Identification of differential expression genes related to anthocyanin biosynthesis in carmine radish (Raphanus sativus L.) fleshy roots using comparative RNA-Seq method.
Identifieur interne : 000158 ( Main/Curation ); précédent : 000157; suivant : 000159Identification of differential expression genes related to anthocyanin biosynthesis in carmine radish (Raphanus sativus L.) fleshy roots using comparative RNA-Seq method.
Auteurs : Jian Gao [République populaire de Chine] ; Wen-Bo Li [République populaire de Chine] ; Hong-Fang Liu [République populaire de Chine] ; Fa-Bo Chen [République populaire de Chine]Source :
- PloS one [ 1932-6203 ] ; 2020.
Descripteurs français
- KwdFr :
- Anthocyanes (biosynthèse), Gene Ontology (MeSH), Gènes de plante (génétique), Légumes (génétique), Légumes (métabolisme), Protéines végétales (génétique), Protéines végétales (métabolisme), Racines de plante (génétique), Racines de plante (métabolisme), Raphanus (génétique), Raphanus (métabolisme), Régulation de l'expression des gènes végétaux (MeSH), Séquençage nucléotidique à haut débit (MeSH), Voies de biosynthèse (génétique).
- MESH :
- biosynthèse : Anthocyanes.
- génétique : Gènes de plante, Légumes, Protéines végétales, Racines de plante, Raphanus, Voies de biosynthèse.
- métabolisme : Légumes, Protéines végétales, Racines de plante, Raphanus.
- Gene Ontology, Régulation de l'expression des gènes végétaux, Séquençage nucléotidique à haut débit.
English descriptors
- KwdEn :
- Anthocyanins (biosynthesis), Biosynthetic Pathways (genetics), Gene Expression Regulation, Plant (MeSH), Gene Ontology (MeSH), Genes, Plant (genetics), High-Throughput Nucleotide Sequencing (MeSH), Plant Proteins (genetics), Plant Proteins (metabolism), Plant Roots (genetics), Plant Roots (metabolism), RNA-Seq (MeSH), Raphanus (genetics), Raphanus (metabolism), Vegetables (genetics), Vegetables (metabolism).
- MESH :
- chemical , biosynthesis : Anthocyanins.
- genetics : Biosynthetic Pathways, Genes, Plant, Plant Proteins, Plant Roots, Raphanus, Vegetables.
- chemical , metabolism : Plant Proteins, Plant Roots, Raphanus, Vegetables.
- Gene Expression Regulation, Plant, Gene Ontology, High-Throughput Nucleotide Sequencing, RNA-Seq.
Abstract
Radish (Raphanus sativus L.), is an important root vegetable crop grown worldwide, and it contains phyto-anthocyanins. However, only limited studies have been conducted to elucidate the molecular mechanisms underlying anthocyanin biosynthesis in the different color variants of the radish fleshy root. In this study, Illumina paired-end RNA-sequencing was employed to characterize the transcriptomic changes in seven different types of radish fleshy roots. Approximately, 126 co-modulated differentially expressed genes were obtained, and most DEGs were more likely to participate in anthocyanin biosynthesis, including two transcription factors RsMYB_9 and RsERF070, and four functional genes RsBRICK1, RsBRI1-like2, RsCOX1, and RsCRK10. In addition, some related genes such as RsCHS, RsCHI, RsANS, RsMT2-4, RsUF3GT, glutathione S-transferase F12, RsUFGT78D2-like and RsUDGT-75C1-like significantly contributed to the regulatory mechanism of anthocyanin biosynthesis in the radish cultivars. Furthermore, gene ontology analysis revealed that the anthocyanin-containing compound biosynthetic process, anthocyanin-containing compound metabolic process, and significantly enriched pathways of the co-modulated DEGs were overrepresented in these cultivars. These results will expand our understanding of the complex molecular mechanism underlying anthocyanin synthesis-related genes in radish.
