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Characterization and evolutionary analysis of Brassica species-diverged sequences containing simple repeat units

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Abstract

Brassica species, B. napus (canola), B. rapa and B. oleracea, are important sources of nutritionally valuable vegetable oil and protein-rich meal for animals and humans. Sequencing of the model plant Arabidopsis thaliana, has opened the way for investigations into the complex structure of the Brassica genomes, offering important insight into their evolution and composition. We use this sequence information for the characterization and functional analysis of SSR sequences that have diverged between the Brassica species. A total of 56 species-diverged sequences containing simple repeat units (SDS-SSR) of B. napus and its diploid progenitor species B. rapa and B. oleracea were isolated and characterized. Of these, 40 sequences showed homology with other Brassica sequences. Using the SSR Locator software, only 23 sequences were found to have SSRs, possibly due to the loss of SSR units in the process of species divergence. Sequence alignments with A. thaliana revealed that these species-diverged SSR sequences were responsible for Brassica divergence for differences between Brassica species in several genomic regions. Six active genes related to transferase, protein, transcription factor and retroelements were found in the SDS-SSRs. These results will further improve our understanding of the characteristics of species-diverged SSR fragments and their contribution to genome differentiation.

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Acknowledgments

This work was supported by National High Technology Research and Development Program of China (863 Program) (2011AA10A104) and Ministry of Agriculture, Modern Agricultural Industrial Technology System Program (CARS-13).

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Authors and Affiliations

  1. College of Agronomy and Biotechnology, Southwest University, Engineering Research Center of South Upland Agriculture of Ministry of Education, Chongqing, 400716, People’s Republic of China

    Lijuan Wei, Meili Xiao, Bi Ma, Kun Lu, Jiana Li & Link Katrin

  2. Centre for Integrative Legume Research and School of Agriculture and Food Sciences, The University of Queensland, Brisbane, 4072, Australia

    Annaliese S. Mason

  3. Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China

    Donghui Fu

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  1. Lijuan Wei
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  2. Meili Xiao
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  4. Bi Ma
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  5. Kun Lu
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Correspondence to Donghui Fu.

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Wei, L., Xiao, M., Mason, A.S. et al. Characterization and evolutionary analysis of Brassica species-diverged sequences containing simple repeat units. Genes Genom 35, 167–175 (2013). https://doi.org/10.1007/s13258-013-0076-6

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  • DOI: https://doi.org/10.1007/s13258-013-0076-6

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