De-novo RNA Sequencing and Metabolite Profiling to Identify Genes Involved in Anthocyanin Biosynthesis in Korean Black Raspberry (Rubus coreanus Miquel)
Identifieur interne : 001186 ( Pmc/Curation ); précédent : 001185; suivant : 001187De-novo RNA Sequencing and Metabolite Profiling to Identify Genes Involved in Anthocyanin Biosynthesis in Korean Black Raspberry (Rubus coreanus Miquel)
Auteurs : Tae Kyung Hyun [Corée du Sud] ; Sarah Lee [Corée du Sud] ; Yeonggil Rim [Corée du Sud] ; Ritesh Kumar [Corée du Sud] ; Xiao Han [Corée du Sud] ; Sang Yeol Lee [Corée du Sud] ; Choong Hwan Lee [Corée du Sud] ; Jae-Yean Kim [Corée du Sud]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
The Korean black raspberry (
Url:
DOI: 10.1371/journal.pone.0088292
PubMed: 24505466
PubMed Central: 3914977
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en"><italic>De-novo</italic> RNA Sequencing and Metabolite Profiling to Identify Genes Involved in Anthocyanin Biosynthesis in Korean Black Raspberry (<italic>Rubus coreanus</italic> Miquel)</title><author><name sortKey="Hyun, Tae Kyung" sort="Hyun, Tae Kyung" uniqKey="Hyun T" first="Tae Kyung" last="Hyun">Tae Kyung Hyun</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju</wicri:regionArea></affiliation></author><author><name sortKey="Lee, Sarah" sort="Lee, Sarah" uniqKey="Lee S" first="Sarah" last="Lee">Sarah Lee</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Division of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Bioscience and Biotechnology, Konkuk University, Seoul</wicri:regionArea></affiliation></author><author><name sortKey="Rim, Yeonggil" sort="Rim, Yeonggil" uniqKey="Rim Y" first="Yeonggil" last="Rim">Yeonggil Rim</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju</wicri:regionArea></affiliation></author><author><name sortKey="Kumar, Ritesh" sort="Kumar, Ritesh" uniqKey="Kumar R" first="Ritesh" last="Kumar">Ritesh Kumar</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju</wicri:regionArea></affiliation></author><author><name sortKey="Han, Xiao" sort="Han, Xiao" uniqKey="Han X" first="Xiao" last="Han">Xiao Han</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju</wicri:regionArea></affiliation></author><author><name sortKey="Lee, Sang Yeol" sort="Lee, Sang Yeol" uniqKey="Lee S" first="Sang Yeol" last="Lee">Sang Yeol Lee</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju</wicri:regionArea></affiliation></author><author><name sortKey="Lee, Choong Hwan" sort="Lee, Choong Hwan" uniqKey="Lee C" first="Choong Hwan" last="Lee">Choong Hwan Lee</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Division of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Bioscience and Biotechnology, Konkuk University, Seoul</wicri:regionArea></affiliation></author><author><name sortKey="Kim, Jae Yean" sort="Kim, Jae Yean" uniqKey="Kim J" first="Jae-Yean" last="Kim">Jae-Yean Kim</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24505466</idno><idno type="pmc">3914977</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3914977</idno><idno type="RBID">PMC:3914977</idno><idno type="doi">10.1371/journal.pone.0088292</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">001187</idno><idno type="wicri:Area/Pmc/Curation">001186</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>De-novo</italic> RNA Sequencing and Metabolite Profiling to Identify Genes Involved in Anthocyanin Biosynthesis in Korean Black Raspberry (<italic>Rubus coreanus</italic> Miquel)</title><author><name sortKey="Hyun, Tae Kyung" sort="Hyun, Tae Kyung" uniqKey="Hyun T" first="Tae Kyung" last="Hyun">Tae Kyung Hyun</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju</wicri:regionArea></affiliation></author><author><name sortKey="Lee, Sarah" sort="Lee, Sarah" uniqKey="Lee S" first="Sarah" last="Lee">Sarah Lee</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Division of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Bioscience and Biotechnology, Konkuk University, Seoul</wicri:regionArea></affiliation></author><author><name sortKey="Rim, Yeonggil" sort="Rim, Yeonggil" uniqKey="Rim Y" first="Yeonggil" last="Rim">Yeonggil Rim</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju</wicri:regionArea></affiliation></author><author><name sortKey="Kumar, Ritesh" sort="Kumar, Ritesh" uniqKey="Kumar R" first="Ritesh" last="Kumar">Ritesh Kumar</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju</wicri:regionArea></affiliation></author><author><name sortKey="Han, Xiao" sort="Han, Xiao" uniqKey="Han X" first="Xiao" last="Han">Xiao