High-Throughput Sequencing and De Novo Assembly of Red and Green Forms of the Perilla frutescens var. crispa Transcriptome
Identifieur interne : 000605 ( Main/Exploration ); précédent : 000604; suivant : 000606High-Throughput Sequencing and De Novo Assembly of Red and Green Forms of the Perilla frutescens var. crispa Transcriptome
Auteurs : Atsushi Fukushima [Japon] ; Michimi Nakamura [Japon] ; Hideyuki Suzuki [Japon] ; Kazuki Saito [Japon] ; Mami Yamazaki [Japon]Source :
- PLoS ONE [ 1932-6203 ] ; 2015.
Abstract
Url:
DOI: 10.1371/journal.pone.0129154
PubMed: 26070213
PubMed Central: 4466401
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">High-Throughput Sequencing and <italic>De Novo</italic> Assembly of Red and Green Forms of the <italic>Perilla frutescens</italic> var. <italic>crispa</italic> Transcriptome</title><author><name sortKey="Fukushima, Atsushi" sort="Fukushima, Atsushi" uniqKey="Fukushima A" first="Atsushi" last="Fukushima">Atsushi Fukushima</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230–0045, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230–0045</wicri:regionArea><wicri:noRegion>230–0045</wicri:noRegion></affiliation></author><author><name sortKey="Nakamura, Michimi" sort="Nakamura, Michimi" uniqKey="Nakamura M" first="Michimi" last="Nakamura">Michimi Nakamura</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba, 263–8522, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba, 263–8522</wicri:regionArea><wicri:noRegion>263–8522</wicri:noRegion></affiliation></author><author><name sortKey="Suzuki, Hideyuki" sort="Suzuki, Hideyuki" uniqKey="Suzuki H" first="Hideyuki" last="Suzuki">Hideyuki Suzuki</name><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, 292–0818, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, 292–0818</wicri:regionArea><wicri:noRegion>292–0818</wicri:noRegion></affiliation></author><author><name sortKey="Saito, Kazuki" sort="Saito, Kazuki" uniqKey="Saito K" first="Kazuki" last="Saito">Kazuki Saito</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230–0045, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230–0045</wicri:regionArea><wicri:noRegion>230–0045</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba, 263–8522, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba, 263–8522</wicri:regionArea><wicri:noRegion>263–8522</wicri:noRegion></affiliation></author><author><name sortKey="Yamazaki, Mami" sort="Yamazaki, Mami" uniqKey="Yamazaki M" first="Mami" last="Yamazaki">Mami Yamazaki</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba, 263–8522, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba, 263–8522</wicri:regionArea><wicri:noRegion>263–8522</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26070213</idno><idno type="pmc">4466401</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4466401</idno><idno type="RBID">PMC:4466401</idno><idno type="doi">10.1371/journal.pone.0129154</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000155</idno><idno type="wicri:Area/Pmc/Curation">000155</idno><idno type="wicri:Area/Pmc/Checkpoint">000474</idno><idno type="wicri:Area/Ncbi/Merge">001B74</idno><idno type="wicri:Area/Ncbi/Curation">001B74</idno><idno type="wicri:Area/Ncbi/Checkpoint">001B74</idno><idno type="wicri:Area/Main/Merge">000605</idno><idno type="wicri:Area/Main/Curation">000605</idno><idno type="wicri:Area/Main/Exploration">000605</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">High-Throughput Sequencing and <italic>De Novo</italic> Assembly of Red and Green Forms of the <italic>Perilla frutescens</italic> var. <italic>crispa</italic> Transcriptome</title><author><name sortKey="Fukushima, Atsushi" sort="Fukushima, Atsushi" uniqKey="Fukushima A" first="Atsushi" last="Fukushima">Atsushi Fukushima</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230–0045, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230–0045</wicri:regionArea><wicri:noRegion>230–0045</wicri:noRegion></affiliation></author><author><name sortKey="Nakamura, Michimi" sort="Nakamura, Michimi" uniqKey="Nakamura M" first="Michimi" last="Nakamura">Michimi Nakamura</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba, 263–8522, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba, 263–8522</wicri:regionArea><wicri:noRegion>263–8522</wicri:noRegion></affiliation></author><author><name sortKey="Suzuki, Hideyuki" sort="Suzuki, Hideyuki" uniqKey="Suzuki H" first="Hideyuki" last="Suzuki">Hideyuki Suzuki</name><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, 292–0818, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, 292–0818</wicri:regionArea><wicri:noRegion>292–0818</wicri:noRegion></affiliation></author><author><name sortKey="Saito, Kazuki" sort="Saito, Kazuki" uniqKey="Saito K" first="Kazuki" last="Saito">Kazuki