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De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress

The study of salt tolerance mechanisms in halophyte plants can provide valuable information for crop breeding and plant engineering programs. The aim of the present study was to investigate whole transcriptome analysis of Aeluropus littoralis in response to salinity stress (200 and 400 mM NaCl) by d...

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Autores principales: Younesi-Melerdi, Elham, Nematzadeh, Ghorban-Ali, Pakdin-Parizi, Ali, Bakhtiarizadeh, Mohammad Reza, Motahari, Seyed Abolfazl
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7272644/
https://www.ncbi.nlm.nih.gov/pubmed/32499577
http://dx.doi.org/10.1038/s41598-020-65947-5
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author Younesi-Melerdi, Elham
Nematzadeh, Ghorban-Ali
Pakdin-Parizi, Ali
Bakhtiarizadeh, Mohammad Reza
Motahari, Seyed Abolfazl
author_facet Younesi-Melerdi, Elham
Nematzadeh, Ghorban-Ali
Pakdin-Parizi, Ali
Bakhtiarizadeh, Mohammad Reza
Motahari, Seyed Abolfazl
author_sort Younesi-Melerdi, Elham
collection PubMed
description The study of salt tolerance mechanisms in halophyte plants can provide valuable information for crop breeding and plant engineering programs. The aim of the present study was to investigate whole transcriptome analysis of Aeluropus littoralis in response to salinity stress (200 and 400 mM NaCl) by de novo RNA-sequencing. To assemble the transcriptome, Trinity v2.4.0 and Bridger tools, were comparatively used with two k-mer sizes (25 and 32 bp). The de novo assembled transcriptome by Bridger (k-mer 32) was chosen as final assembly for subsequent analysis. In general, 103290 transcripts were obtained. The differential expression analysis (log(2)(FC) > 1 and FDR < 0.01) showed that 1861 transcripts expressed differentially, including169 up and 316 down-regulated transcripts in 200 mM NaCl treatment and 1035 up and 430 down-regulated transcripts in 400 mM NaCl treatment compared to control. In addition, 89 transcripts were common in both treatments. The most important over-represented terms in the GO analysis of differentially expressed genes (FDR < 0.05) were chitin response, response to abscisic acid, and regulation of jasmonic acid mediated signaling pathway under 400 mM NaCl treatment and cell cycle, cell division, and mitotic cell cycle process under 200 mM treatment. In addition, the phosphatidylcholine biosynthetic process term was common in both salt treatments. Interestingly, under 400 mM salt treatment, the PRC1 complex that contributes to chromatin remodeling was also enriched along with vacuole as a general salinity stress responsive cell component. Among enriched pathways, the MAPK signaling pathway (ko04016) and phytohormone signal transduction (ko04075) were significantly enriched in 400 mM NaCl treatment, whereas DNA replication (ko03032) was the only pathway that significantly enriched in 200 mM NaCl treatment. Finally, our findings indicate the salt-concentration depended responses of A. littoralis, which well-known salinity stress-related pathways are induced in 400 mM NaCl, while less considered pathways, e.g. cell cycle and DNA replication, are highlighted under 200 mM NaCl treatment.
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spelling pubmed-72726442020-06-05 De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress Younesi-Melerdi, Elham Nematzadeh, Ghorban-Ali Pakdin-Parizi, Ali Bakhtiarizadeh, Mohammad Reza Motahari, Seyed Abolfazl Sci Rep Article The study of salt tolerance mechanisms in halophyte plants can provide valuable information for crop breeding and plant engineering programs. The aim of the present study was to investigate whole transcriptome analysis of Aeluropus littoralis in response to salinity stress (200 and 400 mM NaCl) by de novo RNA-sequencing. To assemble the transcriptome, Trinity v2.4.0 and Bridger tools, were comparatively used with two k-mer sizes (25 and 32 bp). The de novo assembled transcriptome by Bridger (k-mer 32) was chosen as final assembly for subsequent analysis. In general, 103290 transcripts were obtained. The differential expression analysis (log(2)(FC) > 1 and FDR < 0.01) showed that 1861 transcripts expressed differentially, including169 up and 316 down-regulated transcripts in 200 mM NaCl treatment and 1035 up and 430 down-regulated transcripts in 400 mM NaCl treatment compared to control. In addition, 89 transcripts were common in both treatments. The most important over-represented terms in the GO analysis of differentially expressed genes (FDR < 0.05) were chitin response, response to abscisic acid, and regulation of jasmonic acid mediated signaling pathway under 400 mM NaCl treatment and cell cycle, cell division, and mitotic cell cycle process under 200 mM treatment. In addition, the phosphatidylcholine biosynthetic process term was common in both salt treatments. Interestingly, under 400 mM salt treatment, the PRC1 complex that contributes to chromatin remodeling was also enriched along with vacuole as a general salinity stress responsive cell component. Among enriched pathways, the MAPK signaling pathway (ko04016) and phytohormone signal transduction (ko04075) were significantly enriched in 400 mM NaCl treatment, whereas DNA replication (ko03032) was the only pathway that significantly enriched in 200 mM NaCl treatment. Finally, our findings indicate the salt-concentration depended responses of A. littoralis, which well-known salinity stress-related pathways are induced in 400 mM NaCl, while less considered pathways, e.g. cell cycle and DNA replication, are highlighted under 200 mM NaCl treatment. Nature Publishing Group UK 2020-06-04 /pmc/articles/PMC7272644/ /pubmed/32499577 http://dx.doi.org/10.1038/s41598-020-65947-5 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Younesi-Melerdi, Elham
Nematzadeh, Ghorban-Ali
Pakdin-Parizi, Ali
Bakhtiarizadeh, Mohammad Reza
Motahari, Seyed Abolfazl
De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress
title De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress
title_full De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress
title_fullStr De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress
title_full_unstemmed De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress
title_short De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress
title_sort de novo rna sequencing analysis of aeluropus littoralis halophyte plant under salinity stress
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7272644/
https://www.ncbi.nlm.nih.gov/pubmed/32499577
http://dx.doi.org/10.1038/s41598-020-65947-5
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