DOI: 10.1371/journal.pone.0231729
PubMed: 32330148
PubMed Central: PMC7182184
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Bioengineering, Yangtze Normal University, Chongqing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing</wicri:regionArea></affiliation></author><author><name sortKey="Liu, Hong Fang" sort="Liu, Hong Fang" uniqKey="Liu H" first="Hong-Fang" last="Liu">Hong-Fang Liu</name><affiliation wicri:level="1"><nlm:affiliation>School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:affiliation>Green Intelligence Environmental School, Yangtze Normal University, Fuling, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Green Intelligence Environmental School, Yangtze Normal University, Fuling</wicri:regionArea></affiliation></author><author><name sortKey="Chen, Fa Bo" sort="Chen, Fa Bo" uniqKey="Chen F" first="Fa-Bo" last="Chen">Fa-Bo Chen</name><affiliation wicri:level="1"><nlm:affiliation>School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing</wicri:regionArea></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Anthocyanins (biosynthesis)</term><term>Biosynthetic Pathways (genetics)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Gene Ontology (MeSH)</term><term>Genes, Plant (genetics)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (metabolism)</term><term>Plant Roots (genetics)</term><term>Plant Roots (metabolism)</term><term>RNA-Seq (MeSH)</term><term>Raphanus (genetics)</term><term>Raphanus (metabolism)</term><term>Vegetables (genetics)</term><term>Vegetables (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Anthocyanes (biosynthèse)</term><term>Gene Ontology (MeSH)</term><term>Gènes de plante (génétique)</term><term>Légumes (génétique)</term><term>Légumes (métabolisme)</term><term>Protéines végétales (génétique)</term><term>Protéines végétales (métabolisme)</term><term>Racines de plante (génétique)</term><term>Racines de plante (métabolisme)</term><term>Raphanus (génétique)</term><term>Raphanus (métabolisme)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Séquençage nucléotidique à haut débit (MeSH)</term><term>Voies de biosynthèse (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>Anthocyanins</term></keywords><keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr"><term>Anthocyanes</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Biosynthetic Pathways</term><term>Genes, Plant</term><term>Plant Proteins</term><term>Plant Roots</term><term>Raphanus</term><term>Vegetables</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Gènes de plante</term><term>Légumes</term><term>Protéines végétales</term><term>Racines de plante</term><term>Raphanus</term><term>Voies de biosynthèse</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Plant Proteins</term><term>Plant Roots</term><term>Raphanus</term><term>Vegetables</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Légumes</term><term>Protéines végétales</term><term>Racines de plante</term><term>Raphanus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Regulation, Plant</term><term>Gene Ontology</term><term>High-Throughput Nucleotide Sequencing</term><term>RNA-Seq</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Gene Ontology</term><term>Régulation de l'expression des gènes végétaux</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Radish (Raphanus sativus L.), is an important root vegetable crop grown worldwide, and it contains phyto-anthocyanins. However, only limited studies have been conducted to elucidate the molecular mechanisms underlying anthocyanin biosynthesis in the different color variants of the radish fleshy root. In this study, Illumina paired-end RNA-sequencing was employed to characterize the transcriptomic changes in seven different types of radish fleshy roots. Approximately, 126 co-modulated differentially expressed genes were obtained, and most DEGs were more likely to participate in anthocyanin biosynthesis, including two transcription factors RsMYB_9 and RsERF070, and four functional genes RsBRICK1, RsBRI1-like2, RsCOX1, and RsCRK10. In addition, some related genes such as RsCHS, RsCHI, RsANS, RsMT2-4, RsUF3GT, glutathione S-transferase F12, RsUFGT78D2-like and RsUDGT-75C1-like significantly contributed to the regulatory mechanism of anthocyanin biosynthesis in the radish cultivars. Furthermore, gene ontology analysis revealed that the anthocyanin-containing compound biosynthetic process, anthocyanin-containing compound metabolic process, and significantly enriched pathways of the co-modulated DEGs were overrepresented in these cultivars. These results will expand our understanding of the complex molecular mechanism underlying anthocyanin synthesis-related genes in radish.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">32330148</PMID><DateCompleted><Year>2020</Year><Month>07</Month><Day>15</Day></DateCompleted><DateRevised><Year>2020</Year><Month>07</Month><Day>15</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>15</Volume><Issue>4</Issue><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Identification of differential expression genes related to anthocyanin biosynthesis in carmine radish (Raphanus sativus L.) fleshy roots using comparative RNA-Seq method.</ArticleTitle><Pagination><MedlinePgn>e0231729</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0231729</ELocationID><Abstract><AbstractText>Radish (Raphanus sativus L.), is an important root vegetable crop grown worldwide, and it contains phyto-anthocyanins. However, only limited studies have been conducted to elucidate the molecular mechanisms underlying anthocyanin biosynthesis in the different color variants of the radish fleshy root. In this study, Illumina paired-end RNA-sequencing was employed to characterize the transcriptomic changes in seven different types of radish fleshy roots. Approximately, 126 co-modulated differentially expressed genes were obtained, and most DEGs were more likely to participate in anthocyanin biosynthesis, including two transcription factors RsMYB_9 and RsERF070, and four functional genes RsBRICK1, RsBRI1-like2, RsCOX1, and RsCRK10. In addition, some related genes such as RsCHS, RsCHI, RsANS, RsMT2-4, RsUF3GT, glutathione S-transferase F12, RsUFGT78D2-like and RsUDGT-75C1-like significantly contributed to the regulatory mechanism of anthocyanin biosynthesis in the radish cultivars. Furthermore, gene ontology analysis revealed that the anthocyanin-containing compound biosynthetic process, anthocyanin-containing compound metabolic process, and significantly enriched pathways of the co-modulated DEGs were overrepresented in these cultivars. These results will expand our understanding of the complex molecular mechanism underlying anthocyanin synthesis-related genes in radish.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>Jian</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Wen-Bo</ForeName><Initials>WB</Initials><AffiliationInfo><Affiliation>School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Hong-Fang</ForeName><Initials>HF</Initials><AffiliationInfo><Affiliation>School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Green Intelligence Environmental School, Yangtze Normal University, Fuling, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Fa-Bo</ForeName><Initials>FB</Initials><Identifier Source="ORCID">0000-0002-4693-2650</Identifier><AffiliationInfo><Affiliation>School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>04</Month><Day>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D000872">Anthocyanins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000872" MajorTopicYN="N">Anthocyanins</DescriptorName><QualifierName UI="Q000096" MajorTopicYN="Y">biosynthesis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D053898" MajorTopicYN="N">Biosynthetic Pathways</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D063990" MajorTopicYN="N">Gene Ontology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000081246" MajorTopicYN="N">RNA-Seq</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D031224" MajorTopicYN="N">Raphanus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014675" MajorTopicYN="N">Vegetables</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading></MeshHeadingList><CoiStatement>The authors have declared that no competing interests exist.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>10</Month><Day>08</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>03</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>4</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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