Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genus
The accurate diagnosis of diseases caused by pathogenic bacteria requires a stable species classification. Rhodococcus fascians is the only documented member of its ill-defined genus that is capable of causing disease on a wide range of agriculturally important plants. Comparisons of genome sequence...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2014-08-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00406/full |
| _version_ | 1818354055504723968 |
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| author | Allison L. Creason Edward W. Davis Melodie L. Putnam Olivier M. Vandeputte Jeff H Chang |
| author_facet | Allison L. Creason Edward W. Davis Melodie L. Putnam Olivier M. Vandeputte Jeff H Chang |
| author_sort | Allison L. Creason |
| collection | DOAJ |
| description | The accurate diagnosis of diseases caused by pathogenic bacteria requires a stable species classification. Rhodococcus fascians is the only documented member of its ill-defined genus that is capable of causing disease on a wide range of agriculturally important plants. Comparisons of genome sequences generated from isolates of Rhodococcus associated with diseased plants revealed a level of genetic diversity consistent with them representing multiple species. To test this, we generated a tree based on more than 1700 homologous sequences from plant-associated isolates of Rhodococcus, and obtained support from additional approaches that measure and cluster based on genome similarities. Results were consistent in supporting the definition of new Rhodococcus species within clades containing phytopathogenic members. We also used the genome sequences, along with other rhodococcal genome sequences to construct a molecular phylogenetic tree as a framework for resolving the Rhodococcus genus. Results indicated that Rhodococcus has the potential for having 20 species and also confirmed a need to revisit the taxonomic groupings within Rhodococcus. |
| first_indexed | 2024-12-13T19:19:20Z |
| format | Article |
| id | doaj.art-1777634a47c9435980fc38286c23b338 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-13T19:19:20Z |
| publishDate | 2014-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-1777634a47c9435980fc38286c23b3382022-12-21T23:34:12ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2014-08-01510.3389/fpls.2014.00406103878Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genusAllison L. Creason0Edward W. Davis1Melodie L. Putnam2Olivier M. Vandeputte3Jeff H Chang4Oregon State UniversityOregon State UniversityOregon State UniversityUniversite Libre de BruxellesOregon State UniversityThe accurate diagnosis of diseases caused by pathogenic bacteria requires a stable species classification. Rhodococcus fascians is the only documented member of its ill-defined genus that is capable of causing disease on a wide range of agriculturally important plants. Comparisons of genome sequences generated from isolates of Rhodococcus associated with diseased plants revealed a level of genetic diversity consistent with them representing multiple species. To test this, we generated a tree based on more than 1700 homologous sequences from plant-associated isolates of Rhodococcus, and obtained support from additional approaches that measure and cluster based on genome similarities. Results were consistent in supporting the definition of new Rhodococcus species within clades containing phytopathogenic members. We also used the genome sequences, along with other rhodococcal genome sequences to construct a molecular phylogenetic tree as a framework for resolving the Rhodococcus genus. Results indicated that Rhodococcus has the potential for having 20 species and also confirmed a need to revisit the taxonomic groupings within Rhodococcus.http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00406/fullPlant PathogenGram-positiveprokaryotic taxonomyAverage nucleotide identityleafy gall |
| spellingShingle | Allison L. Creason Edward W. Davis Melodie L. Putnam Olivier M. Vandeputte Jeff H Chang Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genus Frontiers in Plant Science Plant Pathogen Gram-positive prokaryotic taxonomy Average nucleotide identity leafy gall |
| title | Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genus |
| title_full | Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genus |
| title_fullStr | Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genus |
| title_full_unstemmed | Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genus |
| title_short | Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genus |
| title_sort | use of whole genome sequences to develop a molecular phylogenetic framework for rhodococcus fascians and the rhodococcus genus |
| topic | Plant Pathogen Gram-positive prokaryotic taxonomy Average nucleotide identity leafy gall |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00406/full |
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