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De Novo Transcriptome Analysis of Medicinally Important Plantago ovata Using RNA-Seq

Identifieur interne : 000290 ( Pmc/Checkpoint ); précédent : 000289; suivant : 000291

De Novo Transcriptome Analysis of Medicinally Important Plantago ovata Using RNA-Seq

Auteurs : Shivanjali Kotwal [Inde] ; Sanjana Kaul [Inde] ; Pooja Sharma [Inde] ; Mehak Gupta [Inde] ; Rama Shankar [Inde] ; Mukesh Jain [Inde] ; Manoj K. Dhar [Inde]

Source :

RBID : PMC:4778938

Abstract

Plantago ovata is an economically and medicinally important plant of the family Plantaginaceae. It is used extensively for the production of seed husk for its application in pharmaceutical, food and cosmetic industries. In the present study, the transcriptome of P. ovata ovary was sequenced using Illumina Genome Analyzer platform to characterize the mucilage biosynthesis pathway in the plant. De novo assembly was carried out using Oases followed by velvet. A total of 46,955 non-redundant transcripts (≥100 bp) using ~29 million high-quality paired end reads were generated. Functional categorization of these transcripts revealed the presence of several genes involved in various biological processes like metabolic pathways, mucilage biosynthesis, biosynthesis of secondary metabolites and antioxidants. In addition, simple sequence-repeat motifs, non-coding RNAs and transcription factors were also identified. Expression profiling of some genes involved in mucilage biosynthetic pathway was performed in different tissues of P. ovata using Real time PCR analysis. The study has resulted in a valuable resource for further studies on gene expression, genomics and functional genomics in P. ovata.


Url:
DOI: 10.1371/journal.pone.0150273
PubMed: 26943165
PubMed Central: 4778938


Affiliations:


