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Identification of sense and antisense transcripts regulated by drought in sugarcane

Sugarcane is an important sugar and energy crop that can be used efficiently for biofuels production. The development of sugarcane cultivars tolerant to drought could allow for the expansion of plantations to sub-prime regions. Knowledge on the mechanisms underlying drought responses and its relatio...

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Autores principales: Lembke, Carolina Gimiliani, Nishiyama, Milton Yutaka, Sato, Paloma Mieko, de Andrade, Rodrigo Fandiño, Souza, Glaucia Mendes
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Netherlands 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369129/
https://www.ncbi.nlm.nih.gov/pubmed/22610347
http://dx.doi.org/10.1007/s11103-012-9922-1
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author Lembke, Carolina Gimiliani
Nishiyama, Milton Yutaka
Sato, Paloma Mieko
de Andrade, Rodrigo Fandiño
Souza, Glaucia Mendes
author_facet Lembke, Carolina Gimiliani
Nishiyama, Milton Yutaka
Sato, Paloma Mieko
de Andrade, Rodrigo Fandiño
Souza, Glaucia Mendes
author_sort Lembke, Carolina Gimiliani
collection PubMed
description Sugarcane is an important sugar and energy crop that can be used efficiently for biofuels production. The development of sugarcane cultivars tolerant to drought could allow for the expansion of plantations to sub-prime regions. Knowledge on the mechanisms underlying drought responses and its relationship with carbon partition would greatly help to define routes to increase yield. In this work we studied sugarcane responses to drought using a custom designed oligonucleotide array with 21,901 different probes. The oligoarrays were designed to contain probes that detect transcription in both sense and antisense orientation. We validated the results obtained using quantitative real-time PCR (qPCR). A total of 987 genes were differentially expressed in at least one sample of sugarcane plants submitted to drought for 24, 72 and 120 h. Among them, 928 were sense transcripts and 59 were antisense transcripts. Genes related to Carbohydrate Metabolism, RNA Metabolism and Signal Transduction were selected for gene expression validation by qPCR that indicated a validation percentage of 90 %. From the probes presented on the array, 75 % of the sense probes and 11.9 % of the antisense probes have signal above background and can be classified as expressed sequences. Our custom sugarcane oligonucleotide array provides sensitivity and good coverage of sugarcane transcripts for the identification of a representative proportion of natural antisense transcripts (NATs) and sense-antisense transcript pairs (SATs). The antisense transcriptome showed, in most cases, co-expression with respective sense transcripts. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11103-012-9922-1) contains supplementary material, which is available to authorized users.
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spelling pubmed-33691292012-06-14 Identification of sense and antisense transcripts regulated by drought in sugarcane Lembke, Carolina Gimiliani Nishiyama, Milton Yutaka Sato, Paloma Mieko de Andrade, Rodrigo Fandiño Souza, Glaucia Mendes Plant Mol Biol Article Sugarcane is an important sugar and energy crop that can be used efficiently for biofuels production. The development of sugarcane cultivars tolerant to drought could allow for the expansion of plantations to sub-prime regions. Knowledge on the mechanisms underlying drought responses and its relationship with carbon partition would greatly help to define routes to increase yield. In this work we studied sugarcane responses to drought using a custom designed oligonucleotide array with 21,901 different probes. The oligoarrays were designed to contain probes that detect transcription in both sense and antisense orientation. We validated the results obtained using quantitative real-time PCR (qPCR). A total of 987 genes were differentially expressed in at least one sample of sugarcane plants submitted to drought for 24, 72 and 120 h. Among them, 928 were sense transcripts and 59 were antisense transcripts. Genes related to Carbohydrate Metabolism, RNA Metabolism and Signal Transduction were selected for gene expression validation by qPCR that indicated a validation percentage of 90 %. From the probes presented on the array, 75 % of the sense probes and 11.9 % of the antisense probes have signal above background and can be classified as expressed sequences. Our custom sugarcane oligonucleotide array provides sensitivity and good coverage of sugarcane transcripts for the identification of a representative proportion of natural antisense transcripts (NATs) and sense-antisense transcript pairs (SATs). The antisense transcriptome showed, in most cases, co-expression with respective sense transcripts. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11103-012-9922-1) contains supplementary material, which is available to authorized users. Springer Netherlands 2012-05-19 2012 /pmc/articles/PMC3369129/ /pubmed/22610347 http://dx.doi.org/10.1007/s11103-012-9922-1 Text en © The Author(s) 2012 https://creativecommons.org/licenses/by/4.0/ This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.
spellingShingle Article
Lembke, Carolina Gimiliani
Nishiyama, Milton Yutaka
Sato, Paloma Mieko
de Andrade, Rodrigo Fandiño
Souza, Glaucia Mendes
Identification of sense and antisense transcripts regulated by drought in sugarcane
title Identification of sense and antisense transcripts regulated by drought in sugarcane
title_full Identification of sense and antisense transcripts regulated by drought in sugarcane
title_fullStr Identification of sense and antisense transcripts regulated by drought in sugarcane
title_full_unstemmed Identification of sense and antisense transcripts regulated by drought in sugarcane
title_short Identification of sense and antisense transcripts regulated by drought in sugarcane
title_sort identification of sense and antisense transcripts regulated by drought in sugarcane
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369129/
https://www.ncbi.nlm.nih.gov/pubmed/22610347
http://dx.doi.org/10.1007/s11103-012-9922-1
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