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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| Format: | Article |
| Language: | English |
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Wiley
2014-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2014/381501 |
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| author | Zhen-hua Dang Qi Qi Hui-rong Zhang Hao-yu Li Shu-Biao Wu Ying-chun Wang |
| author_facet | Zhen-hua Dang Qi Qi Hui-rong Zhang Hao-yu Li Shu-Biao Wu Ying-chun Wang |
| author_sort | Zhen-hua Dang |
| collection | DOAJ |
| 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. |
| format | Article |
| id | doaj-art-2f33fa2dcf11495d894538a3b2b11c6e |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2014-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-2f33fa2dcf11495d894538a3b2b11c6e2025-08-20T03:55:16ZengWileyInternational Journal of Genomics2314-436X2314-43782014-01-01201410.1155/2014/381501381501Identification of Salt-Stress-Induced Genes from the RNA-Seq Data of Reaumuria trigyna Using Differential-Display Reverse Transcription PCRZhen-hua Dang0Qi Qi1Hui-rong Zhang2Hao-yu Li3Shu-Biao Wu4Ying-chun Wang5Key Laboratory of Herbage & Endemic Crop Biotechnology and College of Life Sciences, Inner Mongolia University, Hohhot 010021, ChinaKey Laboratory of Herbage & Endemic Crop Biotechnology and College of Life Sciences, Inner Mongolia University, Hohhot 010021, ChinaKey Laboratory of Herbage & Endemic Crop Biotechnology and College of Life Sciences, Inner Mongolia University, Hohhot 010021, ChinaKey Laboratory of Herbage & Endemic Crop Biotechnology and College of Life Sciences, Inner Mongolia University, Hohhot 010021, ChinaSchool of Environmental and Rural Science, University of New England, Armidale, NSW 2351, AustraliaKey Laboratory of Herbage & Endemic Crop Biotechnology and College of Life Sciences, Inner Mongolia University, Hohhot 010021, ChinaNext 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.http://dx.doi.org/10.1155/2014/381501 |
| spellingShingle | Zhen-hua Dang Qi Qi Hui-rong Zhang Hao-yu Li Shu-Biao Wu Ying-chun Wang Identification of Salt-Stress-Induced Genes from the RNA-Seq Data of Reaumuria trigyna Using Differential-Display Reverse Transcription PCR International Journal of Genomics |
| 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 |
| url | http://dx.doi.org/10.1155/2014/381501 |
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