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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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Netherlands
2012
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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. |
format | Online Article Text |
id | pubmed-3369129 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Springer Netherlands |
record_format | MEDLINE/PubMed |
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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