Han</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju</wicri:regionArea></affiliation></author><author><name sortKey="Lee, Sang Yeol" sort="Lee, Sang Yeol" uniqKey="Lee S" first="Sang Yeol" last="Lee">Sang Yeol Lee</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju</wicri:regionArea></affiliation></author><author><name sortKey="Lee, Choong Hwan" sort="Lee, Choong Hwan" uniqKey="Lee C" first="Choong Hwan" last="Lee">Choong Hwan Lee</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Division of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Bioscience and Biotechnology, Konkuk University, Seoul</wicri:regionArea></affiliation></author><author><name sortKey="Kim, Jae Yean" sort="Kim, Jae Yean" uniqKey="Kim J" first="Jae-Yean" last="Kim">Jae-Yean Kim</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The Korean black raspberry (<italic>Rubus coreanus</italic> Miquel, KB) on ripening is usually consumed as fresh fruit, whereas the unripe KB has been widely used as a source of traditional herbal medicine. Such a stage specific utilization of KB has been assumed due to the changing metabolite profile during fruit ripening process, but so far molecular and biochemical changes during its fruit maturation are poorly understood. To analyze biochemical changes during fruit ripening process at molecular level, firstly, we have sequenced, assembled, and annotated the transcriptome of KB fruits. Over 4.86 Gb of normalized cDNA prepared from fruits was sequenced using Illumina HiSeq™ 2000, and assembled into 43,723 unigenes. Secondly, we have reported that alterations in anthocyanins and proanthocyanidins are the major factors facilitating variations in these stages of fruits. In addition, up-regulation of <italic>F3′H1</italic>, <italic>DFR4</italic> and <italic>LDOX1</italic> resulted in the accumulation of cyanidin derivatives during the ripening process of KB, indicating the positive relationship between the expression of anthocyanin biosynthetic genes and the anthocyanin accumulation. Furthermore, the ability of RcM<italic>CHI2</italic> (<italic>R. coreanus</italic> Miquel chalcone flavanone isomerase 2) gene to complement <italic>Arabidopsis transparent testa 5</italic> mutant supported the feasibility of our transcriptome library to provide the gene resources for improving plant nutrition and pigmentation. Taken together, these datasets obtained from transcriptome library and metabolic profiling would be helpful to define the gene-metabolite relationships in this non-model plant.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bushakra, Jm" uniqKey="Bushakra J">JM Bushakra</name></author><author><name sortKey="Stephens, Mj" uniqKey="Stephens M">MJ Stephens</name></author><author><name sortKey="Atmadjaja, An" uniqKey="Atmadjaja A">AN Atmadjaja</name></author><author><name sortKey="Lewers, Ks" uniqKey="Lewers K">KS Lewers</name></author><author><name sortKey="Symonds, Vv" uniqKey="Symonds V">VV Symonds</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hummer, Ke" uniqKey="Hummer K">KE Hummer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Montrose, Dc" uniqKey="Montrose D">DC Montrose</name></author><author><name sortKey="Horelik, Na" uniqKey="Horelik N">NA 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Braun</name></author><author><name sortKey="Grotewold, E" uniqKey="Grotewold E">E Grotewold</name></author></analytic></biblStruct></listBibl></div1></back></TEI><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, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24505466</article-id><article-id pub-id-type="pmc">3914977</article-id><article-id pub-id-type="publisher-id">PONE-D-13-31052</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0088292</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology</subject><subj-group><subject>Biotechnology</subject><subj-group><subject>Plant Biotechnology</subject></subj-group></subj-group><subj-group><subject>Computational Biology</subject><subj-group><subject>Metabolic Networks</subject></subj-group></subj-group><subj-group><subject>Genetics</subject><subj-group><subject>Plant Genetics</subject></subj-group></subj-group><subj-group><subject>Genomics</subject><subj-group><subject>Genome Analysis Tools</subject><subj-group><subject>Transcriptomes</subject></subj-group></subj-group></subj-group><subj-group><subject>Plant Science</subject><subj-group><subject>Plant Biotechnology</subject><subj-group><subject>Plant Genomics</subject></subj-group></subj-group><subj-group><subject>Plants</subject><subj-group><subject>Fruits</subject></subj-group></subj-group><subj-group><subject>Plant