Identification of MicroRNAs and Target Genes in the Fruit and Shoot Tip of Lycium chinense: A Traditional Chinese Medicinal Plant
Identifieur interne : 000124 ( Pmc/Curation ); précédent : 000123; suivant : 000125Identification of MicroRNAs and Target Genes in the Fruit and Shoot Tip of Lycium chinense: A Traditional Chinese Medicinal Plant
Auteurs : A. B. M. Khaldun [République populaire de Chine] ; Wenjun Huang [République populaire de Chine] ; Sihong Liao [République populaire de Chine] ; Haiyan Lv [République populaire de Chine] ; Ying Wang [République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2015.
Abstract
Although
Url:
DOI: 10.1371/journal.pone.0116334
PubMed: 25587984
PubMed Central: 4294688
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identification of MicroRNAs and Target Genes in the Fruit and Shoot Tip of <italic>Lycium chinense</italic>: A Traditional Chinese Medicinal Plant</title><author><name sortKey="Khaldun, A B M" sort="Khaldun, A B M" uniqKey="Khaldun A" first="A. B. M." last="Khaldun">A. B. M. Khaldun</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>University of the Chinese Academy of Sciences, Beijing, 100039, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>University of the Chinese Academy of Sciences, Beijing, 100039</wicri:regionArea></affiliation></author><author><name sortKey="Huang, Wenjun" sort="Huang, Wenjun" uniqKey="Huang W" first="Wenjun" last="Huang">Wenjun Huang</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074</wicri:regionArea></affiliation></author><author><name sortKey="Liao, Sihong" sort="Liao, Sihong" uniqKey="Liao S" first="Sihong" last="Liao">Sihong Liao</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>University of the Chinese Academy of Sciences, Beijing, 100039, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>University of the Chinese Academy of Sciences, Beijing, 100039</wicri:regionArea></affiliation></author><author><name sortKey="Lv, Haiyan" sort="Lv, Haiyan" uniqKey="Lv H" first="Haiyan" last="Lv">Haiyan Lv</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074</wicri:regionArea></affiliation></author><author><name sortKey="Wang, Ying" sort="Wang, Ying" uniqKey="Wang Y" first="Ying" last="Wang">Ying Wang</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Northwest Center for Agrobiotechnology (Ningxia), Chinese Academy of Sciences, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Northwest Center for Agrobiotechnology (Ningxia), Chinese Academy of Sciences, Beijing</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25587984</idno><idno type="pmc">4294688</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4294688</idno><idno type="RBID">PMC:4294688</idno><idno type="doi">10.1371/journal.pone.0116334</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000124</idno><idno type="wicri:Area/Pmc/Curation">000124</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification of MicroRNAs and Target Genes in the Fruit and Shoot Tip of <italic>Lycium chinense</italic>: A Traditional Chinese Medicinal Plant</title><author><name sortKey="Khaldun, A B M" sort="Khaldun, A B M" uniqKey="Khaldun A" first="A. B. M." last="Khaldun">A. B. M. Khaldun</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>University of the Chinese Academy of Sciences, Beijing, 100039, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>University of the Chinese Academy of Sciences, Beijing, 100039</wicri:regionArea></affiliation></author><author><name sortKey="Huang, Wenjun" sort="Huang, Wenjun" uniqKey="Huang W" first="Wenjun" last="Huang">Wenjun Huang</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074</wicri:regionArea></affiliation></author><author><name sortKey="Liao, Sihong" sort="Liao, Sihong" uniqKey="Liao S" first="Sihong" last="Liao">Sihong Liao</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>University of the Chinese Academy of Sciences, Beijing, 100039, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>University of the Chinese Academy of Sciences, Beijing, 100039</wicri:regionArea></affiliation></author><author><name sortKey="Lv, Haiyan" sort="Lv, Haiyan" uniqKey="Lv H" first="Haiyan" last="Lv">Haiyan Lv</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074</wicri:regionArea></affiliation></author><author><name sortKey="Wang, Ying" sort="Wang, Ying" uniqKey="Wang Y" first="Ying" last="Wang">Ying Wang</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Northwest Center for Agrobiotechnology (Ningxia), Chinese Academy of Sciences, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Northwest Center for Agrobiotechnology (Ningxia), Chinese Academy of Sciences, Beijing</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</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>Although <italic>Lycium chinense</italic> (goji berry) is an important traditional Chinese medicinal plant, little genome information is available for this plant, particularly at the small-RNA level. Recent findings indicate that the evolutionary role of miRNAs is very important for a better understanding of gene regulation in different plant species. To elucidate small RNAs and their potential target genes in fruit and shoot tissues, high-throughput RNA sequencing technology was used followed by qRT-PCR and RLM 5’-RACE experiments. A total of 60 conserved miRNAs belonging to 31 families and 30 putative novel miRNAs were identified. A total of 62 significantly differentially expressed miRNAs were identified, of which 15 (14 known and 1 novel) were shoot-specific, and 12 (7 known and 5 novel) were fruit-specific. Additionally, 28 differentially expressed miRNAs were recorded as up-regulated in fruit tissues. The predicted potential targets were involved in a wide range of metabolic and regulatory pathways. GO (Gene Ontology) enrichment analysis and the KEGG (Kyoto Encyclopedia of Genes and Genomes) database revealed that “metabolic pathways” is the most significant pathway with respect to the rich factor and gene numbers. Moreover, five miRNAs were related to fruit maturation, lycopene biosynthesis and signaling pathways, which might be important for the further study of fruit molecular biology. This study is the first, to detect known and novel miRNAs, and their potential targets, of <italic>L. chinense</italic>. The data and findings that are presented here might be a good source for the functional genomic study of medicinal plants and for understanding the links among diversified biological pathways.