Identification of novel drought-responsive microRNAs and trans-acting siRNAs from Sorghum bicolor (L.) Moench by high-throughput sequencing analysis
Identifieur interne : 000073 ( Pmc/Curation ); précédent : 000072; suivant : 000074Identification of novel drought-responsive microRNAs and trans-acting siRNAs from Sorghum bicolor (L.) Moench by high-throughput sequencing analysis
Auteurs : Amit Katiyar [Inde] ; Shuchi Smita [Inde] ; Senthilkumar K. Muthusamy [Inde] ; Viswanathan Chinnusamy [Inde] ; Dev M. Pandey [Inde] ; Kailash C. Bansal [Inde]Source :
- Frontiers in Plant Science [ 1664-462X ] ; 2015.
Abstract
Small non-coding RNAs (sRNAs) namely microRNAs (miRNAs) and trans-acting small interfering RNAs (tasi-RNAs) play a crucial role in post-transcriptional regulation of gene expression and thus the control plant development and stress responses. In order to identify drought-responsive miRNAs and tasi-RNAs in sorghum, we constructed small RNA libraries from a drought tolerant (M35-1) and susceptible (C43) sorghum genotypes grown under control and drought stress conditions, and sequenced by Illumina Genome Analyzer IIx. Ninety seven conserved and 526 novel miRNAs representing 472 unique miRNA families were identified from sorghum. Ninety-six unique miRNAs were found to be regulated by drought stress, of which 32 were up- and 49 were down-regulated (fold change ≥ 2 or ≤ −2) at least in one genotype, while the remaining 15 miRNAs showed contrasting drought-regulated expression pattern between genotypes. A maximum of 17 and 18 miRNAs was differentially regulated under drought stress condition in the sensitive and tolerant genotypes, respectively. These results suggest that genotype dependent stress responsive regulation of miRNAs may contribute, at least in part, to the differential drought tolerance of sorghum genotypes. We also identified two miR390-directed
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DOI: 10.3389/fpls.2015.00506
PubMed: 26236318
PubMed Central: 4504434
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Moench by high-throughput sequencing analysis</title><author><name sortKey="Katiyar, Amit" sort="Katiyar, Amit" uniqKey="Katiyar A" first="Amit" last="Katiyar">Amit Katiyar</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Biotechnology, Birla Institute of Technology, Mesra</institution><country>Ranchi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Smita, Shuchi" sort="Smita, Shuchi" uniqKey="Smita S" first="Shuchi" last="Smita">Shuchi Smita</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Biotechnology, Birla Institute of Technology, Mesra</institution><country>Ranchi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Muthusamy, Senthilkumar K" sort="Muthusamy, Senthilkumar K" uniqKey="Muthusamy S" first="Senthilkumar K." last="Muthusamy">Senthilkumar K. Muthusamy</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Indian Council of Agricultural Research-National Research Centre on Plant Biotechnology</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Chinnusamy, Viswanathan" sort="Chinnusamy, Viswanathan" uniqKey="Chinnusamy V" first="Viswanathan" last="Chinnusamy">Viswanathan Chinnusamy</name><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>Division of Plant Physiology, Indian Council of Agricultural Research-Indian Agricultural Research Institute</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Pandey, Dev M" sort="Pandey, Dev M" uniqKey="Pandey D" first="Dev M." last="Pandey">Dev M. Pandey</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Biotechnology, Birla Institute of Technology, Mesra</institution><country>Ranchi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Bansal, Kailash C" sort="Bansal, Kailash C" uniqKey="Bansal K" first="Kailash C." last="Bansal">Kailash C. Bansal</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26236318</idno><idno type="pmc">4504434</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4504434</idno><idno type="RBID">PMC:4504434</idno><idno type="doi">10.3389/fpls.2015.00506</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000073</idno><idno type="wicri:Area/Pmc/Curation">000073</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification of novel drought-responsive microRNAs and trans-acting siRNAs from <italic>Sorghum bicolor</italic> (L.) Moench by high-throughput sequencing analysis</title><author><name sortKey="Katiyar, Amit" sort="Katiyar, Amit" uniqKey="Katiyar A" first="Amit" last="Katiyar">Amit Katiyar</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Biotechnology, Birla Institute of Technology, Mesra</institution><country>Ranchi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Smita, Shuchi" sort="Smita, Shuchi" uniqKey="Smita S" first="Shuchi" last="Smita">Shuchi Smita</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Biotechnology, Birla Institute of Technology, Mesra</institution><country>Ranchi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Muthusamy, Senthilkumar K" sort="Muthusamy, Senthilkumar K" uniqKey="Muthusamy S" first="Senthilkumar K." last="Muthusamy">Senthilkumar