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Title 

De novo assembly and characterization of the complete chloroplast genome of radish (Raphanus sativus L.)

Authors 

Y M JeongWon Hyung JungJ H MunNamshin KimH J Yu

Publisher 

Elsevier

Issue Date 

2014

Citation 

Gene, vol. 551, no. 1, pp. 39-48

Keywords 

Brassicaceae familyChloroplast genomeNext-generation sequencingRaphanus sativusSimple sequence repeat

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 Brassica napus. 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

ISSN 

0378-1119

Link 

http://dx.doi.org/10.1016/j.gene.2014.08.038

Appears in Collections

1. Journal Articles > Journal Articles

Registered Date

2017-04-19


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