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Transcriptome Analysis of Syringa oblata Lindl. Inflorescence Identifies Genes Associated with Pigment Biosynthesis and Scent Metabolism

Identifieur interne : 001E05 ( Ncbi/Merge ); précédent : 001E04; suivant : 001E06

Transcriptome Analysis of Syringa oblata Lindl. Inflorescence Identifies Genes Associated with Pigment Biosynthesis and Scent Metabolism

Auteurs : Jian Zheng [République populaire de Chine] ; Zenghui Hu [République populaire de Chine] ; Xuelian Guan [République populaire de Chine] ; Dequan Dou [République populaire de Chine] ; Guo Bai [République populaire de Chine] ; Yu Wang [République populaire de Chine] ; Yingtian Guo [République populaire de Chine] ; Wei Li [République populaire de Chine] ; Pingsheng Leng [République populaire de Chine]

Source :

RBID : PMC:4654506

Abstract

Syringa oblata Lindl. is a woody ornamental plant with high economic value and characteristics that include early flowering, multiple flower colors, and strong fragrance. Despite a long history of cultivation, the genetics and molecular biology of S. oblata are poorly understood. Transcriptome and expression profiling data are needed to identify genes and to better understand the biological mechanisms of floral pigments and scents in this species. Nine cDNA libraries were obtained from three replicates of three developmental stages: inflorescence with enlarged flower buds not protruded, inflorescence with corolla lobes not displayed, and inflorescence with flowers fully opened and emitting strong fragrance. Using the Illumina RNA-Seq technique, 319,425,972 clean reads were obtained and were assembled into 104,691 final unigenes (average length of 853 bp), 41.75% of which were annotated in the NCBI non-redundant protein database. Among the annotated unigenes, 36,967 were assigned to gene ontology categories and 19,956 were assigned to eukaryoticorthologous groups. Using the Kyoto Encyclopedia of Genes and Genomes pathway database, 12,388 unigenes were sorted into 286 pathways. Based on these transcriptomic data, we obtained a large number of candidate genes that were differentially expressed at different flower stages and that were related to floral pigment biosynthesis and fragrance metabolism. This comprehensive transcriptomic analysis provides fundamental information on the genes and pathways involved in flower secondary metabolism and development in S. oblata, providing a useful database for further research on S. oblata and other plants of genus Syringa.


