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

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...

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Autores principales: Kido, Éderson Akio, Ferreira Neto, José Ribamar Costa, Silva, Roberta Lane de Oliveira, Pandolfi, Valesca, Guimarães, Ana Carolina Ribeiro, Veiga, Daniela Truffi, Chabregas, Sabrina Moutinho, Crovella, Sérgio, Benko-Iseppon, Ana Maria
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Scientific World Journal 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353566/
https://www.ncbi.nlm.nih.gov/pubmed/22629208
http://dx.doi.org/10.1100/2012/821062
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author Kido, Éderson Akio
Ferreira Neto, José Ribamar Costa
Silva, Roberta Lane de Oliveira
Pandolfi, Valesca
Guimarães, Ana Carolina Ribeiro
Veiga, Daniela Truffi
Chabregas, Sabrina Moutinho
Crovella, Sérgio
Benko-Iseppon, Ana Maria
author_facet Kido, Éderson Akio
Ferreira Neto, José Ribamar Costa
Silva, Roberta Lane de Oliveira
Pandolfi, Valesca
Guimarães, Ana Carolina Ribeiro
Veiga, Daniela Truffi
Chabregas, Sabrina Moutinho
Crovella, Sérgio
Benko-Iseppon, Ana Maria
author_sort Kido, Éderson Akio
collection PubMed
description 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.
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spelling pubmed-33535662012-05-24 New Insights in the Sugarcane Transcriptome Responding to Drought Stress as Revealed by Supersage Kido, Éderson Akio Ferreira Neto, José Ribamar Costa Silva, Roberta Lane de Oliveira Pandolfi, Valesca Guimarães, Ana Carolina Ribeiro Veiga, Daniela Truffi Chabregas, Sabrina Moutinho Crovella, Sérgio Benko-Iseppon, Ana Maria ScientificWorldJournal Research Article 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. The Scientific World Journal 2012-05-02 /pmc/articles/PMC3353566/ /pubmed/22629208 http://dx.doi.org/10.1100/2012/821062 Text en Copyright © 2012 Éderson Akio Kido et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Kido, Éderson Akio
Ferreira Neto, José Ribamar Costa
Silva, Roberta Lane de Oliveira
Pandolfi, Valesca
Guimarães, Ana Carolina Ribeiro
Veiga, Daniela Truffi
Chabregas, Sabrina Moutinho
Crovella, Sérgio
Benko-Iseppon, Ana Maria
New Insights in the Sugarcane Transcriptome Responding to Drought Stress as Revealed by Supersage
title New Insights in the Sugarcane Transcriptome Responding to Drought Stress as Revealed by Supersage
title_full New Insights in the Sugarcane Transcriptome Responding to Drought Stress as Revealed by Supersage
title_fullStr New Insights in the Sugarcane Transcriptome Responding to Drought Stress as Revealed by Supersage
title_full_unstemmed New Insights in the Sugarcane Transcriptome Responding to Drought Stress as Revealed by Supersage
title_short New Insights in the Sugarcane Transcriptome Responding to Drought Stress as Revealed by Supersage
title_sort new insights in the sugarcane transcriptome responding to drought stress as revealed by supersage
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353566/
https://www.ncbi.nlm.nih.gov/pubmed/22629208
http://dx.doi.org/10.1100/2012/821062
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