RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress

Abstract Background To compensate for the lack of information about the molecular mechanism involved in Arundo donax L. response to salt stress, we de novo sequenced, assembled and analyzed the A. donax leaf transcriptome subjected to two levels of long-term salt stress (namely, S3 severe and S4 ext...

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Main Authors: Angelo Sicilia, Giorgio Testa, Danilo Fabrizio Santoro, Salvatore Luciano Cosentino, Angela Roberta Lo Piero
Format: Article
Language:English
Published: BMC 2019-08-01
Series:BMC Plant Biology
Subjects:
Online Access:http://link.springer.com/article/10.1186/s12870-019-1964-y
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spelling doaj-a222cc04644940e3a53cd4119b0dd5762020-11-25T03:30:27ZengBMCBMC Plant Biology1471-22292019-08-0119112410.1186/s12870-019-1964-yRNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stressAngelo Sicilia0Giorgio Testa1Danilo Fabrizio Santoro2Salvatore Luciano Cosentino3Angela Roberta Lo Piero4Department of Agriculture, Food and Environment, University of CataniaDepartment of Agriculture, Food and Environment, University of CataniaDepartment of Agriculture, Food and Environment, University of CataniaDepartment of Agriculture, Food and Environment, University of CataniaDepartment of Agriculture, Food and Environment, University of CataniaAbstract Background To compensate for the lack of information about the molecular mechanism involved in Arundo donax L. response to salt stress, we de novo sequenced, assembled and analyzed the A. donax leaf transcriptome subjected to two levels of long-term salt stress (namely, S3 severe and S4 extreme). Results The picture that emerges from the identification of differentially expressed genes is consistent with a salt dose-dependent response. Hence, a deeper re-programming of the gene expression occurs in those plants grew at extreme salt level than in those subjected to severe salt stress, probably representing for them an “emergency” state. In particular, we analyzed clusters related to salt sensory and signaling, transcription factors, hormone regulation, Reactive Oxygen Species (ROS) scavenging, osmolyte biosynthesis and biomass production, all of them showing different regulation either versus untreated plants or between the two treatments. Importantly, the photosynthesis is strongly impaired in samples treated with both levels of salinity stress. However, in extreme salt conditions, a dramatic switch from C3 Calvin cycle to C4 photosynthesis is likely to occur, this probably being the more impressive finding of our work. Conclusions Considered the distinct response to salt doses, genes either involved in severe or in extreme salt response could constitute useful markers of the physiological status of A. donax to deepen our understanding of its biology and productivity in salinized soil. Finally, many of the unigenes identified in the present study have the potential to be used for the development of A. donax varieties with improved productivity and stress tolerance, in particular the knock out of the GTL1 gene acting as negative regulator of water use efficiency has been proposed as good target for genome editing.http://link.springer.com/article/10.1186/s12870-019-1964-yBioenergy cropsDe novo assemblyGiant reedLeaf transcriptomeRNA-seqSalt stress
collection DOAJ
language English
format Article
sources DOAJ
author Angelo Sicilia
Giorgio Testa
Danilo Fabrizio Santoro
Salvatore Luciano Cosentino
Angela Roberta Lo Piero
spellingShingle Angelo Sicilia
Giorgio Testa
Danilo Fabrizio Santoro
Salvatore Luciano Cosentino
Angela Roberta Lo Piero
RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress
BMC Plant Biology
Bioenergy crops
De novo assembly
Giant reed
Leaf transcriptome
RNA-seq
Salt stress
author_facet Angelo Sicilia
Giorgio Testa
Danilo Fabrizio Santoro
Salvatore Luciano Cosentino
Angela Roberta Lo Piero
author_sort Angelo Sicilia
title RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress
title_short RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress
title_full RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress
title_fullStr RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress
title_full_unstemmed RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress
title_sort rnaseq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress
publisher BMC
series BMC Plant Biology
issn 1471-2229
publishDate 2019-08-01
description Abstract Background To compensate for the lack of information about the molecular mechanism involved in Arundo donax L. response to salt stress, we de novo sequenced, assembled and analyzed the A. donax leaf transcriptome subjected to two levels of long-term salt stress (namely, S3 severe and S4 extreme). Results The picture that emerges from the identification of differentially expressed genes is consistent with a salt dose-dependent response. Hence, a deeper re-programming of the gene expression occurs in those plants grew at extreme salt level than in those subjected to severe salt stress, probably representing for them an “emergency” state. In particular, we analyzed clusters related to salt sensory and signaling, transcription factors, hormone regulation, Reactive Oxygen Species (ROS) scavenging, osmolyte biosynthesis and biomass production, all of them showing different regulation either versus untreated plants or between the two treatments. Importantly, the photosynthesis is strongly impaired in samples treated with both levels of salinity stress. However, in extreme salt conditions, a dramatic switch from C3 Calvin cycle to C4 photosynthesis is likely to occur, this probably being the more impressive finding of our work. Conclusions Considered the distinct response to salt doses, genes either involved in severe or in extreme salt response could constitute useful markers of the physiological status of A. donax to deepen our understanding of its biology and productivity in salinized soil. Finally, many of the unigenes identified in the present study have the potential to be used for the development of A. donax varieties with improved productivity and stress tolerance, in particular the knock out of the GTL1 gene acting as negative regulator of water use efficiency has been proposed as good target for genome editing.
topic Bioenergy crops
De novo assembly
Giant reed
Leaf transcriptome
RNA-seq
Salt stress
url http://link.springer.com/article/10.1186/s12870-019-1964-y
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