title: De novo assembly and characterization of the complete chloroplast genome of radish (Raphanus sativus L.).
abstract: Radish (Raphanus sativus L.) is an edible root vegetable crop that is cultivated worldwide and whose genome has been sequenced. Here we report the complete nucleotide sequence of the radish cultivar WK10039 chloroplast (cp) genome, along with a de novo assembly strategy using whole genome shotgun sequence reads obtained by next generation sequencing. The radish cp genome is 153,368 bp in length and has a typical quadripartite structure, composed of a pair of inverted repeat regions (26,217 bp each), a large single copy region (83,170 bp), and a small single copy region (17,764 bp). The radish cp genome contains 87 predicted protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Sequence analysis revealed the presence of 91 simple sequence repeats (SSRs) in the radish cp genome. Phylogenetic analysis of 62 protein-coding gene sequences from the 17 cp genomes of the Brassicaceae family suggested that the radish cp genome is most closely related to the cp genomes of Brassica rapa and Brassicanapus. Comparisons with the B. rapa and B. napus cp genomes revealed highly divergent intergenic sequences and introns that can potentially be developed as diagnostic cp markers. Synonymous and nonsynonymous substitutions of cp genes suggested that nucleotide substitutions have occurred at similar rates in most genes. The complete sequence of the radish cp genome would serve as a valuable resource for the development of new molecular markers and the study of the phylogenetic relationships of Raphanus species in the Brassicaceae family.
authors.affiliation: Department of Life Science, The Catholic University of Korea, Bucheon 420-743, Republic of Korea.
authors.forename: Young-Min
authors.initials: YM
authors.lastname: Jeong
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea.
authors.forename: Won-Hyung
authors.initials: WH
authors.lastname: Chung
authors.affiliation: Department of Bioscience and Bioinformatics, Myongji University, Yongin 449-728, Republic of Korea.
authors.forename: Jeong-Hwan
authors.initials: JH
authors.lastname: Mun
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea. Electronic address: n@rna.kr.
authors.forename: Namshin
authors.initials: N
authors.lastname: Kim
authors.affiliation: Department of Life Science, The Catholic University of Korea, Bucheon 420-743, Republic of Korea. Electronic address: yuheeju@catholic.ac.kr.
authors.forename: Hee-Ju
authors.initials: HJ
authors.lastname: Yu
mesh_terms: D029688:Brassica napus / Q000235:genetics; D054628:Genome, Chloroplast; D018745:Genome, Plant; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D012343:RNA, Transfer; D031224:Raphanus / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D012343:RNA, Transfer
keywords: Brassicaceae family; Chloroplast genome; Next-generation sequencing; Raphanus sativus; Simple sequence repeat