Genetics</subject><subject>Plant Genomics</subject></subj-group></subj-group></subj-group></article-categories><title-group><article-title><italic>De-novo</italic> RNA Sequencing and Metabolite Profiling to Identify Genes Involved in Anthocyanin Biosynthesis in Korean Black Raspberry (<italic>Rubus coreanus</italic> Miquel)</article-title><alt-title alt-title-type="running-head">RNA-Seq and Metabolomics in Korean Black Raspberry</alt-title></title-group><contrib-group><contrib contrib-type="author" equal-contrib="yes"><name><surname>Hyun</surname><given-names>Tae Kyung</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author" equal-contrib="yes"><name><surname>Lee</surname><given-names>Sarah</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Rim</surname><given-names>Yeonggil</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Kumar</surname><given-names>Ritesh</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Han</surname><given-names>Xiao</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lee</surname><given-names>Sang Yeol</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lee</surname><given-names>Choong Hwan</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Kim</surname><given-names>Jae-Yean</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Division of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Ouzounis</surname><given-names>Christos A.</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>The Centre for Research and Technology, Hellas, Greece</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>chlee123@konkuk.ac.kr</email> (CHL); <email>kimjy@gnu.ac.kr</email> (JYK)</corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: TKH SL SYL CHL JYK. Performed the experiments: TKH SL YR RK XH. Analyzed the data: TKH SL CHL JYK. Contributed reagents/materials/analysis tools: SYL CHL JYK. Wrote the paper: TKH SL RK CHL JYK.</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>5</day><month>2</month><year>2014</year></pub-date><volume>9</volume><issue>2</issue><elocation-id>e88292</elocation-id><history><date date-type="received"><day>26</day><month>7</month><year>2013</year></date><date date-type="accepted"><day>7</day><month>1</month><year>2014</year></date></history><permissions><copyright-year>2014</copyright-year><copyright-holder>Hyun et al</copyright-holder><license><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><abstract><p>The Korean black raspberry (<italic>Rubus coreanus</italic> Miquel, KB) on ripening is usually consumed as fresh fruit, whereas the unripe KB has been widely used as a source of traditional herbal medicine. Such a stage specific utilization of KB has been assumed due to the changing metabolite profile during fruit ripening process, but so far molecular and biochemical changes during its fruit maturation are poorly understood. To analyze biochemical changes during fruit ripening process at molecular level, firstly, we have sequenced, assembled, and annotated the transcriptome of KB fruits. Over 4.86 Gb of normalized cDNA prepared from fruits was sequenced using Illumina HiSeq™ 2000, and assembled into 43,723 unigenes. Secondly, we have reported that alterations in anthocyanins and proanthocyanidins are the major factors facilitating variations in these stages of fruits. In addition, up-regulation of <italic>F3′H1</italic>, <italic>DFR4</italic> and <italic>LDOX1</italic> resulted in the accumulation of cyanidin derivatives during the ripening process of KB, indicating the positive relationship between the expression of anthocyanin biosynthetic genes and the anthocyanin accumulation. Furthermore, the ability of RcM<italic>CHI2</italic> (<italic>R. coreanus</italic> Miquel chalcone flavanone isomerase 2) gene to complement <italic>Arabidopsis transparent testa 5</italic> mutant supported the feasibility of our transcriptome library to provide the gene resources for improving plant nutrition and pigmentation. Taken together, these datasets obtained from transcriptome library and metabolic profiling would be helpful to define the gene-metabolite relationships in this non-model plant.</p></abstract><funding-group><funding-statement>This work was supported by Science and Technology and a grant from the Next-Generation BioGreen 21 Program (SSAC grant PJ009495; PJ00952004), Rural Development Administration, Republic of Korea. 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><page-count count="13"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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