, Volume 35, Issue 2, pp 167-175
Date: 29 Jan 2013

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.