Deciphering Transcriptional Programming during Pod and Seed Development Using RNA-Seq in Pigeonpea (Cajanus cajan)
Identifieur interne : 001101 ( Pmc/Curation ); précédent : 001100; suivant : 001102Deciphering Transcriptional Programming during Pod and Seed Development Using RNA-Seq in Pigeonpea (Cajanus cajan)
Auteurs : Lekha T. Pazhamala [Inde] ; Gaurav Agarwal [Inde] ; Prasad Bajaj [Inde] ; Vinay Kumar [Inde] ; Akanksha Kulshreshtha [Inde] ; Rachit K. Saxena [Inde] ; Rajeev K. Varshney [Inde, Australie]Source :
- PLoS ONE [ 1932-6203 ] ; 2016.
Abstract
Seed development is an important event in plant life cycle that has interested humankind since ages, especially in crops of economic importance. Pigeonpea is an important grain legume of the semi-arid tropics, used mainly for its protein rich seeds. In order to understand the transcriptional programming during the pod and seed development, RNA-seq data was generated from embryo sac from the day of anthesis (0 DAA), seed and pod wall (5, 10, 20 and 30 DAA) of pigeonpea variety “Asha” (ICPL 87119) using Illumina HiSeq 2500. About 684 million sequencing reads have been generated from nine samples, which resulted in the identification of 27,441 expressed genes after sequence analysis. These genes have been studied for their differentially expression, co-expression, temporal and spatial gene expression. We have also used the RNA-seq data to identify important seed-specific transcription factors, biological processes and associated pathways during seed development process in pigeonpea. The comprehensive gene expression study from flowering to mature pod development in pigeonpea would be crucial in identifying candidate genes involved in seed traits directly or indirectly related to yield and quality. The dataset will serve as an important resource for gene discovery and deciphering the molecular mechanisms underlying various seed related traits.
Url:
DOI: 10.1371/journal.pone.0164959
PubMed: 27760186
PubMed Central: 5070767
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Pazhamala</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324</wicri:regionArea></affiliation></author><author><name sortKey="Agarwal, Gaurav" sort="Agarwal, Gaurav" uniqKey="Agarwal G" first="Gaurav" last="Agarwal">Gaurav Agarwal</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324</wicri:regionArea></affiliation></author><author><name sortKey="Bajaj, Prasad" sort="Bajaj, Prasad" uniqKey="Bajaj P" first="Prasad" last="Bajaj">Prasad Bajaj</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324</wicri:regionArea></affiliation></author><author><name sortKey="Kumar, Vinay" sort="Kumar, Vinay" uniqKey="Kumar V" first="Vinay" last="Kumar">Vinay Kumar</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324</wicri:regionArea></affiliation></author><author><name sortKey="Kulshreshtha, Akanksha" sort="Kulshreshtha, Akanksha" uniqKey="Kulshreshtha A" first="Akanksha" last="Kulshreshtha">Akanksha Kulshreshtha</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324</wicri:regionArea></affiliation></author><author><name sortKey="Saxena, Rachit K" sort="Saxena, Rachit K" uniqKey="Saxena R" first="Rachit K." last="Saxena">Rachit K. 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Varshney</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>School of Plant Biology and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>School of Plant Biology and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Seed development is an important event in plant life cycle that has interested humankind since ages, especially in crops of economic importance. Pigeonpea is an important grain legume of the semi-arid tropics, used mainly for its protein rich seeds. In order to understand the transcriptional programming during the pod and seed development, RNA-seq data was generated from embryo sac from the day of anthesis (0 DAA), seed and pod wall (5, 10, 20 and 30 DAA) of pigeonpea variety “Asha” (ICPL 87119) using Illumina HiSeq 2500. About 684 million sequencing reads have been generated from nine samples, which resulted in the identification of 27,441 expressed genes after sequence analysis. These genes have been studied for their differentially expression, co-expression, temporal and spatial gene expression. We have also used the RNA-seq data to identify important seed-specific transcription factors, biological processes and associated pathways during seed development process in pigeonpea. The comprehensive gene expression study from flowering to mature pod development in pigeonpea would be crucial in identifying candidate genes involved in seed traits directly or indirectly related to yield and quality. The dataset will serve as an important resource for gene discovery and deciphering the molecular mechanisms underlying various seed related traits.