title: The Arabidopsis root transcriptome by serial analysis of gene expression. Gene identification using the genome sequence.
abstract: Large-scale identification of genes expressed in roots of the model plant Arabidopsis was performed by serial analysis of gene expression (SAGE), on a total of 144,083 sequenced tags, representing at least 15,964 different mRNAs. For tag to gene assignment, we developed a computational approach based on 26,620 genes annotated from the complete sequence of the genome. The procedure selected warrants the identification of the genes corresponding to the majority of the tags found experimentally, with a high level of reliability, and provides a reference database for SAGE studies in Arabidopsis. This new resource allowed us to characterize the expression of more than 3,000 genes, for which there is no expressed sequence tag (EST) or cDNA in the databases. Moreover, 85% of the tags were specific for one gene. To illustrate this advantage of SAGE for functional genomics, we show that our data allow an unambiguous analysis of most of the individual genes belonging to 12 different ion transporter multigene families. These results indicate that, compared with EST-based tag to gene assignment, the use of the annotated genome sequence greatly improves gene identification in SAGE studies. However, more than 6,000 different tags remained with no gene match, suggesting that a significant proportion of transcripts present in the roots originate from yet unknown or wrongly annotated genes. The root transcriptome characterized in this study markedly differs from those obtained in other organs, and provides a unique resource for investigating the functional specificities of the root system. As an example of the use of SAGE for transcript profiling in Arabidopsis, we report here the identification of 270 genes differentially expressed between roots of plants grown either with NO3- or NH4NO3 as N source.
authors.affiliation: Biochimie et Physiologie Moléculaire des Plantes, Unité Mixte de Recherche 5004, Agro-M/Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/UM2, Place Viala, 34060 Montpellier 1, France.
authors.forename: Cécile
authors.initials: C
authors.lastname: Fizames
authors.forename: Stéphane
authors.initials: S
authors.lastname: Muños
authors.forename: Céline
authors.initials: C
authors.lastname: Cazettes
authors.forename: Philippe
authors.initials: P
authors.lastname: Nacry
authors.forename: Jossia
authors.initials: J
authors.lastname: Boucherez
authors.forename: Frédéric
authors.initials: F
authors.lastname: Gaymard
authors.forename: David
authors.initials: D
authors.lastname: Piquemal
authors.forename: Valérie
authors.initials: V
authors.lastname: Delorme
authors.forename: Thérèse
authors.initials: T
authors.lastname: Commes
authors.forename: Patrick
authors.initials: P
authors.lastname: Doumas
authors.forename: Richard
authors.initials: R
authors.lastname: Cooke
authors.forename: Jacques
authors.initials: J
authors.lastname: Marti
authors.forename: Hervé
authors.initials: H
authors.lastname: Sentenac
authors.forename: Alain
authors.initials: A
authors.lastname: Gojon
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D001483:Base Sequence; D018744:DNA, Plant / Q000235:genetics; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D015870:Gene Expression; D018745:Genome, Plant; D007473:Ion Channels / Q000235:genetics; D017136:Ion Transport / Q000235:genetics; D009584:Nitrogen / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics
chemical_list: D018744:DNA, Plant; D007473:Ion Channels; D012333:RNA, Messenger; D018749:RNA, Plant; D009584:Nitrogen