Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray) generated from the shotgun libraries previously used in the sequencing of this bacterial genome

dc.contributor.authorMoreira, Leandro M
dc.contributor.authorDe Laia, Marcelo L [UNESP]
dc.contributor.authorDe Souza, Robson F
dc.contributor.authorZaini, Paulo A
dc.contributor.authorDa Silva, Ana Cr
dc.contributor.authorDa Silva, Aline M
dc.contributor.authorFerro, Jesus A [UNESP]
dc.contributor.institutionUniversidade Federal de Ouro Preto (UFOP)
dc.contributor.institutionUniversidade de São Paulo (USP)
dc.contributor.institutionUniversidade Federal dos Vales do Jequitinhonha e Mucuri (UFVJM)
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.contributor.institutionAlellyx Applied Genomics
dc.date.accessioned2014-05-27T11:24:42Z
dc.date.available2014-05-27T11:24:42Z
dc.date.issued2010-06-25
dc.description.abstractBackground. From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC), clones that were representative of the largest possible number of coding sequences (CDSs) were selected to create a DNA microarray platform on glass slides (XACarray). The creation of the XACarray allowed for the establishment of a tool that is capable of providing data for the analysis of global genome expression in this organism. Findings. The inserts from the selected clones were amplified by PCR with the universal oligonucleotide primers M13R and M13F. The obtained products were purified and fixed in duplicate on glass slides specific for use in DNA microarrays. The number of spots on the microarray totaled 6,144 and included 768 positive controls and 624 negative controls per slide. Validation of the platform was performed through hybridization of total DNA probes from XAC labeled with different fluorophores, Cy3 and Cy5. In this validation assay, 86% of all PCR products fixed on the glass slides were confirmed to present a hybridization signal greater than twice the standard deviation of the deviation of the global median signal-to-noise ration. Conclusions. Our validation of the XACArray platform using DNA-DNA hybridization revealed that it can be used to evaluate the expression of 2,365 individual CDSs from all major functional categories, which corresponds to 52.7% of the annotated CDSs of the XAC genome. As a proof of concept, we used this platform in a previously work to verify the absence of genomic regions that could not be detected by sequencing in related strains of Xanthomonas. © 2010 Moreira et al; licensee BioMed Central Ltd.en
dc.description.affiliationDepartamento de Cincias Biolágicas (DECBI) Instituto de Cincias Exatas e Biolágicas Universidade Federal de Ouro Preto, Ouro Preto, MG
dc.description.affiliationNcleo de Pesquisas em Cincias Biolágicas (NUPEB) Universidade Federal de Ouro Preto, Ouro Preto, MG
dc.description.affiliationDepartamento de Bioquímica Instituto de Química, Universidade de so Paulo, So Paulo, SP
dc.description.affiliationDepartamento de Engenharia Florestal Faculdade de Cincias Agrrias Universidade Federal Dos Vales Do Jequitinhonha e Mucuri, Diamantina, MG
dc.description.affiliationDepartamento de Tecnologia Faculdade de Cincias Agrrias e Veterinrias de Jaboticabal UNESP - Univ. Estadual Paulista, Jaboticabal, SP
dc.description.affiliationAlellyx Applied Genomics, Rua James Clerk Maxwell 320, Campinas SP
dc.description.affiliationUnespDepartamento de Tecnologia Faculdade de Cincias Agrrias e Veterinrias de Jaboticabal UNESP - Univ. Estadual Paulista, Jaboticabal, SP
dc.identifierhttp://dx.doi.org/10.1186/1756-0500-3-150
dc.identifier.citationBMC Research Notes, v. 3.
dc.identifier.doi10.1186/1756-0500-3-150
dc.identifier.file2-s2.0-77953799039.pdf
dc.identifier.issn1756-0500
dc.identifier.scopus2-s2.0-77953799039
dc.identifier.urihttp://hdl.handle.net/11449/71733
dc.language.isoeng
dc.relation.ispartofBMC Research Notes
dc.relation.ispartofsjr0,691
dc.rights.accessRightsAcesso aberto
dc.sourceScopus
dc.subjectBacteria (microorganisms)
dc.subjectXanthomonas
dc.subjectXanthomonas axonopodis
dc.subjectXanthomonas axonopodis pv. citri
dc.titleDevelopment and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray) generated from the shotgun libraries previously used in the sequencing of this bacterial genomeen
dc.typeArtigo
dcterms.licensehttp://www.biomedcentral.com/about/license
unesp.campusUniversidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabalpt
unesp.departmentTecnologia - FCAVpt

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