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/Corpus ); 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 ; Wen-Bo Li ; Hong-Fang Liu ; Fa-Bo ChenSource :
- PloS one [ 1932-6203 ] ; 2020.
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
Links to Exploration step
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<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>
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<keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>Anthocyanins</term>
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<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>
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<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>
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