Saito</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230–0045, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230–0045</wicri:regionArea><wicri:noRegion>230–0045</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba, 263–8522, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba, 263–8522</wicri:regionArea><wicri:noRegion>263–8522</wicri:noRegion></affiliation></author><author><name sortKey="Yamazaki, Mami" sort="Yamazaki, Mami" uniqKey="Yamazaki M" first="Mami" last="Yamazaki">Mami Yamazaki</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba, 263–8522, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba, 263–8522</wicri:regionArea><wicri:noRegion>263–8522</wicri:noRegion></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><italic>Perilla frutescens</italic> var. <italic>crispa</italic> (Labiatae) has two chemo-varietal forms, i.e. red and green forms of perilla, that differ in the production of anthocyanins. To facilitate molecular biological and biochemical studies in perilla-specialized metabolism we used Illumina RNA-sequencing technology in our comprehensive comparison of the transcriptome map of the leaves of red and green forms of perilla. Sequencing generated over 1.2 billion short reads with an average length of 101 nt. <italic>De novo</italic> transcriptome assembly yielded 47,788 and 47,840 unigenes in the red and green forms of perilla plants, respectively. Comparison of the assembled unigenes and existing perilla cDNA sequences showed highly reliable alignment. All unigenes were annotated with gene ontology (GO) and Enzyme Commission numbers and entered into the Kyoto Encyclopedia of Genes and Genomes. We identified 68 differentially expressed genes (DEGs) in red and green forms of perilla. GO enrichment analysis of the DEGs showed that genes involved in the anthocyanin metabolic process were enriched. Differential expression analysis revealed that the transcript level of anthocyanin biosynthetic unigenes encoding flavonoid 3’-hydroxylase, dihydroflavonol 4-reductase, and anthocyanidin synthase was significantly higher in red perilla, while the transcript level of unigenes encoding limonene synthase was significantly higher in green perilla. Our data serve as a basis for future research on perilla bio-engineering and provide a shortcut for the characterization of new functional genes in <italic>P</italic>. <italic>frutescens</italic>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Winkel Shirley, B" uniqKey="Winkel Shirley B">B Winkel-Shirley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Moura, Jc" uniqKey="Moura J">JC Moura</name></author><author><name sortKey="Bonine, Ca" uniqKey="Bonine C">CA Bonine</name></author><author><name sortKey="De Oliveira Fernandes Viana, J" uniqKey="De Oliveira Fernandes Viana J">J de Oliveira Fernandes Viana</name></author><author><name sortKey="Dornelas, Mc" uniqKey="Dornelas M">MC Dornelas</name></author><author><name sortKey="Mazzafera, P" uniqKey="Mazzafera P">P Mazzafera</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Koes, R" uniqKey="Koes R">R 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Pages</name></author><author><name sortKey="Aboyoun, P" uniqKey="Aboyoun P">P Aboyoun</name></author><author><name sortKey="Gentleman, R" uniqKey="Gentleman R">R Gentleman</name></author><author><name sortKey="Debroy, S" uniqKey="Debroy S">S DebRoy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Robinson, Md" uniqKey="Robinson M">MD Robinson</name></author><author><name sortKey="Oshlack, A" uniqKey="Oshlack A">A Oshlack</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Robinson, Md" uniqKey="Robinson M">MD Robinson</name></author><author><name sortKey="Mccarthy, Dj" uniqKey="Mccarthy D">DJ McCarthy</name></author><author><name sortKey="Smyth, Gk" uniqKey="Smyth G">GK Smyth</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Anders, S" uniqKey="Anders S">S Anders</name></author><author><name sortKey="Huber, W" uniqKey="Huber W">W Huber</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Japon</li></country></list><tree><country name="Japon"><noRegion><name sortKey="Fukushima, Atsushi" sort="Fukushima, Atsushi" uniqKey="Fukushima A" first="Atsushi" last="Fukushima">Atsushi Fukushima</name></noRegion><name sortKey="Nakamura, Michimi" sort="Nakamura, Michimi" uniqKey="Nakamura M" first="Michimi" last="Nakamura">Michimi Nakamura</name><name sortKey="Saito, Kazuki" sort="Saito, Kazuki" uniqKey="Saito K" first="Kazuki" last="Saito">Kazuki Saito</name><name sortKey="Saito, Kazuki" sort="Saito, Kazuki" uniqKey="Saito K" first="Kazuki" last="Saito">Kazuki Saito</name><name sortKey="Suzuki, Hideyuki" sort="Suzuki, Hideyuki" uniqKey="Suzuki H" first="Hideyuki" last="Suzuki">Hideyuki Suzuki</name><name sortKey="Yamazaki, Mami" sort="Yamazaki, Mami" uniqKey="Yamazaki M" first="Mami" last="Yamazaki">Mami Yamazaki</name></country></tree></affiliations></record>Pour manipuler 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