Url:
DOI: 10.1371/journal.pone.0142542
PubMed: 26587670
PubMed Central: 4654506

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Le document en format XML

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Lindl. Inflorescence Identifies Genes Associated with Pigment Biosynthesis and Scent Metabolism</title>
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<p>
<italic>Syringa oblata</italic>
Lindl. is a woody ornamental plant with high economic value and characteristics that include early flowering, multiple flower colors, and strong fragrance. Despite a long history of cultivation, the genetics and molecular biology of
<italic>S</italic>
.
<italic>oblata</italic>
are poorly understood. Transcriptome and expression profiling data are needed to identify genes and to better understand the biological mechanisms of floral pigments and scents in this species. Nine cDNA libraries were obtained from three replicates of three developmental stages: inflorescence with enlarged flower buds not protruded, inflorescence with corolla lobes not displayed, and inflorescence with flowers fully opened and emitting strong fragrance. Using the Illumina RNA-Seq technique, 319,425,972 clean reads were obtained and were assembled into 104,691 final unigenes (average length of 853 bp), 41.75% of which were annotated in the NCBI non-redundant protein database. Among the annotated unigenes, 36,967 were assigned to gene ontology categories and 19,956 were assigned to eukaryoticorthologous groups. Using the Kyoto Encyclopedia of Genes and Genomes pathway database, 12,388 unigenes were sorted into 286 pathways. Based on these transcriptomic data, we obtained a large number of candidate genes that were differentially expressed at different flower stages and that were related to floral pigment biosynthesis and fragrance metabolism. This comprehensive transcriptomic analysis provides fundamental information on the genes and pathways involved in flower secondary metabolism and development in
<italic>S</italic>
.
<italic>oblata</italic>
, providing a useful database for further research on
<italic>S</italic>
.
<italic>oblata</italic>
and other plants of genus
<italic>Syringa</italic>
.</p>
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<pmc article-type="research-article">
<pmc-dir>properties open_access</pmc-dir>
<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">26587670</article-id>
<article-id pub-id-type="pmc">4654506</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0142542</article-id>
<article-id pub-id-type="publisher-id">PONE-D-15-32087</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group>
<article-title>Transcriptome Analysis of
<italic>Syringa oblata</italic>
Lindl. Inflorescence Identifies Genes Associated with Pigment Biosynthesis and Scent Metabolism</article-title>
<alt-title alt-title-type="running-head">Transcriptome Analysis of Flower Pigment and Scent in
<italic>Syringa oblata</italic>
</alt-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Zheng</surname>
<given-names>Jian</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff002">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Hu</surname>
<given-names>Zenghui</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Guan</surname>
<given-names>Xuelian</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Dou</surname>
<given-names>Dequan</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Bai</surname>
<given-names>Guo</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Wang</surname>
<given-names>Yu</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Guo</surname>
<given-names>Yingtian</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Li</surname>
<given-names>Wei</given-names>
</name>
<xref ref-type="aff" rid="aff003">
<sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Leng</surname>
<given-names>Pingsheng</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
<xref rid="cor001" ref-type="corresp">*</xref>
</contrib>
</contrib-group>
<aff id="aff001">
<label>1</label>
<addr-line>College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China</addr-line>
</aff>
<aff id="aff002">
<label>2</label>
<addr-line>Beijing Engineering Research Center of rural landscape planning and design, Beijing, 102206, China</addr-line>
</aff>
<aff id="aff003">
<label>3</label>
<addr-line>College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266100, China</addr-line>
</aff>
<contrib-group>
<contrib contrib-type="editor">
<name>
<surname>Li</surname>
<given-names>Maoteng</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1">
<addr-line>Huazhong University of Science and Technology, CHINA</addr-line>
</aff>
<author-notes>
<fn fn-type="conflict" id="coi001">
<p>
<bold>Competing Interests: </bold>
The authors declare that they have no competing interests exist.</p>
</fn>
<fn fn-type="con" id="contrib001">
<p>Conceived and designed the experiments: PL. Performed the experiments: JZ XG DD GB YW YG. Analyzed the data: JZ ZH WL. Contributed reagents/materials/analysis tools: JZ ZH. Wrote the paper: JZ.</p>
</fn>
<corresp id="cor001">* E-mail:
<email>zhengjian770116@163.com</email>
</corresp>
</author-notes>
<pub-date pub-type="epub">
<day>20</day>
<month>11</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="collection">
<year>2015</year>
</pub-date>
<volume>10</volume>
<issue>11</issue>
<elocation-id>e0142542</elocation-id>
<history>
<date date-type="received">
<day>21</day>
<month>7</month>
<year>2015</year>
</date>
<date date-type="accepted">
<day>25</day>
<month>10</month>
<year>2015</year>
</date>
</history>
<permissions>
<copyright-year>2015</copyright-year>
<copyright-holder>Zheng 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.0142542.pdf"></self-uri>
<abstract>
<p>
<italic>Syringa oblata</italic>
Lindl. is a woody ornamental plant with high economic value and characteristics that include early flowering, multiple flower colors, and strong fragrance. Despite a long history of cultivation, the genetics and molecular biology of
<italic>S</italic>
.
<italic>oblata</italic>
are poorly understood. Transcriptome and expression profiling data are needed to identify genes and to better understand the biological mechanisms of floral pigments and scents in this species. Nine cDNA libraries were obtained from three replicates of three developmental stages: inflorescence with enlarged flower buds not protruded, inflorescence with corolla lobes not displayed, and inflorescence with flowers fully opened and emitting strong fragrance. Using the Illumina RNA-Seq technique, 319,425,972 clean reads were obtained and were assembled into 104,691 final unigenes (average length of 853 bp), 41.75% of which were annotated in the NCBI non-redundant protein database. Among the annotated unigenes, 36,967 were assigned to gene ontology categories and 19,956 were assigned to eukaryoticorthologous groups. Using the Kyoto Encyclopedia of Genes and Genomes pathway database, 12,388 unigenes were sorted into 286 pathways. Based on these transcriptomic data, we obtained a large number of candidate genes that were differentially expressed at different flower stages and that were related to floral pigment biosynthesis and fragrance metabolism. This comprehensive transcriptomic analysis provides fundamental information on the genes and pathways involved in flower secondary metabolism and development in
<italic>S</italic>
.
<italic>oblata</italic>
, providing a useful database for further research on
<italic>S</italic>
.
<italic>oblata</italic>
and other plants of genus
<italic>Syringa</italic>
.</p>
</abstract>
<funding-group>
<funding-statement>Funding was provided by The Importation and Development of High-Caliber Talents Project of Beijing Municipal Institutions (CIT&TCD20154043); The Project of Construction of Innovative Teams and Teacher Career Development for Universities and Colleges Under Beijing Municipality (CIT& IDHT20150503); The Building Project of Beijing Laboratory of Urban and Rural Ecological Environment (PXM2015-014207-000014). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement>
</funding-group>
<counts>
<fig-count count="8"></fig-count>
<table-count count="2"></table-count>
<page-count count="20"></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. The read data are deposited at the NCBI Short Read Archive under the accession SRP063913.</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. The read data are deposited at the NCBI Short Read Archive under the accession SRP063913.</p>
</notes>
</front>
</pmc>
<affiliations>
<list>
<country>
<li>République populaire de Chine</li>
</country>
</list>
<tree>
<country name="République populaire de Chine">
<noRegion>
<name sortKey="Zheng, Jian" sort="Zheng, Jian" uniqKey="Zheng J" first="Jian" last="Zheng">Jian Zheng</name>
</noRegion>
<name sortKey="Bai, Guo" sort="Bai, Guo" uniqKey="Bai G" first="Guo" last="Bai">Guo Bai</name>
<name sortKey="Dou, Dequan" sort="Dou, Dequan" uniqKey="Dou D" first="Dequan" last="Dou">Dequan Dou</name>
<name sortKey="Guan, Xuelian" sort="Guan, Xuelian" uniqKey="Guan X" first="Xuelian" last="Guan">Xuelian Guan</name>
<name sortKey="Guo, Yingtian" sort="Guo, Yingtian" uniqKey="Guo Y" first="Yingtian" last="Guo">Yingtian Guo</name>
<name sortKey="Hu, Zenghui" sort="Hu, Zenghui" uniqKey="Hu Z" first="Zenghui" last="Hu">Zenghui Hu</name>
<name sortKey="Leng, Pingsheng" sort="Leng, Pingsheng" uniqKey="Leng P" first="Pingsheng" last="Leng">Pingsheng Leng</name>
<name sortKey="Li, Wei" sort="Li, Wei" uniqKey="Li W" first="Wei" last="Li">Wei Li</name>
<name sortKey="Wang, Yu" sort="Wang, Yu" uniqKey="Wang Y" first="Yu" last="Wang">Yu Wang</name>
<name sortKey="Zheng, Jian" sort="Zheng, Jian" uniqKey="Zheng J" first="Jian" last="Zheng">Jian Zheng</name>
</country>
</tree>
</affiliations>
</record>

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