A spatial dissection of the Arabidopsis floral transcriptome by MPSS

Persistent Link:
http://hdl.handle.net/10150/610079
Title:
A spatial dissection of the Arabidopsis floral transcriptome by MPSS
Author:
Peiffer, Jason; Kaushik, Shail; Sakai, Hajime; Arteaga-Vazquez, Mario; Sanchez-Leon, Nidia; Ghazal, Hassan; Vielle-Calzada, Jean; Meyers, Blake
Affiliation:
Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA; DuPont Crop Genetics, Wilmington, DE 19880, USA; National Laboratory of Genomics for Biodiversity and Department of Genetic Engineering, CINVESTAV Campus, Guanajuato, Irapuato, Mexico; Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14850, USA; Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; University Mohammed I, Laboratory of Genetics and Biotechnology, Faculty of Sciences, Oujda and Pluridisciplinary Faculty of Nador, Morocco
Issue Date:
2008
Publisher:
BioMed Central
Citation:
BMC Plant Biology 2008, 8:43 doi:10.1186/1471-2229-8-43
Journal:
BMC Plant Biology
Rights:
© 2008 Peiffer et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:We have further characterized floral organ-localized gene expression in the inflorescence of Arabidopsis thaliana by comparison of massively parallel signature sequencing (MPSS) data. Six libraries of RNA sequence tags from immature inflorescence tissues were constructed and matched to their respective loci in the annotated Arabidopsis genome. These signature libraries survey the floral transcriptome of wild-type tissue as well as the floral homeotic mutants, apetala1, apetala3, agamous, a superman/apetala1 double mutant, and differentiated ovules dissected from the gynoecia of wild-type inflorescences. Comparing and contrasting these MPSS floral expression libraries enabled demarcation of transcripts enriched in the petals, stamens, stigma-style, gynoecia, and those with predicted enrichment within the sepal/sepal-petals, petal-stamens, or gynoecia-stamens.RESULTS:By comparison of expression libraries, a total of 572 genes were found to have organ-enriched expression within the inflorescence. The bulk of characterized organ-enriched transcript diversity was noted in the gynoecia and stamens, whereas fewer genes demonstrated sepal or petal-localized expression. Validation of the computational analyses was performed by comparison with previously published expression data, in situ hybridizations, promoter-reporter fusions, and reverse transcription PCR. A number of well-characterized genes were accurately delineated within our system of transcript filtration. Moreover, empirical validations confirm MPSS predictions for several genes with previously uncharacterized expression patterns.CONCLUSION:This extensive MPSS analysis confirms and supplements prior microarray floral expression studies and illustrates the utility of sequence survey-based expression analysis in functional genomics. Spatial floral expression data accrued by MPSS and similar methods will be advantageous in the elucidation of more comprehensive genetic regulatory networks governing floral development.
EISSN:
1471-2229
DOI:
10.1186/1471-2229-8-43
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2229/8/43

Full metadata record

DC FieldValue Language
dc.contributor.authorPeiffer, Jasonen
dc.contributor.authorKaushik, Shailen
dc.contributor.authorSakai, Hajimeen
dc.contributor.authorArteaga-Vazquez, Marioen
dc.contributor.authorSanchez-Leon, Nidiaen
dc.contributor.authorGhazal, Hassanen
dc.contributor.authorVielle-Calzada, Jeanen
dc.contributor.authorMeyers, Blakeen
dc.date.accessioned2016-05-20T08:58:04Z-
dc.date.available2016-05-20T08:58:04Z-
dc.date.issued2008en
dc.identifier.citationBMC Plant Biology 2008, 8:43 doi:10.1186/1471-2229-8-43en
dc.identifier.doi10.1186/1471-2229-8-43en
dc.identifier.urihttp://hdl.handle.net/10150/610079-
dc.description.abstractBACKGROUND:We have further characterized floral organ-localized gene expression in the inflorescence of Arabidopsis thaliana by comparison of massively parallel signature sequencing (MPSS) data. Six libraries of RNA sequence tags from immature inflorescence tissues were constructed and matched to their respective loci in the annotated Arabidopsis genome. These signature libraries survey the floral transcriptome of wild-type tissue as well as the floral homeotic mutants, apetala1, apetala3, agamous, a superman/apetala1 double mutant, and differentiated ovules dissected from the gynoecia of wild-type inflorescences. Comparing and contrasting these MPSS floral expression libraries enabled demarcation of transcripts enriched in the petals, stamens, stigma-style, gynoecia, and those with predicted enrichment within the sepal/sepal-petals, petal-stamens, or gynoecia-stamens.RESULTS:By comparison of expression libraries, a total of 572 genes were found to have organ-enriched expression within the inflorescence. The bulk of characterized organ-enriched transcript diversity was noted in the gynoecia and stamens, whereas fewer genes demonstrated sepal or petal-localized expression. Validation of the computational analyses was performed by comparison with previously published expression data, in situ hybridizations, promoter-reporter fusions, and reverse transcription PCR. A number of well-characterized genes were accurately delineated within our system of transcript filtration. Moreover, empirical validations confirm MPSS predictions for several genes with previously uncharacterized expression patterns.CONCLUSION:This extensive MPSS analysis confirms and supplements prior microarray floral expression studies and illustrates the utility of sequence survey-based expression analysis in functional genomics. Spatial floral expression data accrued by MPSS and similar methods will be advantageous in the elucidation of more comprehensive genetic regulatory networks governing floral development.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2229/8/43en
dc.rights© 2008 Peiffer et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleA spatial dissection of the Arabidopsis floral transcriptome by MPSSen
dc.typeArticleen
dc.identifier.eissn1471-2229en
dc.contributor.departmentDepartment of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USAen
dc.contributor.departmentDuPont Crop Genetics, Wilmington, DE 19880, USAen
dc.contributor.departmentNational Laboratory of Genomics for Biodiversity and Department of Genetic Engineering, CINVESTAV Campus, Guanajuato, Irapuato, Mexicoen
dc.contributor.departmentDepartment of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14850, USAen
dc.contributor.departmentDepartment of Plant Sciences, University of Arizona, Tucson, AZ 85721, USAen
dc.contributor.departmentUniversity Mohammed I, Laboratory of Genetics and Biotechnology, Faculty of Sciences, Oujda and Pluridisciplinary Faculty of Nador, Moroccoen
dc.identifier.journalBMC Plant Biologyen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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