Young-Min Jeong

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

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.

The complete mitochondrial genome of cultivated radish WK10039 (Raphanus sativus L.)

Abstract We determined the complete nucleotide sequence of the mitochondrial genome of radish cultivar WK10039 (Raphanus sativus L.). The total length of the mtDNA sequence is 244,054 bp, with GC content of 45.3%. The radish mtDNA contains 82 protein-coding genes, 17 tRNA genes, and 3 rRNA genes. Among the protein-coding genes, 34 encode proteins with known functions. There are two 5529 bp repeats in the radish mitochondrial genome that may contribute to DNA recombination resulting in at least three different forms of mtDNA in radish.

Identification of candidate domestication regions in the radish genome based on high-depth resequencing analysis of 17 genotypes

Key messageThis study provides high-quality variation data of diverse radish genotypes. Genome-wide SNP comparison along with RNA-seq analysis identified candidate genes related to domestication that have potential as trait-related markers for genetics and breeding of radish.AbstractRadish (Raphanus sativus L.) is an annual root vegetable crop that also encompasses diverse wild species. Radish has a long history of domestication, but the origins and selective sweep of cultivated radishes remain controversial. Here, we present comprehensive whole-genome resequencing analysis of radish to explore genomic variation between the radish genotypes and to identify genetic bottlenecks due to domestication in Asian cultivars. High-depth resequencing and multi-sample genotyping analysis of ten cultivated and seven wild accessions obtained 4.0 million high-quality homozygous single-nucleotide polymorphisms (SNPs)/insertions or deletions. Variation analysis revealed that Asian cultivated radish types are closely related to wild Asian accessions, but are distinct from European/American cultivated radishes, supporting the notion that Asian cultivars were domesticated from wild Asian genotypes. SNP comparison between Asian genotypes identified 153 candidate domestication regions (CDRs) containing 512 genes. Network analysis of the genes in CDRs functioning in plant signaling pathways and biochemical processes identified group of genes related to root architecture, cell wall, sugar metabolism, and glucosinolate biosynthesis. Expression profiling of the genes during root development suggested that domestication-related selective advantages included a main taproot with few branched lateral roots, reduced cell wall rigidity and favorable taste. Overall, this study provides evolutionary insights into domestication-related genetic selection in radish as well as identification of gene candidates with the potential to act as trait-related markers for background selection of elite lines in molecular breeding.

Assembly of a radish core collection for evaluation and preservation of genetic diversity

The radish is both an agronomically important root vegetable crop and a wild species of genus Raphanus in the Brassicaceae family. To date, at least four independent draft genome assemblies, marker development studies, and an analysis of radish evolution have been performed; however, there is no core collection of germplasm representing the genetic diversity in radish with minimum genetic redundancy. We report the assembly of a radish core collection consisting of 125 accessions. These accessions were selected by using 25 sequence-tagged site insertion/deletion markers to genotype 70 alleles in 886 accessions obtained from three germplasm banks in Korea, Japan, and Germany. An unweighted pair-group method with arithmetic mean (UPGMA) analysis of the genotyping data classified the accessions into 125 groups based on a Jaccard’s similarity coefficient of 0.72. One representative accession from each group was selected for a core collection that included 125 accessions, corresponding to 14.1% of the whole collection and including all 70 alleles. Principal coordinates analysis demonstrated that the genetic distribution within the core collection was similar to that of the whole collection, and 94% of the total variance within the whole collection could be explained using the analysis of molecular variance from the core collection. The UPGMA and STRUCTURE software analyses identified three major groups of accessions within the core collection, which were the Asian cultivated radish, the European cultivated radish, and the wild radish. The radish core collection developed in this study will be an important plant resource in future research and radish breeding.

Comparative Analysis of the Radish Genome with Brassica Genomes

Raphanus sativus L. includes an annual root vegetable crop, radish, and diverse wild species. R. sativus has a long history of domestication, but its phylogenetic position in the tribe Brassiceae is controversial. A comprehensive analysis of the R. sativus genome will provide fundamental information about the structure of its genome, evolutionary features of polyploidy, and significant insight for phylogenetic delimitation of this species. Diverse genomic resources, including a high-density genetic map, clone libraries, cytogenetic data, and transcriptome data, have been developed to sequence the genome. Recently, the R. sativus cv. ‘WK10039’ (2n = 18, 510.8 Mb) genome was sequenced and assembled into nine chromosome pseudomolecules spanning >98% of the gene space. Comparative mapping of the tPCK-like ancestral genome based on conserved ortholog set markers and proteome comparison revealed that the R. sativus genome has intermediate characteristics between the Brassica A/C and B genomes with triplicated segments, suggesting an internal origin from the genus Brassica. The evolutionary characteristics shared between R. sativus and diploid Brassica species provide genomic evidence for species delimitation of R. sativus and reconstruction of the mesohexaploid ancestral genome.