Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic tools

Detalhes bibliográficos
Autor(a) principal: Kishi, Luciano Takeshi [UNESP]
Data de Publicação: 2016
Outros Autores: Fernandes, Camila Cesário [UNESP], Omori, Wellington Pine [UNESP], Campanharo, João Carlos [UNESP], De Macedo Lemos, Eliana Gertrudes de Macedo [UNESP]
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1186/s12866-016-0882-5
http://hdl.handle.net/11449/173713
Resumo: Background: Evidence based on genomic sequences is extremely important to confirm the phylogenetic relationships within the Rhizobium group. SEMIA3007 was analyzed within the Mesorhizobium groups to define the underlying causes of taxonomic identification. We previously used biochemical tests and phenotypic taxonomic methods to identify bacteria, which can lead to erroneous classification. An improved understanding of bacterial strains such as the Mesorhizobium genus would increase our knowledge of classification and evolution of these species. Results: In this study, we sequenced the complete genome of SEMIA3007 and compared it with five other Mesorhizobium and two Rhizobium genomes. The genomes of isolated SEMIA3007 showed several orthologs with M. huakuii, M. erdmanii and M. loti. We identified SEMIA3007 as a Mesorhizobium by comparing the 16S rRNA gene and the complete genome. Conclusion: Our ortholog, 16S rRNA gene and average nucleotide identity values (ANI) analysis all demonstrate SEMIA3007 is not Rhizobium leguminosarum bv. viceae. The results of the phylogenetic analysis clearly show SEMIA3007 is part of the Mesorhizobium group and suggest a reclassification is warranted.
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spelling Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic toolsComparative analysisCore genomeGenome sequencingOrtholog genesPhylogenetic analysisBackground: Evidence based on genomic sequences is extremely important to confirm the phylogenetic relationships within the Rhizobium group. SEMIA3007 was analyzed within the Mesorhizobium groups to define the underlying causes of taxonomic identification. We previously used biochemical tests and phenotypic taxonomic methods to identify bacteria, which can lead to erroneous classification. An improved understanding of bacterial strains such as the Mesorhizobium genus would increase our knowledge of classification and evolution of these species. Results: In this study, we sequenced the complete genome of SEMIA3007 and compared it with five other Mesorhizobium and two Rhizobium genomes. The genomes of isolated SEMIA3007 showed several orthologs with M. huakuii, M. erdmanii and M. loti. We identified SEMIA3007 as a Mesorhizobium by comparing the 16S rRNA gene and the complete genome. Conclusion: Our ortholog, 16S rRNA gene and average nucleotide identity values (ANI) analysis all demonstrate SEMIA3007 is not Rhizobium leguminosarum bv. viceae. The results of the phylogenetic analysis clearly show SEMIA3007 is part of the Mesorhizobium group and suggest a reclassification is warranted.Departamento de Tecnologia Laboratório de Bioquímica de Microrganismos e Planta - LBMP UNESP - Universidade Estadual Paulista Faculdade de Ciências Agrárias e Veterinárias, Via de Acesso Prof. Paulo Donato Castellane s/nDepartamento de Tecnologia Laboratório de Bioquímica de Microrganismos e Planta - LBMP UNESP - Universidade Estadual Paulista Faculdade de Ciências Agrárias e Veterinárias, Via de Acesso Prof. Paulo Donato Castellane s/nUniversidade Estadual Paulista (Unesp)Kishi, Luciano Takeshi [UNESP]Fernandes, Camila Cesário [UNESP]Omori, Wellington Pine [UNESP]Campanharo, João Carlos [UNESP]De Macedo Lemos, Eliana Gertrudes de Macedo [UNESP]2018-12-11T17:07:24Z2018-12-11T17:07:24Z2016-11-04info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article1-8application/pdfhttp://dx.doi.org/10.1186/s12866-016-0882-5BMC Microbiology, v. 16, n. 1, p. 1-8, 2016.1471-2180http://hdl.handle.net/11449/17371310.1186/s12866-016-0882-52-s2.0-849940177422-s2.0-84994017742.pdfScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBMC Microbiology1,242info:eu-repo/semantics/openAccess2024-06-07T15:31:16Zoai:repositorio.unesp.br:11449/173713Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-06-07T15:31:16Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic tools
title Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic tools
spellingShingle Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic tools
Kishi, Luciano Takeshi [UNESP]
Comparative analysis
Core genome
Genome sequencing
Ortholog genes
Phylogenetic analysis
title_short Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic tools
title_full Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic tools
title_fullStr Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic tools
title_full_unstemmed Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic tools
title_sort Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic tools
author Kishi, Luciano Takeshi [UNESP]
author_facet Kishi, Luciano Takeshi [UNESP]
Fernandes, Camila Cesário [UNESP]
Omori, Wellington Pine [UNESP]
Campanharo, João Carlos [UNESP]
De Macedo Lemos, Eliana Gertrudes de Macedo [UNESP]
author_role author
author2 Fernandes, Camila Cesário [UNESP]
Omori, Wellington Pine [UNESP]
Campanharo, João Carlos [UNESP]
De Macedo Lemos, Eliana Gertrudes de Macedo [UNESP]
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Universidade Estadual Paulista (Unesp)
dc.contributor.author.fl_str_mv Kishi, Luciano Takeshi [UNESP]
Fernandes, Camila Cesário [UNESP]
Omori, Wellington Pine [UNESP]
Campanharo, João Carlos [UNESP]
De Macedo Lemos, Eliana Gertrudes de Macedo [UNESP]
dc.subject.por.fl_str_mv Comparative analysis
Core genome
Genome sequencing
Ortholog genes
Phylogenetic analysis
topic Comparative analysis
Core genome
Genome sequencing
Ortholog genes
Phylogenetic analysis
description Background: Evidence based on genomic sequences is extremely important to confirm the phylogenetic relationships within the Rhizobium group. SEMIA3007 was analyzed within the Mesorhizobium groups to define the underlying causes of taxonomic identification. We previously used biochemical tests and phenotypic taxonomic methods to identify bacteria, which can lead to erroneous classification. An improved understanding of bacterial strains such as the Mesorhizobium genus would increase our knowledge of classification and evolution of these species. Results: In this study, we sequenced the complete genome of SEMIA3007 and compared it with five other Mesorhizobium and two Rhizobium genomes. The genomes of isolated SEMIA3007 showed several orthologs with M. huakuii, M. erdmanii and M. loti. We identified SEMIA3007 as a Mesorhizobium by comparing the 16S rRNA gene and the complete genome. Conclusion: Our ortholog, 16S rRNA gene and average nucleotide identity values (ANI) analysis all demonstrate SEMIA3007 is not Rhizobium leguminosarum bv. viceae. The results of the phylogenetic analysis clearly show SEMIA3007 is part of the Mesorhizobium group and suggest a reclassification is warranted.
publishDate 2016
dc.date.none.fl_str_mv 2016-11-04
2018-12-11T17:07:24Z
2018-12-11T17:07:24Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://dx.doi.org/10.1186/s12866-016-0882-5
BMC Microbiology, v. 16, n. 1, p. 1-8, 2016.
1471-2180
http://hdl.handle.net/11449/173713
10.1186/s12866-016-0882-5
2-s2.0-84994017742
2-s2.0-84994017742.pdf
url http://dx.doi.org/10.1186/s12866-016-0882-5
http://hdl.handle.net/11449/173713
identifier_str_mv BMC Microbiology, v. 16, n. 1, p. 1-8, 2016.
1471-2180
10.1186/s12866-016-0882-5
2-s2.0-84994017742
2-s2.0-84994017742.pdf
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv BMC Microbiology
1,242
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 1-8
application/pdf
dc.source.none.fl_str_mv Scopus
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
repository.mail.fl_str_mv
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