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Transcriptome Characterization and Sequencing-Based Identification of Salt-Responsive Genes in Millettia pinnata, a Semi-Mangrove Plant
Semi-mangroves form a group of transitional species between glycophytes and halophytes, and hold unique potential for learning molecular mechanisms underlying plant salt tolerance. Millettia pinnata is a semi-mangrove plant that can survive a wide range of saline conditions in the absence of special...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3325082/ https://www.ncbi.nlm.nih.gov/pubmed/22351699 http://dx.doi.org/10.1093/dnares/dss004 |
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author | Huang, Jianzi Lu, Xiang Yan, Hao Chen, Shouyi Zhang, Wanke Huang, Rongfeng Zheng, Yizhi |
author_facet | Huang, Jianzi Lu, Xiang Yan, Hao Chen, Shouyi Zhang, Wanke Huang, Rongfeng Zheng, Yizhi |
author_sort | Huang, Jianzi |
collection | PubMed |
description | Semi-mangroves form a group of transitional species between glycophytes and halophytes, and hold unique potential for learning molecular mechanisms underlying plant salt tolerance. Millettia pinnata is a semi-mangrove plant that can survive a wide range of saline conditions in the absence of specialized morphological and physiological traits. By employing the Illumina sequencing platform, we generated ∼192 million short reads from four cDNA libraries of M. pinnata and processed them into 108 598 unisequences with a high depth of coverage. The mean length and total length of these unisequences were 606 bp and 65.8 Mb, respectively. A total of 54 596 (50.3%) unisequences were assigned Nr annotations. Functional classification revealed the involvement of unisequences in various biological processes related to metabolism and environmental adaptation. We identified 23 815 candidate salt-responsive genes with significantly differential expression under seawater and freshwater treatments. Based on the reverse transcription–polymerase chain reaction (RT–PCR) and real-time PCR analyses, we verified the changes in expression levels for a number of candidate genes. The functional enrichment analyses for the candidate genes showed tissue-specific patterns of transcriptome remodelling upon salt stress in the roots and the leaves. The transcriptome of M. pinnata will provide valuable gene resources for future application in crop improvement. In addition, this study sets a good example for large-scale identification of salt-responsive genes in non-model organisms using the sequencing-based approach. |
format | Online Article Text |
id | pubmed-3325082 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-33250822012-04-12 Transcriptome Characterization and Sequencing-Based Identification of Salt-Responsive Genes in Millettia pinnata, a Semi-Mangrove Plant Huang, Jianzi Lu, Xiang Yan, Hao Chen, Shouyi Zhang, Wanke Huang, Rongfeng Zheng, Yizhi DNA Res Full Papers Semi-mangroves form a group of transitional species between glycophytes and halophytes, and hold unique potential for learning molecular mechanisms underlying plant salt tolerance. Millettia pinnata is a semi-mangrove plant that can survive a wide range of saline conditions in the absence of specialized morphological and physiological traits. By employing the Illumina sequencing platform, we generated ∼192 million short reads from four cDNA libraries of M. pinnata and processed them into 108 598 unisequences with a high depth of coverage. The mean length and total length of these unisequences were 606 bp and 65.8 Mb, respectively. A total of 54 596 (50.3%) unisequences were assigned Nr annotations. Functional classification revealed the involvement of unisequences in various biological processes related to metabolism and environmental adaptation. We identified 23 815 candidate salt-responsive genes with significantly differential expression under seawater and freshwater treatments. Based on the reverse transcription–polymerase chain reaction (RT–PCR) and real-time PCR analyses, we verified the changes in expression levels for a number of candidate genes. The functional enrichment analyses for the candidate genes showed tissue-specific patterns of transcriptome remodelling upon salt stress in the roots and the leaves. The transcriptome of M. pinnata will provide valuable gene resources for future application in crop improvement. In addition, this study sets a good example for large-scale identification of salt-responsive genes in non-model organisms using the sequencing-based approach. Oxford University Press 2012-04 2012-02-19 /pmc/articles/PMC3325082/ /pubmed/22351699 http://dx.doi.org/10.1093/dnares/dss004 Text en © The Author 2012. Published by Oxford University Press on behalf of Kazusa DNA Research Institute http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Full Papers Huang, Jianzi Lu, Xiang Yan, Hao Chen, Shouyi Zhang, Wanke Huang, Rongfeng Zheng, Yizhi Transcriptome Characterization and Sequencing-Based Identification of Salt-Responsive Genes in Millettia pinnata, a Semi-Mangrove Plant |
title | Transcriptome Characterization and Sequencing-Based Identification of Salt-Responsive Genes in Millettia pinnata, a Semi-Mangrove Plant |
title_full | Transcriptome Characterization and Sequencing-Based Identification of Salt-Responsive Genes in Millettia pinnata, a Semi-Mangrove Plant |
title_fullStr | Transcriptome Characterization and Sequencing-Based Identification of Salt-Responsive Genes in Millettia pinnata, a Semi-Mangrove Plant |
title_full_unstemmed | Transcriptome Characterization and Sequencing-Based Identification of Salt-Responsive Genes in Millettia pinnata, a Semi-Mangrove Plant |
title_short | Transcriptome Characterization and Sequencing-Based Identification of Salt-Responsive Genes in Millettia pinnata, a Semi-Mangrove Plant |
title_sort | transcriptome characterization and sequencing-based identification of salt-responsive genes in millettia pinnata, a semi-mangrove plant |
topic | Full Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3325082/ https://www.ncbi.nlm.nih.gov/pubmed/22351699 http://dx.doi.org/10.1093/dnares/dss004 |
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