De novo transcriptome sequencing of radish (Raphanus sativusL.) and analysis of major genes involved in glucosinolate metabolism

BMC Genomics

Research Article

Xianwen Zhu¹  Yiqin Gong²  Liang Xu²  Liwang Liu²  Zhe Liu²  Lulu Zhai²  Rugang Yu²  Yan Pan²  Yan Wang³ 

[1] Department of Plant Sciences, North Dakota State University, 58108, Fargo, ND, USA;National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, P.R. China;Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R. China, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, P.R. China;National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, P.R. China;Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R. China, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, P.R. China;Institute of Vegetable Crops, Wenzhou Academy of Agricultural Sciences; Wenzhou Vocation College of Science & Technology, 325014, Wenzhou, P.R. China;

关键词: Radish;    De novo;    RNA-Seq;    Transcriptome;    Glucosinolate metabolic pathways;   

DOI  :  10.1186/1471-2164-14-836

 received in 2013-06-17, accepted in 2013-11-14,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundRadish (Raphanus sativus L.), is an important root vegetable crop worldwide. Glucosinolates in the fleshy taproot significantly affect the flavor and nutritional quality of radish. However, little is known about the molecular mechanisms underlying glucosinolate metabolism in radish taproots. The limited availability of radish genomic information has greatly hindered functional genomic analysis and molecular breeding in radish.ResultsIn this study, a high-throughput, large-scale RNA sequencing technology was employed to characterize the de novo transcriptome of radish roots at different stages of development. Approximately 66.11 million paired-end reads representing 73,084 unigenes with a N50 length of 1,095 bp, and a total length of 55.73 Mb were obtained. Comparison with the publicly available protein database indicates that a total of 67,305 (about 92.09% of the assembled unigenes) unigenes exhibit similarity (e –value ≤ 1.0e-5) to known proteins. The functional annotation and classification including Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the main activated genes in radish taproots are predominately involved in basic physiological and metabolic processes, biosynthesis of secondary metabolite pathways, signal transduction mechanisms and other cellular components and molecular function related terms. The majority of the genes encoding enzymes involved in glucosinolate (GS) metabolism and regulation pathways were identified in the unigene dataset by targeted searches of their annotations. A number of candidate radish genes in the glucosinolate metabolism related pathways were also discovered, from which, eight genes were validated by T-A cloning and sequencing while four were validated by quantitative RT-PCR expression profiling.ConclusionsThe ensuing transcriptome dataset provides a comprehensive sequence resource for molecular genetics research in radish. It will serve as an important public information platform to further understanding of the molecular mechanisms involved in biosynthesis and metabolism of the related nutritional and flavor components during taproot formation in radish.

【 授权许可】

Unknown   
© Wang et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.