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

Gene
Young-Min JeongHee-Ju Yu

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...Continue Reading

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Related Concepts

Phylogeny
Plant Proteins
Transfer RNA
Genome, Plant
Tetranucleotide Repeats
Turnip
Raphanus
Genome, Chloroplast
High-Throughput Nucleotide Sequencing
Base Sequence

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