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Varshney, Rk" uniqKey="Varshney R">RK Varshney</name></author><author><name sortKey="Terauchi, R" uniqKey="Terauchi R">R Terauchi</name></author><author><name sortKey="Mccouch, Sr" uniqKey="Mccouch S">SR McCouch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pazhamala, L" uniqKey="Pazhamala L">L Pazhamala</name></author><author><name sortKey="Saxena, Rk" uniqKey="Saxena R">RK Saxena</name></author><author><name sortKey="Singh, Vk" uniqKey="Singh V">VK Singh</name></author><author><name sortKey="Sameerkumar, Cv" uniqKey="Sameerkumar C">CV Sameerkumar</name></author><author><name sortKey="Kumar, V" uniqKey="Kumar V">V Kumar</name></author><author><name sortKey="Sinha, P" uniqKey="Sinha P">P 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, CA USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27760186</article-id><article-id pub-id-type="pmc">5070767</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0164959</article-id><article-id pub-id-type="publisher-id">PONE-D-16-17693</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Gene Expression</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Plant Science</subject><subj-group><subject>Plant Anatomy</subject><subj-group><subject>Seeds</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Plant Science</subject><subj-group><subject>Plant Anatomy</subject><subj-group><subject>Fruit and Seed Anatomy</subject><subj-group><subject>Plant Embryo Anatomy</subject><subj-group><subject>Embryo Sac</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Plant Science</subject><subj-group><subject>Plant Anatomy</subject><subj-group><subject>Plant Embryo Anatomy</subject><subj-group><subject>Embryo Sac</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Developmental Biology</subject><subj-group><subject>Embryogenesis</subject><subj-group><subject>Plant Embryogenesis</subject><subj-group><subject>Plant Embryo Anatomy</subject><subj-group><subject>Embryo Sac</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Developmental Biology</subject><subj-group><subject>Plant Growth and Development</subject><subj-group><subject>Plant Development</subject><subj-group><subject>Plant Embryogenesis</subject><subj-group><subject>Plant Embryo Anatomy</subject><subj-group><subject>Embryo Sac</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Plant Science</subject><subj-group><subject>Plant Growth and Development</subject><subj-group><subject>Plant Development</subject><subj-group><subject>Plant Embryogenesis</subject><subj-group><subject>Plant Embryo Anatomy</subject><subj-group><subject>Embryo Sac</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and life sciences</subject><subj-group><subject>Molecular biology</subject><subj-group><subject>Molecular biology techniques</subject><subj-group><subject>Sequencing techniques</subject><subj-group><subject>RNA sequencing</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and analysis methods</subject><subj-group><subject>Molecular biology techniques</subject><subj-group><subject>Sequencing techniques</subject><subj-group><subject>RNA sequencing</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Gene Expression</subject><subj-group><subject>Gene Regulation</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Cell Biology</subject><subj-group><subject>Cell Processes</subject><subj-group><subject>Cell Cycle and Cell Division</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and life sciences</subject><subj-group><subject>Biochemistry</subject><subj-group><subject>Proteins</subject><subj-group><subject>DNA-binding proteins</subject><subj-group><subject>Transcription Factors</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Gene Expression</subject><subj-group><subject>Gene Regulation</subject><subj-group><subject>Transcription Factors</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Biochemistry</subject><subj-group><subject>Proteins</subject><subj-group><subject>Regulatory Proteins</subject><subj-group><subject>Transcription Factors</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Computational Biology</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Gene Ontologies</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Genomics</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Gene Ontologies</subject></subj-group></subj-group></subj-group></subj-group></subj-group></article-categories><title-group><article-title>Deciphering Transcriptional Programming during Pod and Seed Development Using RNA-Seq in Pigeonpea (<italic>Cajanus cajan</italic>)</article-title><alt-title alt-title-type="running-head">Transcriptomic Study of Pigeonpea Pod and Seed Development</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Pazhamala</surname><given-names>Lekha T.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Agarwal</surname><given-names>Gaurav</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bajaj</surname><given-names>Prasad</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Kumar</surname><given-names>Vinay</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Kulshreshtha</surname><given-names>Akanksha</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Saxena</surname><given-names>Rachit K.