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Hou, K" uniqKey="Hou K">K Hou</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Qian, J Y" uniqKey="Qian J">J-Y Qian</name></author><author><name sortKey="Liu, D" uniqKey="Liu D">D Liu</name></author><author><name sortKey="Huang, Ag" uniqKey="Huang A">AG Huang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oh, Y" uniqKey="Oh Y">Y Oh</name></author><author><name sortKey="Cho, W" uniqKey="Cho W">W Cho</name></author><author><name sortKey="Im, G" uniqKey="Im G">G Im</name></author><author><name sortKey="Jeong, Y" uniqKey="Jeong Y">Y Jeong</name></author><author><name sortKey="Hwang, Y" uniqKey="Hwang 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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">25587984</article-id><article-id pub-id-type="pmc">4294688</article-id><article-id pub-id-type="publisher-id">PONE-D-14-35852</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0116334</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Identification of MicroRNAs and Target Genes in the Fruit and Shoot Tip of <italic>Lycium chinense</italic>: A Traditional Chinese Medicinal Plant</article-title><alt-title alt-title-type="running-head">MicroRNAs in <italic>Lycium chinense</italic></alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Khaldun</surname><given-names>A. B. M.</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="other" rid="econtrib001"><sup>‡</sup></xref></contrib><contrib contrib-type="author"><name><surname>Huang</surname><given-names>Wenjun</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="other" rid="econtrib001"><sup>‡</sup></xref></contrib><contrib contrib-type="author"><name><surname>Liao</surname><given-names>Sihong</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>Lv</surname><given-names>Haiyan</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Ying</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff003"><sup>3</sup></xref><xref ref-type="corresp" rid="cor001">*</xref></contrib></contrib-group><aff id="aff001"><label>1</label><addr-line>Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China</addr-line></aff><aff id="aff002"><label>2</label><addr-line>University of the Chinese Academy of Sciences, Beijing, 100039, China</addr-line></aff><aff id="aff003"><label>3</label><addr-line>Northwest Center for Agrobiotechnology (Ningxia), Chinese Academy of Sciences, Beijing, China</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Yang</surname><given-names>Zhi Min</given-names></name><role>Academic Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Nanjing Agricultural University, CHINA</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: ABMK YW. Performed the experiments: ABMK WH HL SL. Analyzed the data: ABMK WH. Contributed reagents/materials/analysis tools: YW HL SL. Wrote the paper: ABMK YW WH.</p></fn><fn fn-type="equal" id="econtrib001"><p>‡ These authors contributed equally to this work.</p></fn><corresp id="cor001">* E-mail: <email>yingwang@wbgcas.cn</email></corresp></author-notes><pub-date pub-type="collection"><year>2015</year></pub-date><pub-date pub-type="epub"><day>14</day><month>1</month><year>2015</year></pub-date><volume>10</volume><issue>1</issue><elocation-id>e0116334</elocation-id><history><date date-type="received"><day>29</day><month>8</month><year>2014</year></date><date date-type="accepted"><day>5</day><month>12</month><year>2014</year></date></history><permissions><copyright-year>2015</copyright-year><copyright-holder>Khaldun 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.0116334.pdf"></self-uri><abstract><p>Although <italic>Lycium chinense</italic> (goji berry) is an important traditional Chinese medicinal plant, little genome information is available for this plant, particularly at the small-RNA level. Recent findings indicate that the evolutionary role of miRNAs is very important for a better understanding of gene regulation in different plant species. To elucidate small RNAs and their potential target genes in fruit and shoot tissues, high-throughput RNA sequencing technology was used followed by qRT-PCR and RLM 5’-RACE experiments. A total of 60 conserved miRNAs belonging to 31 families and 30 putative novel miRNAs were identified. A total of 62 significantly differentially expressed miRNAs were identified, of which 15 (14 known and 1 novel) were shoot-specific, and 12 (7 known and 5 novel) were fruit-specific. Additionally, 28 differentially expressed miRNAs were recorded as up-regulated in fruit tissues. The predicted potential targets were involved in a wide range of metabolic and regulatory pathways. GO (Gene Ontology) enrichment analysis and the KEGG (Kyoto Encyclopedia of Genes and Genomes) database revealed that “metabolic pathways” is the most significant pathway with respect to the rich factor and gene numbers. Moreover, five miRNAs were related to fruit maturation, lycopene biosynthesis and signaling pathways, which might be important for the further study of fruit molecular biology. This study is the first, to detect known and novel miRNAs, and their potential targets, of <italic>L. chinense</italic>. The data and findings that are presented here might be a good source for the functional genomic study of medicinal plants and for understanding the links among diversified biological pathways.</p></abstract><funding-group><funding-statement>This work was supported by National Natural Science Foundation of China (Grant no. 31200242 and 31470391) and Scientific Research Equipment Project of Chinese Academy of Sciences (YZ201227) (YW). 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="7"></fig-count><table-count count="4"></table-count><page-count count="21"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>The data set studied in this article are available at NCBI (SRA) public repository under the accession number SRP043345.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>The data set studied in this article are available at NCBI (SRA) public repository under the accession number SRP043345.</p></notes></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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