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Identification of Salt-Stress-Induced Genes from the RNA-Seq Data of Reaumuria trigyna Using Differential-Display Reverse Transcription PCR

Next generation sequencing (NGS) technologies have been used to generate huge amounts of sequencing data from many organisms. However, the correct choice of candidate genes and prevention of false-positive results computed from digital gene expression (DGE) of RNA-seq data are vital when using these...

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Autores principales: Dang, Zhen-hua, Qi, Qi, Zhang, Hui-rong, Li, Hao-yu, Wu, Shu-Biao, Wang, Ying-chun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4322826/
https://www.ncbi.nlm.nih.gov/pubmed/25692129
http://dx.doi.org/10.1155/2014/381501
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author Dang, Zhen-hua
Qi, Qi
Zhang, Hui-rong
Li, Hao-yu
Wu, Shu-Biao
Wang, Ying-chun
author_facet Dang, Zhen-hua
Qi, Qi
Zhang, Hui-rong
Li, Hao-yu
Wu, Shu-Biao
Wang, Ying-chun
author_sort Dang, Zhen-hua
collection PubMed
description Next generation sequencing (NGS) technologies have been used to generate huge amounts of sequencing data from many organisms. However, the correct choice of candidate genes and prevention of false-positive results computed from digital gene expression (DGE) of RNA-seq data are vital when using these genetic resources. We indirectly identified 18 salt-stress-induced Reaumuria trigyna transcripts from the transcriptome sequencing data using differential-display reverse transcription PCR (DDRT-PCR) combined with local BLAST searches. Highly consistent with the DGE results, the quantitative real-time PCR expression patterns of these transcripts showed strong upregulation by salt stress, suggesting that these genes may play important roles in R. trigyna's survival under high-salt environments. The method presented here successfully identified responsive genes from the massive amount of RNA-seq data. Thus, we suggest that DDRT-PCR could be employed to mine NGS data in a wide range of applications in transcriptomic studies. In addition, the genes identified in the present study are promising candidates for further elucidation of the salt tolerance mechanisms in R. trigyna.
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spelling pubmed-43228262015-02-17 Identification of Salt-Stress-Induced Genes from the RNA-Seq Data of Reaumuria trigyna Using Differential-Display Reverse Transcription PCR Dang, Zhen-hua Qi, Qi Zhang, Hui-rong Li, Hao-yu Wu, Shu-Biao Wang, Ying-chun Int J Genomics Research Article Next generation sequencing (NGS) technologies have been used to generate huge amounts of sequencing data from many organisms. However, the correct choice of candidate genes and prevention of false-positive results computed from digital gene expression (DGE) of RNA-seq data are vital when using these genetic resources. We indirectly identified 18 salt-stress-induced Reaumuria trigyna transcripts from the transcriptome sequencing data using differential-display reverse transcription PCR (DDRT-PCR) combined with local BLAST searches. Highly consistent with the DGE results, the quantitative real-time PCR expression patterns of these transcripts showed strong upregulation by salt stress, suggesting that these genes may play important roles in R. trigyna's survival under high-salt environments. The method presented here successfully identified responsive genes from the massive amount of RNA-seq data. Thus, we suggest that DDRT-PCR could be employed to mine NGS data in a wide range of applications in transcriptomic studies. In addition, the genes identified in the present study are promising candidates for further elucidation of the salt tolerance mechanisms in R. trigyna. Hindawi Publishing Corporation 2014 2014-11-26 /pmc/articles/PMC4322826/ /pubmed/25692129 http://dx.doi.org/10.1155/2014/381501 Text en Copyright © 2014 Zhen-hua Dang 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
Dang, Zhen-hua
Qi, Qi
Zhang, Hui-rong
Li, Hao-yu
Wu, Shu-Biao
Wang, Ying-chun
Identification of Salt-Stress-Induced Genes from the RNA-Seq Data of Reaumuria trigyna Using Differential-Display Reverse Transcription PCR
title Identification of Salt-Stress-Induced Genes from the RNA-Seq Data of Reaumuria trigyna Using Differential-Display Reverse Transcription PCR
title_full Identification of Salt-Stress-Induced Genes from the RNA-Seq Data of Reaumuria trigyna Using Differential-Display Reverse Transcription PCR
title_fullStr Identification of Salt-Stress-Induced Genes from the RNA-Seq Data of Reaumuria trigyna Using Differential-Display Reverse Transcription PCR
title_full_unstemmed Identification of Salt-Stress-Induced Genes from the RNA-Seq Data of Reaumuria trigyna Using Differential-Display Reverse Transcription PCR
title_short Identification of Salt-Stress-Induced Genes from the RNA-Seq Data of Reaumuria trigyna Using Differential-Display Reverse Transcription PCR
title_sort identification of salt-stress-induced genes from the rna-seq data of reaumuria trigyna using differential-display reverse transcription pcr
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4322826/
https://www.ncbi.nlm.nih.gov/pubmed/25692129
http://dx.doi.org/10.1155/2014/381501
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