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Varshney</surname><given-names>Rajeev K.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff002"><sup>2</sup></xref><xref ref-type="corresp" rid="cor001">*</xref></contrib></contrib-group><aff id="aff001"><label>1</label><addr-line>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324, India</addr-line></aff><aff id="aff002"><label>2</label><addr-line>School of Plant Biology and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Parida</surname><given-names>Swarup Kumar</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>National Institute for Plant Genome Research, INDIA</addr-line></aff><author-notes><fn fn-type="COI-statement" id="coi001"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p><list list-type="simple"><list-item><p><bold>Conceptualization:</bold> RKV RKS LTP.</p></list-item><list-item><p><bold>Data curation:</bold> PB GA.</p></list-item><list-item><p><bold>Formal analysis:</bold> PB GA.</p></list-item><list-item><p><bold>Funding acquisition:</bold> RKV.</p></list-item><list-item><p><bold>Investigation:</bold> LTP RKS.</p></list-item><list-item><p><bold>Methodology:</bold> RKS LTP AK.</p></list-item><list-item><p><bold>Project administration:</bold> RKS RKV LTP.</p></list-item><list-item><p><bold>Resources:</bold> RKV.</p></list-item><list-item><p><bold>Software:</bold> PB GA.</p></list-item><list-item><p><bold>Supervision:</bold> RKS RKV.</p></list-item><list-item><p><bold>Validation:</bold> LTP RKS AK VK.</p></list-item><list-item><p><bold>Visualization:</bold> PB LTP.</p></list-item><list-item><p><bold>Writing – original draft:</bold> LTP RKS RKV PB.</p></list-item><list-item><p><bold>Writing – review & editing:</bold> LTP RKS RKV PB.</p></list-item></list></p></fn><corresp id="cor001">* E-mail: <email>r.k.varshney@cgiar.org</email></corresp></author-notes><pub-date pub-type="epub"><day>19</day><month>10</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>11</volume><issue>10</issue><elocation-id>e0164959</elocation-id><history><date date-type="received"><day>2</day><month>5</month><year>2016</year></date><date date-type="accepted"><day>4</day><month>10</month><year>2016</year></date></history><permissions><copyright-statement>© 2016 Pazhamala et al</copyright-statement><copyright-year>2016</copyright-year><copyright-holder>Pazhamala et al</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 <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="pone.0164959.pdf"></self-uri><abstract><p>Seed development is an important event in plant life cycle that has interested humankind since ages, especially in crops of economic importance. Pigeonpea is an important grain legume of the semi-arid tropics, used mainly for its protein rich seeds. In order to understand the transcriptional programming during the pod and seed development, RNA-seq data was generated from embryo sac from the day of anthesis (0 DAA), seed and pod wall (5, 10, 20 and 30 DAA) of pigeonpea variety “Asha” (ICPL 87119) using Illumina HiSeq 2500. About 684 million sequencing reads have been generated from nine samples, which resulted in the identification of 27,441 expressed genes after sequence analysis. These genes have been studied for their differentially expression, co-expression, temporal and spatial gene expression. We have also used the RNA-seq data to identify important seed-specific transcription factors, biological processes and associated pathways during seed development process in pigeonpea. The comprehensive gene expression study from flowering to mature pod development in pigeonpea would be crucial in identifying candidate genes involved in seed traits directly or indirectly related to yield and quality. The dataset will serve as an important resource for gene discovery and deciphering the molecular mechanisms underlying various seed related traits.</p></abstract><funding-group><funding-statement>This work has been undertaken as part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of CGIAR Consortium.</funding-statement></funding-group><counts><fig-count count="8"></fig-count><table-count count="1"></table-count><page-count count="17"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>All raw sequencing data have been deposited in NCBI Sequence Read Archive (SRA) database (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/bioproject/344973">http://www.ncbi.nlm.nih.gov/bioproject/344973</ext-link>).</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>All raw sequencing data have been deposited in NCBI Sequence Read Archive (SRA) database (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/bioproject/344973">http://www.ncbi.nlm.nih.gov/bioproject/344973</ext-link>).</p></notes></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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