De-novo RNA Sequencing and Metabolite Profiling to Identify Genes Involved in Anthocyanin Biosynthesis in Korean Black Raspberry (Rubus coreanus Miquel)
Identifieur interne : 000C37 ( Main/Exploration ); précédent : 000C36; suivant : 000C38De-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
Affiliations:
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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><wicri:noRegion>Jinju</wicri:noRegion></affiliation></author><author><name sortKey="Lee, Sarah" sort="Lee, Sarah" uniqKey="Lee S" first="Sarah" last="Lee">Sarah Lee</name><affiliation wicri:level="3"><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><placeName><settlement type="city">Séoul</settlement></placeName></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><wicri:noRegion>Jinju</wicri:noRegion></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><wicri:noRegion>Jinju</wicri:noRegion></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><wicri:noRegion>Jinju</wicri:noRegion></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><wicri:noRegion>Jinju</wicri:noRegion></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="3"><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><placeName><settlement type="city">Séoul</settlement></placeName></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><wicri:noRegion>Jinju</wicri:noRegion></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><idno type="wicri:Area/Pmc/Checkpoint">000941</idno><idno type="wicri:Area/Ncbi/Merge">001585</idno><idno type="wicri:Area/Ncbi/Curation">001585</idno><idno type="wicri:Area/Ncbi/Checkpoint">001585</idno><idno type="wicri:Area/Main/Merge">000C40</idno><idno type="wicri:Area/Main/Curation">000C37</idno><idno type="wicri:Area/Main/Exploration">000C37</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><wicri:noRegion>Jinju</wicri:noRegion></affiliation></author><author><name sortKey="Lee, Sarah" sort="Lee, Sarah" uniqKey="Lee S" first="Sarah" last="Lee">Sarah Lee</name><affiliation wicri:level="3"><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><placeName><settlement type="city">Séoul</settlement></placeName></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><wicri:noRegion>Jinju</wicri:noRegion></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><wicri:noRegion>Jinju</wicri:noRegion></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><wicri:noRegion>Jinju</wicri:noRegion></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><wicri:noRegion>Jinju</wicri:noRegion></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="3"><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><placeName><settlement type="city">Séoul</settlement></placeName></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><wicri:noRegion>Jinju</wicri:noRegion></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><affiliations><list><country><li>Corée du Sud</li></country><settlement><li>Séoul</li></settlement></list><tree><country name="Corée du Sud"><noRegion><name sortKey="Hyun, Tae Kyung" sort="Hyun, Tae Kyung" uniqKey="Hyun T" first="Tae Kyung" last="Hyun">Tae Kyung Hyun</name></noRegion><name sortKey="Han, Xiao" sort="Han, Xiao" uniqKey="Han X" first="Xiao" last="Han">Xiao Han</name><name sortKey="Kim, Jae Yean" sort="Kim, Jae Yean" uniqKey="Kim J" first="Jae-Yean" last="Kim">Jae-Yean Kim</name><name sortKey="Kumar, Ritesh" sort="Kumar, Ritesh" uniqKey="Kumar R" first="Ritesh" last="Kumar">Ritesh Kumar</name><name sortKey="Lee, Choong Hwan" sort="Lee, Choong Hwan" uniqKey="Lee C" first="Choong Hwan" last="Lee">Choong Hwan Lee</name><name sortKey="Lee, Sang Yeol" sort="Lee, Sang Yeol" uniqKey="Lee S" first="Sang Yeol" last="Lee">Sang Yeol Lee</name><name sortKey="Lee, Sarah" sort="Lee, Sarah" uniqKey="Lee S" first="Sarah" last="Lee">Sarah Lee</name><name sortKey="Rim, Yeonggil" sort="Rim, Yeonggil" uniqKey="Rim Y" first="Yeonggil" last="Rim">Yeonggil Rim</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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