1. Identification of differential expression genes related to anthocyanin biosynthesis in carmine radish (Raphanus sativus L.) fleshy roots using comparative RNA-Seq method
- Author
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Wenbo Li, Fabo Chen, Hong-Fang Liu, and Jian Gao
- Subjects
0106 biological sciences ,0301 basic medicine ,Inbred Strains ,Raphanus ,Gene Expression ,RNA-Seq ,Vegetable Crops ,01 natural sciences ,Plant Roots ,Biochemistry ,Transcriptome ,Anthocyanins ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Gene expression ,Vegetables ,Plant Proteins ,Regulation of gene expression ,Multidisciplinary ,food and beverages ,High-Throughput Nucleotide Sequencing ,Eukaryota ,Agriculture ,Genomics ,Plants ,Experimental Organism Systems ,Biosynthetic process ,Medicine ,Transcriptome Analysis ,Research Article ,Science ,DNA transcription ,Crops ,Brassica ,Biology ,Genes, Plant ,Research and Analysis Methods ,Biosynthesis ,03 medical and health sciences ,DNA-binding proteins ,Genetics ,Gene Regulation ,Gene ,fungi ,Organisms ,Biology and Life Sciences ,Proteins ,Computational Biology ,biology.organism_classification ,Genome Analysis ,Biosynthetic Pathways ,Regulatory Proteins ,030104 developmental biology ,Gene Ontology ,chemistry ,Anthocyanin ,Animal Studies ,Radish ,010606 plant biology & botany ,Transcription Factors ,Crop Science - 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.
- Published
- 2019