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 NO 3 Ϫ or NH 4 NO 3 as N source.

The Fast and Transient Transcriptional Network of Gravity and Mechanical Stimulation in the Arabidopsis Root Apex

“…The highest abundance of transcripts based on normalized fluorescence intensity data was found for genes involved in protein synthesis (ribosomal proteins, elongation factor 1-a, HSP70) and degradation (aspartic proteinase, E2, ubiquitin-conjugating enzyme), detoxification (glutathione transferases, metallothioneins), and maintenance of reduced proteinacious Cys (thioredoxin H). These genes were also identified with highest transcript abundance based on fluorescence intensity in Arabidopsis root tips by Birnbaum et al (2003) and showed high abundance as a function of frequency of sequenced tags in SAGE libraries of Arabidopsis root tips (Fizames et al, 2004), which validates our overall expression data.…”

Rooteomics: The Challenge of Discovering Plant Defense-Related Proteins in Roots

“…This is also true for root proteins. An interesting result was obtained by Fizames et al [63], who analyzed root transcriptomics of Arabidopsis plants using the SAGE (Serial Analysis of Gene Expression) technique. These authors reported 6000 different transcript tags, which showed no match to the Arabidopsis genes and suggest that a significant amount of transcripts present in roots originate from unknown or wrongly annotated genes.…”

Nitrite Acts as a Transcriptome Signal at Micromolar Concentrations in Arabidopsis Roots

“…Ammonium has been shown to affect the expression of several hundred genes in Arabidopsis roots (Fizames et al, 2004). High ammonium levels (20 mM or greater) have been used as a nitrogen source for several nitrate transcriptome studies (Wang et al, 2000).…”