Comparative analysis of the radish genome based on a conserved ortholog set (COS) of Brassica
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This manuscript provides a Brassica conserved ortholog set (COS) that can be used as diagnostic cross-species markers as well as tools for genetic mapping and genome comparison of the Brassicaceae.
A conserved ortholog set (COS) is a collection of genes that are conserved in both sequence and copy number between closely related genomes. COS is a useful resource for developing gene-based markers and is suitable for comparative genome mapping. We developed a COS for Brassica based on proteome comparisons of Arabidopsis thaliana, B. rapa, and B. oleracea to establish a basis for comparative genome analysis of crop species in the Brassicaceae. A total of 1,194 conserved orthologous single-copy genes were identified from the genomes based on whole-genome BLASTP analysis. Gene ontology analysis showed that most of them encoded proteins with unknown function and chloroplast-related genes were enriched. In addition, 152 Brassica COS primer sets were applied to 16 crop and wild species of the Brassicaceae and 57.9–92.8 % of them were successfully amplified across the species representing that a Brassica COS can be used as diagnostic cross-species markers of diverse Brassica species. We constructed a genetic map of Raphanus sativus by analyzing the segregation of 322 COS genes in an F2 population (93 individuals) of Korean cultivars (WK10039 × WK10024). Comparative genome analysis based on the COS genes showed conserved genome structures between R. sativus and B. rapa with lineage-specific rearrangement and fractionation of triplicated subgenome blocks indicating close evolutionary relationship and differentiation of the genomes. The Brassica COS developed in this study will play an important role in genetic, genomic, and breeding studies of crop Brassicaceae species.
KeywordsBrassica Species Restriction Fragment Length Polymorphism Marker Ancestral Karyotype Polyploidy Event Comparative Genome Mapping
This work was supported by grants from the Next-Generation Biogreen21 program (PJ008019), Rural Development Administration, Korea to HJY and 2013 Research Fund of Myongji University to JHM. We thank Dr. Shengyi Liu (Oil Crops Research Institute of CAAS, China) for kindly providing sequence information of Brassica oleracea, Sin-Gi Park (National Academy of Agricultural Science of RDA, Korea) for bioinformatics support, and Dr. Suhyoung Park (National Institute of Horticultural and Herbal Science of RDA, Korea) for providing plant material.
Conflict of interest
The authors declare that they have no conflict of interest.
The authors declare that the experiments complied with current laws of the country in which they were performed.
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