ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2022
An improved Raphanus sativus cv. WK10039 genome localizes centromeres, uncovers variation of DNA methylation and resolves arrangement of the ancestral Brassica genome blocks in radish chromosomes.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Expanding the triangle of U: comparative analysis of the Hirschfeldia incana genome provides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits.Annals of botany · 2026Article
- Structure and evolution of the Forsythieae genome elucidated by chromosome-level genome comparison of Abeliophyllum distichum and Forsythia ovata (Oleaceae).Communications biology · 2025Article
- Telomere-to-telomere Phragmites australis reference genome assembly with a B chromosome provides insights into its evolution and polysaccharide biosynthesis.Communications biology · 2025Article
- Chromosome-level assemblies of the endemic Korean species Abeliophyllum distichum and Forsythia ovata.Scientific data · 2024Article
- A novel SNP within the Rsa10025320 gene is highly associated with hollowness in red-skinned radish fleshy roots.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Identification and variation of a new restorer of fertility gene that induces cleavage in orf138 mRNA of Ogura male sterility in radish.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Profiling genome-wide methylation in two maples: Fine-scale approaches to detection with nanopore technology.Evolutionary applications · 2024Article
- Genome ofFrontiers in genetics · 2024Article
- Quantitative trait locus (QTL) analysis and fine-mapping forBreeding science · 2023Article
- Effect of structural variation in the promoter region ofFrontiers in plant science · 2023Article
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Abstract
key messageThis study presents an improved genome of Raphanus sativus cv. WK10039 uncovering centromeres and differentially methylated regions of radish chromosomes. Comprehensive genome comparison of radish and diploid Brassica species of U's triangle reveals that R. sativus arose from the Brassica B genome lineage and is a sibling species of B. nigra. Radish (Raphanus sativus L.) is a key root vegetable crop closely related to the Brassica crop species of the family Brassicaceae. We reported a draft genome of R. sativus cv. WK10039 (Rs1.0), which had 54.6 Mb gaps. To study the radish genome and explore previously unknown regions, we generated an improved genome assembly (Rs2.0) by long-read sequencing and high-resolution genome-wide mapping of chromatin interactions. Rs2.0 was 434.9 Mb in size with 0.27 Mb gaps, and the N50 scaffold length was 37.3 Mb (40-fold larger assembly compared to Rs1.0). Approximately 38% of Rs2.0 was comprised of repetitive sequences, and 52,768 protein-coding genes and 4845 non-protein-coding genes were predicted and annotated. The improved contiguity and coverage of Rs2.0, along with the detection of highly methylated regions, enabled localization of centromeres where R. sativus-specific centromere-associated repeats, full-length OTA and CRM LTR-Gypsy retrotransposons, hAT-Ac, CMC-EnSpm and Helitron DNA transposons, and sequences highly homologous to B. nigra centromere-specific CENH3-associated CL sequences were enriched. Whole-genome bisulfite sequencing combined with mRNA sequencing identified differential epigenetic marks in the radish genome related to tissue development. Synteny comparison and genomic distance analysis of radish and three diploid Brassica species of U's triangle suggested that the radish genome arose from the Brassica B genome lineage through unique rearrangement of the triplicated ancestral Brassica genome after splitting of the Brassica A/C and B genomes.
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