 1797484253026451456 |
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| author | Kayla Gisela Silva Leonor Martins Miguel Teixeira Joël F. Pothier Fernando Tavares |
| author_facet | Kayla Gisela Silva Leonor Martins Miguel Teixeira Joël F. Pothier Fernando Tavares |
| author_sort | Kayla Gisela Silva |
| collection | DOAJ |
| description | <i>Xanthomonas euroxanthea</i> is a bacterial species encompassing both pathogenic and non-pathogenic strains and is frequently found colonizing the same host plants as <i>X. arboricola</i>. This presents the need to develop a detection and genotyping assay able to track these bacteria in microbial consortia with other xanthomonads. Eight <i>X. euroxanthea</i>-specific DNA markers (XEA1-XEA8) were selected by comparative genomics and validated in silico regarding their specificity and consistency using BLASTn, synteny analysis, CG content, codon usage (CAI/eCAI values) and genomic proximity to plasticity determinants. In silico, the selected eight DNA markers were found to be specific and conserved across the genomes of 11 <i>X. euroxanthea</i> strains, and in particular, five DNA markers (XEA4, XEA5, XEA6, XEA7 and XEA8) were unfailingly found in these genomes. A multiplex of PCR targeting markers XEA1 (819 bp), XEA8 (648 bp) and XEA5 (295 bp) was shown to successfully detect <i>X. euroxanthea</i> down to 1 ng of DNA (per PCR reaction). The topology of trees generated with the concatenated sequences of three markers (XEA5, XEA6 and XEA8) and four housekeeping genes (<i>gyrB</i>, <i>rpoD</i>, <i>fyuA</i> and <i>acnB</i>) underlined the equal discriminatory power of these features and thus the suitability of the DNA markers to discriminate <i>X. euroxanthea</i> lineages. Overall, this study displays a DNA-marker-based method for the detection and genotyping of <i>X. euroxanthea</i> strains, contributing to monitoring for its presence in <i>X. arboricola</i>-colonizing habitats. The present study proposes a workflow for the selection of species-specific detection markers. Prospectively, this assay could contribute to unveil alternative host species of <i>Xanthomonas euroxanthea</i>; and improve the control of phytopathogenic strains. |
| first_indexed | 2024-03-09T23:00:51Z |
| format | Article |
| id | doaj.art-3c28b0399454417d9d8dfd726abf553e |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T23:00:51Z |
| publishDate | 2022-05-01 |
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| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-3c28b0399454417d9d8dfd726abf553e2023-11-23T18:02:39ZengMDPI AGMicroorganisms2076-26072022-05-01106107810.3390/microorganisms10061078DNA Markers for Detection and Genotyping of <i>Xanthomonas euroxanthea</i>Kayla Gisela Silva0Leonor Martins1Miguel Teixeira2Joël F. Pothier3Fernando Tavares4CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, PortugalEnvironmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820 Wädenswil, SwitzerlandCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal<i>Xanthomonas euroxanthea</i> is a bacterial species encompassing both pathogenic and non-pathogenic strains and is frequently found colonizing the same host plants as <i>X. arboricola</i>. This presents the need to develop a detection and genotyping assay able to track these bacteria in microbial consortia with other xanthomonads. Eight <i>X. euroxanthea</i>-specific DNA markers (XEA1-XEA8) were selected by comparative genomics and validated in silico regarding their specificity and consistency using BLASTn, synteny analysis, CG content, codon usage (CAI/eCAI values) and genomic proximity to plasticity determinants. In silico, the selected eight DNA markers were found to be specific and conserved across the genomes of 11 <i>X. euroxanthea</i> strains, and in particular, five DNA markers (XEA4, XEA5, XEA6, XEA7 and XEA8) were unfailingly found in these genomes. A multiplex of PCR targeting markers XEA1 (819 bp), XEA8 (648 bp) and XEA5 (295 bp) was shown to successfully detect <i>X. euroxanthea</i> down to 1 ng of DNA (per PCR reaction). The topology of trees generated with the concatenated sequences of three markers (XEA5, XEA6 and XEA8) and four housekeeping genes (<i>gyrB</i>, <i>rpoD</i>, <i>fyuA</i> and <i>acnB</i>) underlined the equal discriminatory power of these features and thus the suitability of the DNA markers to discriminate <i>X. euroxanthea</i> lineages. Overall, this study displays a DNA-marker-based method for the detection and genotyping of <i>X. euroxanthea</i> strains, contributing to monitoring for its presence in <i>X. arboricola</i>-colonizing habitats. The present study proposes a workflow for the selection of species-specific detection markers. Prospectively, this assay could contribute to unveil alternative host species of <i>Xanthomonas euroxanthea</i>; and improve the control of phytopathogenic strains.https://www.mdpi.com/2076-2607/10/6/1078<i>Xanthomonas euroxanthea</i>taxa-specific DNA markersmultiplex PCRcomparative genomicsgenotyping |
| spellingShingle | Kayla Gisela Silva Leonor Martins Miguel Teixeira Joël F. Pothier Fernando Tavares DNA Markers for Detection and Genotyping of <i>Xanthomonas euroxanthea</i> Microorganisms <i>Xanthomonas euroxanthea</i> taxa-specific DNA markers multiplex PCR comparative genomics genotyping |
| title | DNA Markers for Detection and Genotyping of <i>Xanthomonas euroxanthea</i> |
| title_full | DNA Markers for Detection and Genotyping of <i>Xanthomonas euroxanthea</i> |
| title_fullStr | DNA Markers for Detection and Genotyping of <i>Xanthomonas euroxanthea</i> |
| title_full_unstemmed | DNA Markers for Detection and Genotyping of <i>Xanthomonas euroxanthea</i> |
| title_short | DNA Markers for Detection and Genotyping of <i>Xanthomonas euroxanthea</i> |
| title_sort | dna markers for detection and genotyping of i xanthomonas euroxanthea i |
| topic | <i>Xanthomonas euroxanthea</i> taxa-specific DNA markers multiplex PCR comparative genomics genotyping |
| url | https://www.mdpi.com/2076-2607/10/6/1078 |
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