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Le document en format XML

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Transcriptome Analysis of Medicinally Important
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Transcriptome Analysis of Medicinally Important
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Using RNA-Seq</title>
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<name sortKey="Kotwal, Shivanjali" sort="Kotwal, Shivanjali" uniqKey="Kotwal S" first="Shivanjali" last="Kotwal">Shivanjali Kotwal</name>
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<italic>Plantago ovata</italic>
is an economically and medicinally important plant of the family Plantaginaceae. It is used extensively for the production of seed husk for its application in pharmaceutical, food and cosmetic industries. In the present study, the transcriptome of
<italic>P</italic>
.
<italic>ovata</italic>
ovary was sequenced using Illumina Genome Analyzer platform to characterize the mucilage biosynthesis pathway in the plant.
<italic>De novo</italic>
assembly was carried out using Oases followed by velvet. A total of 46,955 non-redundant transcripts (≥100 bp) using ~29 million high-quality paired end reads were generated. Functional categorization of these transcripts revealed the presence of several genes involved in various biological processes like metabolic pathways, mucilage biosynthesis, biosynthesis of secondary metabolites and antioxidants. In addition, simple sequence-repeat motifs, non-coding RNAs and transcription factors were also identified. Expression profiling of some genes involved in mucilage biosynthetic pathway was performed in different tissues of
<italic>P</italic>
.
<italic>ovata</italic>
using Real time PCR analysis. The study has resulted in a valuable resource for further studies on gene expression, genomics and functional genomics in
<italic>P</italic>
.
<italic>ovata</italic>
.</p>
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<article-title>
<italic>De Novo</italic>
Transcriptome Analysis of Medicinally Important
<italic>Plantago ovata</italic>
Using RNA-Seq</article-title>
<alt-title alt-title-type="running-head">Transcriptome Analysis in
<italic>Plantago</italic>
</alt-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Kotwal</surname>
<given-names>Shivanjali</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Kaul</surname>
<given-names>Sanjana</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
<xref ref-type="corresp" rid="cor001">*</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Sharma</surname>
<given-names>Pooja</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Gupta</surname>
<given-names>Mehak</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Shankar</surname>
<given-names>Rama</given-names>
</name>
<xref ref-type="aff" rid="aff002">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Jain</surname>
<given-names>Mukesh</given-names>
</name>
<xref ref-type="aff" rid="aff002">
<sup>2</sup>
</xref>
<xref ref-type="author-notes" rid="currentaff001">
<sup>¤</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Dhar</surname>
<given-names>Manoj K.</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff001">
<label>1</label>
<addr-line>School of Biotechnology, University of Jammu, Jammu, Jammu & Kashmir, 180006, India</addr-line>
</aff>
<aff id="aff002">
<label>2</label>
<addr-line>National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India</addr-line>
</aff>
<contrib-group>
<contrib contrib-type="editor">
<name>
<surname>Trivedi</surname>
<given-names>Prabodh Kumar</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1">
<addr-line>CSIR-National Botanical Research Institute, INDIA</addr-line>
</aff>
<author-notes>
<fn fn-type="conflict" id="coi001">
<p>
<bold>Competing Interests: </bold>
The authors have declared that no competing interests exist.</p>
</fn>
<fn fn-type="con" id="contrib001">
<p>Conceived and designed the experiments: MKD S. Kaul. Performed the experiments: S. Kotwal PS MG. Analyzed the data: S. Kotwal RS. Contributed reagents/materials/analysis tools: S. Kaul MJ. Wrote the paper: S. Kotwal RS MKD.</p>
</fn>
<fn fn-type="current-aff" id="currentaff001">
<label>¤</label>
<p>Current address: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India</p>
</fn>
<corresp id="cor001">* E-mail:
<email>sanrozie@rediffmail.com</email>
</corresp>
</author-notes>
<pub-date pub-type="epub">
<day>4</day>
<month>3</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="collection">
<year>2016</year>
</pub-date>
<volume>11</volume>
<issue>3</issue>
<elocation-id>e0150273</elocation-id>
<history>
<date date-type="received">
<day>7</day>
<month>9</month>
<year>2015</year>
</date>
<date date-type="accepted">
<day>11</day>
<month>2</month>
<year>2016</year>
</date>
</history>
<permissions>
<copyright-statement>© 2016 Kotwal et al</copyright-statement>
<copyright-year>2016</copyright-year>
<copyright-holder>Kotwal 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:type="simple" xlink:href="pone.0150273.pdf"></self-uri>
<abstract>
<p>
<italic>Plantago ovata</italic>
is an economically and medicinally important plant of the family Plantaginaceae. It is used extensively for the production of seed husk for its application in pharmaceutical, food and cosmetic industries. In the present study, the transcriptome of
<italic>P</italic>
.
<italic>ovata</italic>
ovary was sequenced using Illumina Genome Analyzer platform to characterize the mucilage biosynthesis pathway in the plant.
<italic>De novo</italic>
assembly was carried out using Oases followed by velvet. A total of 46,955 non-redundant transcripts (≥100 bp) using ~29 million high-quality paired end reads were generated. Functional categorization of these transcripts revealed the presence of several genes involved in various biological processes like metabolic pathways, mucilage biosynthesis, biosynthesis of secondary metabolites and antioxidants. In addition, simple sequence-repeat motifs, non-coding RNAs and transcription factors were also identified. Expression profiling of some genes involved in mucilage biosynthetic pathway was performed in different tissues of
<italic>P</italic>
.
<italic>ovata</italic>
using Real time PCR analysis. The study has resulted in a valuable resource for further studies on gene expression, genomics and functional genomics in
<italic>P</italic>
.
<italic>ovata</italic>
.</p>
</abstract>
<funding-group>
<funding-statement>The authors are grateful to Department of Biotechnology (DBT), Govt. of India for financial assistance in the form of a research project to MKD. Ms. Shivanjali Kotwal is grateful to the Department of Science and Technology (DST), Govt. of India for an INSPIRE fellowship.</funding-statement>
</funding-group>
<counts>
<fig-count count="8"></fig-count>
<table-count count="5"></table-count>
<page-count count="23"></page-count>
</counts>
<custom-meta-group>
<custom-meta id="data-availability">
<meta-name>Data Availability</meta-name>
<meta-value>All relevant data are within the paper and its Supporting Information files.</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
<notes>
<title>Data Availability</title>
<p>All relevant data are within the paper and its Supporting Information files.</p>
</notes>
</front>
</pmc>
<affiliations>
<list>
<country>
<li>Inde</li>
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<name sortKey="Jain, Mukesh" sort="Jain, Mukesh" uniqKey="Jain M" first="Mukesh" last="Jain">Mukesh Jain</name>
<name sortKey="Kaul, Sanjana" sort="Kaul, Sanjana" uniqKey="Kaul S" first="Sanjana" last="Kaul">Sanjana Kaul</name>
<name sortKey="Shankar, Rama" sort="Shankar, Rama" uniqKey="Shankar R" first="Rama" last="Shankar">Rama Shankar</name>
<name sortKey="Sharma, Pooja" sort="Sharma, Pooja" uniqKey="Sharma P" first="Pooja" last="Sharma">Pooja Sharma</name>
</country>
</tree>
</affiliations>
</record>

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