Journal Article

New Insights in the Sugarcane Transcriptome Responding to Drought Stress as Revealed by Supersage

Ferreira Neto, José Ribamar Costa, Guimarães, Ana Carolina Ribeiro, Chabregas, Sabrina Moutinho, Crovella, Sérgio, Benko-Iseppon, Ana Maria, Silva, Roberta Lane de Oliveira, Veiga, Daniela Truffi, Kido, Éderson Akio, Pandolfi, Valesca

2012

Overview

In the scope of the present work, four SuperSAGE libraries have been generated, using bulked root tissues from four drought-tolerant accessions as compared with four bulked sensitive genotypes, aiming to generate a panel of differentially expressed stress-responsive genes. Both groups were submitted to 24 hours of water deficit stress. The SuperSAGE libraries produced 8,787,315 tags (26 bp) that, after exclusion of singlets, allowed the identification of 205,975 unitags. Most relevant BlastN matches comprised 567,420 tags, regarding 75,404 unitags with 164,860 different ESTs. To optimize the annotation efficiency, the Gene Ontology (GO) categorization was carried out for 186,191 ESTs (BlastN against Uniprot-SwissProt), permitting the categorization of 118,208 ESTs (63.5%). In an attempt to elect a group of the best tags to be validated by RTqPCR, the GO categorization of the tag-related ESTs allowed the in silico identification of 213 upregulated unitags responding basically to abiotic stresses, from which 145 presented no hits after BlastN analysis, probably concerning new genes still uncovered in previous studies. The present report analyzes the sugarcane transcriptome under drought stress, using a combination of high-throughput transcriptome profiling by SuperSAGE with the Solexa sequencing technology, allowing the identification of potential target genes during the stress response.

• Publisher: Hindawi Puplishing Corporation,The Scientific World Journal,John Wiley & Sons, Inc,Hindawi Limited,Wiley
• Subject: Abiotic stress / Annotations / Botanical research / Classification / Crops / Drought / Drought resistance / Droughts / Gene expression / Gene Expression Profiling - methods / Gene sequencing / Genes / Genetic aspects / Genetic research / Genetic transcription / Genetically altered foods / Genotypes / Health aspects / Heat-Shock Response - physiology / Identification / Irrigation / Kinases / Oryza / Physiology / Plant biology / Plant Proteins - metabolism / Plant sciences / Productivity / Proteins / Rice / Saccharum - metabolism / Saccharum officinarum / Signal transduction / Stresses / Sucrose / Sugarcane / Tags / Target recognition / Tobacco / Transcriptome - physiology / Water deficit