K. Muthusamy</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Indian Council of Agricultural Research-National Research Centre on Plant Biotechnology</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Chinnusamy, Viswanathan" sort="Chinnusamy, Viswanathan" uniqKey="Chinnusamy V" first="Viswanathan" last="Chinnusamy">Viswanathan Chinnusamy</name><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>Division of Plant Physiology, Indian Council of Agricultural Research-Indian Agricultural Research Institute</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Pandey, Dev M" sort="Pandey, Dev M" uniqKey="Pandey D" first="Dev M." last="Pandey">Dev M. Pandey</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Biotechnology, Birla Institute of Technology, Mesra</institution><country>Ranchi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Bansal, Kailash C" sort="Bansal, Kailash C" uniqKey="Bansal K" first="Kailash C." last="Bansal">Kailash C. Bansal</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in Plant Science</title><idno type="eISSN">1664-462X</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Small non-coding RNAs (sRNAs) namely microRNAs (miRNAs) and trans-acting small interfering RNAs (tasi-RNAs) play a crucial role in post-transcriptional regulation of gene expression and thus the control plant development and stress responses. In order to identify drought-responsive miRNAs and tasi-RNAs in sorghum, we constructed small RNA libraries from a drought tolerant (M35-1) and susceptible (C43) sorghum genotypes grown under control and drought stress conditions, and sequenced by Illumina Genome Analyzer IIx. Ninety seven conserved and 526 novel miRNAs representing 472 unique miRNA families were identified from sorghum. Ninety-six unique miRNAs were found to be regulated by drought stress, of which 32 were up- and 49 were down-regulated (fold change ≥ 2 or ≤ −2) at least in one genotype, while the remaining 15 miRNAs showed contrasting drought-regulated expression pattern between genotypes. A maximum of 17 and 18 miRNAs was differentially regulated under drought stress condition in the sensitive and tolerant genotypes, respectively. These results suggest that genotype dependent stress responsive regulation of miRNAs may contribute, at least in part, to the differential drought tolerance of sorghum genotypes. We also identified two miR390-directed <italic>TAS3</italic> gene homologs and the auxin response factors as tasi-RNA targets. We predicted more than 1300 unique target genes for the novel and conserved miRNAs. These target genes were predicted to be involved in different cellular, metabolic, response to stimulus, biological regulation, and developmental processes. Genome-wide identification of stress-responsive miRNAs, tasi-RNAs and their targets identified in this study will be useful in unraveling the molecular mechanisms underlying drought stress responses and genetic improvement of biomass production and stress tolerance in sorghum.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Allen, E" uniqKey="Allen E">E. Allen</name></author><author><name sortKey="Xie, Z" uniqKey="Xie Z">Z. Xie</name></author><author><name sortKey="Gustafson, A M" uniqKey="Gustafson A">A. M. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Plant Sci</journal-id><journal-id journal-id-type="iso-abbrev">Front Plant Sci</journal-id><journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id><journal-title-group><journal-title>Frontiers in Plant Science</journal-title></journal-title-group><issn pub-type="epub">1664-462X</issn><publisher><publisher-name>Frontiers Media S.A.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26236318</article-id><article-id pub-id-type="pmc">4504434</article-id><article-id pub-id-type="doi">10.3389/fpls.2015.00506</article-id><article-categories><subj-group subj-group-type="heading"><subject>Plant Science</subject><subj-group><subject>Original Research</subject></subj-group></subj-group></article-categories><title-group><article-title>Identification of novel drought-responsive microRNAs and trans-acting siRNAs from <italic>Sorghum bicolor</italic> (L.) Moench by high-throughput sequencing analysis</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Katiyar</surname><given-names>Amit</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="author-notes" rid="fn003"><sup>†</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/213655/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Smita</surname><given-names>Shuchi</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="author-notes" rid="fn004"><sup>†</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/251718/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Muthusamy</surname><given-names>Senthilkumar K.</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref><xref ref-type="author-notes" rid="fn005"><sup>†</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/247225/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Chinnusamy</surname><given-names>Viswanathan</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/87006/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Pandey</surname><given-names>Dev M.