TY - JOUR
T1 - A spatial dissection of the Arabidopsis floral transcriptome by MPSS
AU - Peiffer, Jason A.
AU - Kaushik, Shail
AU - Sakai, Hajime
AU - Arteaga-Vazquez, Mario
AU - Sanchez-Leon, Nidia
AU - Ghazal, Hassan
AU - Vielle-Calzada, Jean Philippe
AU - Meyers, Blake C.
N1 - Funding Information:
This research was funded in part by NSF Plant Genome Research award #0110528 (B.C.M.) and an NSF Research Experiences for Undergraduates (REU) award to Jason Peiffer. We are grateful for the bioinformatics assistance and advice of Dr. Kan Nobuta, as well as support and advice from additional members of the Meyers Lab and members of Dr. Pam Green's lab. Dan Rodriguez and Cesar Alvarez-Mejía assisted with reverse transcription PCR and ovule-specific reporter gene constructs. M.A.V. and N.S.L. were recipients of a Ph.D fellowship from Consejo Nacional de Ciencia y Tec-nología (CONACyT). Research in JPVC lab was supported by Fondos Mix- tos Guanajuato, CONACyT, and the Howard Hughes Medical Institute. We would like to thank Dr. Thomas Jack for providing ap3-6 seed stock, as well as the Arabidopsis Biological Resource Center at The Ohio State University for ag seed stock.
PY - 2008
Y1 - 2008
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=43649086637&partnerID=8YFLogxK
U2 - 10.1186/1471-2229-8-43
DO - 10.1186/1471-2229-8-43
M3 - Article
C2 - 18426585
AN - SCOPUS:43649086637
SN - 1471-2229
VL - 8
JO - BMC Plant Biology
JF - BMC Plant Biology
M1 - 43
ER -