Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance
Identifieur interne : 000394 ( Main/Exploration ); précédent : 000393; suivant : 000395Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance
Auteurs : Joann Diray-Arce [États-Unis] ; Mark Clement [États-Unis] ; Bilquees Gul [Pakistan] ; M Ajmal Khan [Qatar] ; Brent L. Nielsen [États-Unis]Source :
- BMC Genomics [ 1471-2164 ] ; 2015.
Abstract
Improvement of crop production is needed to feed the growing world population as the amount and quality of agricultural land decreases and soil salinity increases. This has stimulated research on salt tolerance in plants. Most crops tolerate a limited amount of salt to survive and produce biomass, while halophytes (salt-tolerant plants) have the ability to grow with saline water utilizing specific biochemical mechanisms. However, little is known about the genes involved in salt tolerance. We have characterized the transcriptome of
Twelve sequencing libraries prepared from control (0 mM NaCl treated) and optimum (300 mM NaCl treated) plants were sequenced using Illumina Hiseq 2000 to investigate differential gene expression between shoots and roots of
This work has identified potential genes involved in salt tolerance in
The online version of this article (doi:10.1186/s12864-015-1553-x) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-015-1553-x
PubMed: 25943316
PubMed Central: 4422317
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Transcriptome assembly, profiling and differential gene expression analysis of the halophyte <italic>Suaeda fruticosa</italic> provides insights into salt tolerance</title><author><name sortKey="Diray Arce, Joann" sort="Diray Arce, Joann" uniqKey="Diray Arce J" first="Joann" last="Diray-Arce">Joann Diray-Arce</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Utah</region></placeName><wicri:cityArea>Department of Microbiology and Molecular Biology, Brigham Young University, Provo</wicri:cityArea></affiliation></author><author><name sortKey="Clement, Mark" sort="Clement, Mark" uniqKey="Clement M" first="Mark" last="Clement">Mark Clement</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Department of Computer Science, Brigham Young University, Provo, UT 84602 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Utah</region></placeName><wicri:cityArea>Department of Computer Science, Brigham Young University, Provo</wicri:cityArea></affiliation></author><author><name sortKey="Gul, Bilquees" sort="Gul, Bilquees" uniqKey="Gul B" first="Bilquees" last="Gul">Bilquees Gul</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, Pakistan</nlm:aff><country xml:lang="fr">Pakistan</country><wicri:regionArea>Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi</wicri:regionArea><wicri:noRegion>Karachi</wicri:noRegion></affiliation></author><author><name sortKey="Khan, M Ajmal" sort="Khan, M Ajmal" uniqKey="Khan M" first="M Ajmal" last="Khan">M Ajmal Khan</name><affiliation wicri:level="1"><nlm:aff id="Aff4">College of Arts and Sciences, Qatar University, Doha, Qatar</nlm:aff><country xml:lang="fr">Qatar</country><wicri:regionArea>College of Arts and Sciences, Qatar University, Doha</wicri:regionArea><wicri:noRegion>Doha</wicri:noRegion></affiliation></author><author><name sortKey="Nielsen, Brent L" sort="Nielsen, Brent L" uniqKey="Nielsen B" first="Brent L" last="Nielsen">Brent L. Nielsen</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Utah</region></placeName><wicri:cityArea>Department of Microbiology and Molecular Biology, Brigham Young University, Provo</wicri:cityArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25943316</idno><idno type="pmc">4422317</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4422317</idno><idno type="RBID">PMC:4422317</idno><idno type="doi">10.1186/s12864-015-1553-x</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000584</idno><idno type="wicri:Area/Pmc/Curation">000583</idno><idno type="wicri:Area/Pmc/Checkpoint">000308</idno><idno type="wicri:Area/Ncbi/Merge">001B16</idno><idno type="wicri:Area/Ncbi/Curation">001B16</idno><idno type="wicri:Area/Ncbi/Checkpoint">001B16</idno><idno type="wicri:Area/Main/Merge">000394</idno><idno type="wicri:Area/Main/Curation">000394</idno><idno type="wicri:Area/Main/Exploration">000394</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Transcriptome assembly, profiling and differential gene expression analysis of the halophyte <italic>Suaeda fruticosa</italic> provides insights into salt tolerance</title><author><name sortKey="Diray Arce, Joann" sort="Diray Arce, Joann" uniqKey="Diray Arce J" first="Joann" last="Diray-Arce">Joann Diray-Arce</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Utah</region></placeName><wicri:cityArea>Department of Microbiology and Molecular Biology, Brigham Young University, Provo</wicri:cityArea></affiliation></author><author><name sortKey="Clement, Mark" sort="Clement, Mark" uniqKey="Clement M" first="Mark" last="Clement">Mark Clement</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Department of Computer Science, Brigham Young University, Provo, UT 84602 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Utah</region></placeName><wicri:cityArea>Department of Computer Science, Brigham Young University, Provo</wicri:cityArea></affiliation></author><author><name sortKey="Gul, Bilquees" sort="Gul, Bilquees" uniqKey="Gul B" first="Bilquees" last="Gul">Bilquees Gul</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, Pakistan</nlm:aff><country xml:lang="fr">Pakistan</country><wicri:regionArea>Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi</wicri:regionArea><wicri:noRegion>Karachi</wicri:noRegion></affiliation></author><author><name