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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.

Abstract

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.

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Acknowledgments

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.

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The authors declare that the experiments complied with current laws of the country in which they were performed.

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Authors and Affiliations

  1. Department of Life Science, The Catholic University of Korea, Bucheon, 420-743, Korea

    Young-Min Jeong, Hee Chung & Hee-Ju Yu

  2. Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 305-806, Korea

    Won-Hyong Chung & Namshin Kim

  3. The Agricultural Genome Center, National Academy of Agricultural Science Rural Development Administration, Suwon, 441-707, Korea

    Beom-Seok Park

  4. Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, Korea

    Ki-Byung Lim

  5. Department of Bioscience and Bioinformatics, Myongji University, Yongin, 449-728, Korea

    Jeong-Hwan Mun

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  1. Young-Min Jeong
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Communicated by Isobel Parkin.

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Supplemental Fig. S1 Functional classification of the Brassica COS genes based on gene ontology mapping using TAIR database. GO of whole At genes was compared as control and Z test was used to examine statistical analysis. A. Cellular component categories. B. Molecular function categories. C. Biological process categories.

Supplemental Fig. S2 PCR amplification of six COS genes in selected species of Brassicaceae. At, A. thaliana; Rs, R. sativus; A, B. rapa (A genome); B, B. nigra (B genome); C, B. olearacea (C genome); AB, B. juncea (AB genome); AC, B. napus (AC genome); BC, B. carinata (BC genome); A + B, genomic DNA mixture of A and B; A + C, genomic DNA mixture of A and C; B + C, genomic DNA mixture of B and C.

Supplemental Fig. S3 Phylogenetic tree of 13 species of Brassicaceae. Tree was generated using MEGA5 program by Maximum Likelihood analysis of COS0015, COS245, and COS566 genes. The stability of tree nodes was tested by bootstrap analysis with 1,000 replicates. Bootstrap values are indicated on the branches and the branch length reflects the estimated number of substitutions per 100 sites. A local cluster of 5 wild Mediterranean Brassica species, Br, and Bo is indicated in a green box.

Supplemental Fig. S4 Circos diagram of syntenic genome block pairs between Rs and Br. Conserved orthologous blocks in Rs are plotted against their syntenic counterpart in Br. The numbers in Rs linkage groups indicate genetic distance in cM whereas those in Br chromosomes indicate 5 Mb intervals. The syntenic counterparts of conserved blocks between the genomes are interconnected by colored lines. Br, B. rapa; Rs, R. sativus.

Supplemental Fig. S5 Circos diagram of COS gene pairs between Rs and Br corresponding eight ancient chromosomes. A. AK1, B. AK2, C. AK3, D. AK4, E. AK5, F. AK6, G. AK7, H. AK8. Conserved orthologous genes in Rs are plotted against their syntenic counterpart in Br. The numbers in Rs linkage groups indicate genetic distance in cM whereas those in Br chromosomes indicate 5 Mb intervals. The syntenic counterparts of conserved gene pair between the genomes are interconnected by colored lines. The line colors indicate three differentially fractionated subgenome types in the Br genome. Br, B. rapa; Rs, R. sativus.

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Jeong, YM., Chung, WH., Chung, H. et al. Comparative analysis of the radish genome based on a conserved ortholog set (COS) of Brassica . Theor Appl Genet 127, 1975–1989 (2014). https://doi.org/10.1007/s00122-014-2354-3

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