de novo transcriptomic profiling of differentially expressed genes in grass halophyte Urochondra setulosa under high salinity

Abstract Soil salinity is one of the major limiting factors for crop productivity across the world. Halophytes have recently been a source of attraction for exploring the survival and tolerance mechanisms at extreme saline conditions. Urochondra setulosa is one of the obligate grass halophyte that c...

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Autores principales:	Anita Mann, Naresh Kumar, Ashwani Kumar, Charu Lata, Arvind Kumar, Babu Lal Meena, Dwijesh Mishra, Monendra Grover, Sonam Gaba, C. Parameswaran, Nitin Mantri
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d54db91b408845299f1246b1434e4fc5
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spelling	oai:doaj.org-article:d54db91b408845299f1246b1434e4fc52021-12-02T11:35:59Zde novo transcriptomic profiling of differentially expressed genes in grass halophyte Urochondra setulosa under high salinity10.1038/s41598-021-85220-72045-2322https://doaj.org/article/d54db91b408845299f1246b1434e4fc52021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85220-7https://doaj.org/toc/2045-2322Abstract Soil salinity is one of the major limiting factors for crop productivity across the world. Halophytes have recently been a source of attraction for exploring the survival and tolerance mechanisms at extreme saline conditions. Urochondra setulosa is one of the obligate grass halophyte that can survive in up to 1000 mM NaCl. The de novo transcriptome of Urochondra leaves at different salt concentrations of 300–500 mM NaCl was generated on Illumina HiSeq. Approximately 352.78 million high quality reads with an average contig length of 1259 bp were assembled de novo. A total of 120,231 unigenes were identified. On an average, 65% unigenes were functionally annotated to known proteins. Approximately 35% unigenes were specific to Urochondra. Differential expression revealed significant enrichment (P < 0.05) of transcription factors, transporters and metabolites suggesting the transcriptional regulation of ion homeostasis and signalling at high salt concentrations in this grass. Also, about 143 unigenes were biologically related to salt stress responsive genes. Randomly selected genes of important pathways were validated for functional characterization. This study provides useful information to understand the gene regulation at extremely saline levels. The study offers the first comprehensive evaluation of Urochondra setulosa leaf transcriptome. Examining non-model organisms that can survive in harsh environment can provide novel insights into the stress coping mechanisms which can be useful to develop improved agricultural crops.Anita MannNaresh KumarAshwani KumarCharu LataArvind KumarBabu Lal MeenaDwijesh MishraMonendra GroverSonam GabaC. ParameswaranNitin MantriNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Anita Mann Naresh Kumar Ashwani Kumar Charu Lata Arvind Kumar Babu Lal Meena Dwijesh Mishra Monendra Grover Sonam Gaba C. Parameswaran Nitin Mantri de novo transcriptomic profiling of differentially expressed genes in grass halophyte Urochondra setulosa under high salinity
description	Abstract Soil salinity is one of the major limiting factors for crop productivity across the world. Halophytes have recently been a source of attraction for exploring the survival and tolerance mechanisms at extreme saline conditions. Urochondra setulosa is one of the obligate grass halophyte that can survive in up to 1000 mM NaCl. The de novo transcriptome of Urochondra leaves at different salt concentrations of 300–500 mM NaCl was generated on Illumina HiSeq. Approximately 352.78 million high quality reads with an average contig length of 1259 bp were assembled de novo. A total of 120,231 unigenes were identified. On an average, 65% unigenes were functionally annotated to known proteins. Approximately 35% unigenes were specific to Urochondra. Differential expression revealed significant enrichment (P < 0.05) of transcription factors, transporters and metabolites suggesting the transcriptional regulation of ion homeostasis and signalling at high salt concentrations in this grass. Also, about 143 unigenes were biologically related to salt stress responsive genes. Randomly selected genes of important pathways were validated for functional characterization. This study provides useful information to understand the gene regulation at extremely saline levels. The study offers the first comprehensive evaluation of Urochondra setulosa leaf transcriptome. Examining non-model organisms that can survive in harsh environment can provide novel insights into the stress coping mechanisms which can be useful to develop improved agricultural crops.
format	article
author	Anita Mann Naresh Kumar Ashwani Kumar Charu Lata Arvind Kumar Babu Lal Meena Dwijesh Mishra Monendra Grover Sonam Gaba C. Parameswaran Nitin Mantri
author_facet	Anita Mann Naresh Kumar Ashwani Kumar Charu Lata Arvind Kumar Babu Lal Meena Dwijesh Mishra Monendra Grover Sonam Gaba C. Parameswaran Nitin Mantri
author_sort	Anita Mann
title	de novo transcriptomic profiling of differentially expressed genes in grass halophyte Urochondra setulosa under high salinity
title_short	de novo transcriptomic profiling of differentially expressed genes in grass halophyte Urochondra setulosa under high salinity
title_full	de novo transcriptomic profiling of differentially expressed genes in grass halophyte Urochondra setulosa under high salinity
title_fullStr	de novo transcriptomic profiling of differentially expressed genes in grass halophyte Urochondra setulosa under high salinity
title_full_unstemmed	de novo transcriptomic profiling of differentially expressed genes in grass halophyte Urochondra setulosa under high salinity
title_sort	de novo transcriptomic profiling of differentially expressed genes in grass halophyte urochondra setulosa under high salinity
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/d54db91b408845299f1246b1434e4fc5
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de novo transcriptomic profiling of differentially expressed genes in grass halophyte Urochondra setulosa under high salinity

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