sortKey="Khan, M Ajmal" sort="Khan, M Ajmal" uniqKey="Khan M" first="M Ajmal" last="Khan">M Ajmal Khan</name><affiliation wicri:level="1"><nlm:aff id="Aff4">College of Arts and Sciences, Qatar University, Doha, Qatar</nlm:aff><country xml:lang="fr">Qatar</country><wicri:regionArea>College of Arts and Sciences, Qatar University, Doha</wicri:regionArea><wicri:noRegion>Doha</wicri:noRegion></affiliation></author><author><name sortKey="Nielsen, Brent L" sort="Nielsen, Brent L" uniqKey="Nielsen B" first="Brent L" last="Nielsen">Brent L. Nielsen</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Utah</region></placeName><wicri:cityArea>Department of Microbiology and Molecular Biology, Brigham Young University, Provo</wicri:cityArea></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Improvement of crop production is needed to feed the growing world population as the amount and quality of agricultural land decreases and soil salinity increases. This has stimulated research on salt tolerance in plants. Most crops tolerate a limited amount of salt to survive and produce biomass, while halophytes (salt-tolerant plants) have the ability to grow with saline water utilizing specific biochemical mechanisms. However, little is known about the genes involved in salt tolerance. We have characterized the transcriptome of <italic>Suaeda fruticosa</italic>, a halophyte that has the ability to sequester salts in its leaves. <italic>Suaeda fruticosa</italic> is an annual shrub in the family Chenopodiaceae found in coastal and inland regions of Pakistan and Mediterranean shores. This plant is an obligate halophyte that grows optimally from 200–400 mM NaCl and can grow at up to 1000 mM NaCl. High throughput sequencing technology was performed to provide understanding of genes involved in the salt tolerance mechanism. De novo assembly of the transcriptome and analysis has allowed identification of differentially expressed and unique genes present in this non-conventional crop.</p></sec><sec><title>Results</title><p>Twelve sequencing libraries prepared from control (0 mM NaCl treated) and optimum (300 mM NaCl treated) plants were sequenced using Illumina Hiseq 2000 to investigate differential gene expression between shoots and roots of <italic>Suaeda fruticosa</italic>. The transcriptome was assembled de novo using Velvet and Oases k-45 and clustered using CDHIT-EST. There are 54,526 unigenes; among these 475 genes are downregulated and 44 are upregulated when samples from plants grown under optimal salt are compared with those grown without salt. BLAST analysis identified the differentially expressed genes, which were categorized in gene ontology terms and their pathways.</p></sec><sec><title>Conclusions</title><p>This work has identified potential genes involved in salt tolerance in <italic>Suaeda fruticosa</italic>, and has provided an outline of tools to use for de novo transcriptome analysis. The assemblies that were used provide coverage of a considerable proportion of the transcriptome, which allows analysis of differential gene expression and identification of genes that may be involved in salt tolerance. The transcriptome may serve as a reference sequence for study of other succulent halophytes.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-015-1553-x) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Labidi, N" uniqKey="Labidi N">N Labidi</name></author><author><name sortKey="Ammari, M" uniqKey="Ammari M">M Ammari</name></author><author><name sortKey="Mssedi, D" uniqKey="Mssedi D">D Mssedi</name></author><author><name sortKey="Benzerti, M" uniqKey="Benzerti M">M Benzerti</name></author><author><name sortKey="Snoussi, S" uniqKey="Snoussi S">S Snoussi</name></author><author><name sortKey="Abdelly, C" uniqKey="Abdelly C">C Abdelly</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Weber, Dj" 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uniqKey="Chen J">J Chen</name></author><author><name sortKey="Xie, W" uniqKey="Xie W">W Xie</name></author><author><name sortKey="Wang, L" uniqKey="Wang L">L Wang</name></author><author><name sortKey="Zhang, Q" uniqKey="Zhang Q">Q Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lopes Caitar, V" uniqKey="Lopes Caitar V">V Lopes-Caitar</name></author><author><name sortKey="De Carvalho, M" uniqKey="De Carvalho M">M de Carvalho</name></author><author><name sortKey="Darben, L" uniqKey="Darben L">L Darben</name></author><author><name sortKey="Kuwahara, M" uniqKey="Kuwahara M">M Kuwahara</name></author><author><name sortKey="Nepomuceno, A" uniqKey="Nepomuceno A">A Nepomuceno</name></author><author><name sortKey="Dias, W" uniqKey="Dias W">W Dias</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Pakistan</li><li>Qatar</li><li>États-Unis</li></country><region><li>Utah</li></region></list><tree><country name="États-Unis"><region name="Utah"><name sortKey="Diray Arce, Joann" sort="Diray Arce, Joann" uniqKey="Diray Arce J" first="Joann" last="Diray-Arce">Joann Diray-Arce</name></region><name sortKey="Clement, Mark" sort="Clement, Mark" uniqKey="Clement M" first="Mark" last="Clement">Mark Clement</name><name sortKey="Nielsen, Brent L" sort="Nielsen, Brent L" uniqKey="Nielsen B" first="Brent L" last="Nielsen">Brent L. Nielsen</name></country><country name="Pakistan"><noRegion><name sortKey="Gul, Bilquees" sort="Gul, Bilquees" uniqKey="Gul B" first="Bilquees" last="Gul">Bilquees Gul</name></noRegion></country><country name="Qatar"><noRegion><name sortKey="Khan, M Ajmal" sort="Khan, M Ajmal" uniqKey="Khan M" first="M Ajmal" last="Khan">M Ajmal Khan</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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