</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/44140/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Bansal</surname><given-names>Kailash C.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><sup>1</sup><institution>Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources</institution><country>New Delhi, India</country></aff><aff id="aff2"><sup>2</sup><institution>Department of Biotechnology, Birla Institute of Technology, Mesra</institution><country>Ranchi, India</country></aff><aff id="aff3"><sup>3</sup><institution>Indian Council of Agricultural Research-National Research Centre on Plant Biotechnology</institution><country>New Delhi, India</country></aff><aff id="aff4"><sup>4</sup><institution>Division of Plant Physiology, Indian Council of Agricultural Research-Indian Agricultural Research Institute</institution><country>New Delhi, India</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: Rajeev K. Varshney, International Crops Research Institute for the Semi-Arid Tropics, India</p></fn><fn fn-type="edited-by"><p>Reviewed by: Eduard Akhunov, Kansas State University, USA; Manoj K. Sharma, Jawaharlal Nehru University, India</p></fn><corresp id="fn001">*Correspondence: Kailash C. Bansal, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources (NBPGR), IARI Pusa Campus, New Delhi 110012, India <email xlink:type="simple">kailashbansal@hotmail.com</email></corresp><fn fn-type="other" id="fn002"><p>This article was submitted to Plant Genetics and Genomics, a section of the journal Frontiers in Plant Science</p></fn><fn fn-type="present-address" id="fn003"><p>†Present Address: Amit Katiyar, Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India</p></fn><fn fn-type="present-address" id="fn004"><p>Shuchi Smita, Centre for Agricultural Bio-Informatics, Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India</p></fn><fn fn-type="present-address" id="fn005"><p>Senthilkumar K. Muthusamy, Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Karnal, India</p></fn></author-notes><pub-date pub-type="epub"><day>09</day><month>7</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>6</volume><elocation-id>506</elocation-id><history><date date-type="received"><day>24</day><month>2</month><year>2015</year></date><date date-type="accepted"><day>23</day><month>6</month><year>2015</year></date></history><permissions><copyright-statement>Copyright © 2015 Katiyar, Smita, Muthusamy, Chinnusamy, Pandey and Bansal.</copyright-statement><copyright-year>2015</copyright-year><copyright-holder>Katiyar, Smita, Muthusamy, Chinnusamy, Pandey and Bansal</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p></license></permissions><abstract><p>Small non-coding RNAs (sRNAs) namely microRNAs (miRNAs) and trans-acting small interfering RNAs (tasi-RNAs) play a crucial role in post-transcriptional regulation of gene expression and thus the control plant development and stress responses. In order to identify drought-responsive miRNAs and tasi-RNAs in sorghum, we constructed small RNA libraries from a drought tolerant (M35-1) and susceptible (C43) sorghum genotypes grown under control and drought stress conditions, and sequenced by Illumina Genome Analyzer IIx. Ninety seven conserved and 526 novel miRNAs representing 472 unique miRNA families were identified from sorghum. Ninety-six unique miRNAs were found to be regulated by drought stress, of which 32 were up- and 49 were down-regulated (fold change ≥ 2 or ≤ −2) at least in one genotype, while the remaining 15 miRNAs showed contrasting drought-regulated expression pattern between genotypes. A maximum of 17 and 18 miRNAs was differentially regulated under drought stress condition in the sensitive and tolerant genotypes, respectively. These results suggest that genotype dependent stress responsive regulation of miRNAs may contribute, at least in part, to the differential drought tolerance of sorghum genotypes. We also identified two miR390-directed <italic>TAS3</italic> gene homologs and the auxin response factors as tasi-RNA targets. We predicted more than 1300 unique target genes for the novel and conserved miRNAs. These target genes were predicted to be involved in different cellular, metabolic, response to stimulus, biological regulation, and developmental processes. Genome-wide identification of stress-responsive miRNAs, tasi-RNAs and their targets identified in this study will be useful in unraveling the molecular mechanisms underlying drought stress responses and genetic improvement of biomass production and stress tolerance in sorghum.</p></abstract><kwd-group><kwd>sorghum</kwd><kwd>microRNAs</kwd><kwd>tasiRNA</kwd><kwd>drought</kwd><kwd>next-generation sequencing</kwd><kwd>transcriptome</kwd></kwd-group><counts><fig-count count="6"></fig-count><table-count count="2"></table-count><equation-count count="0"></equation-count><ref-count count="69"></ref-count><page-count count="21"></page-count><word-count count="13821"></word-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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