Genes & Genomics

, Volume 35, Issue 2, pp 167–175

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

  • Lijuan Wei
  • Meili Xiao
  • Annaliese S. Mason
  • Bi Ma
  • Kun Lu
  • Jiana Li
  • Link Katrin
  • Donghui Fu
Research Article

DOI: 10.1007/s13258-013-0076-6

Cite this article as:
Wei, L., Xiao, M., Mason, A.S. et al. Genes Genom (2013) 35: 167. doi:10.1007/s13258-013-0076-6
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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.

Keywords

Brassica Species-diverged sequences SSR 

Supplementary material

13258_2013_76_MOESM1_ESM.xls (44 kb)
Supplementary Table 1 Nomenclature, code, and origin of the selected Brassica cultivars and accessions (XLS 44 kb)
13258_2013_76_MOESM2_ESM.xls (48 kb)
Supplementary Table 2 Basic information on species-diverged sequences (XLS 48 kb)
13258_2013_76_MOESM3_ESM.xls (60 kb)
Supplementary Table 3 The information of homologous sequences of species-diverged fragments (XLS 59 kb)
13258_2013_76_MOESM4_ESM.xls (26 kb)
Supplementary Table 4 Degree and characteristics of divergence of the species-diverged sequences (XLS 26 kb)
13258_2013_76_MOESM5_ESM.xls (23 kb)
Supplementary Table 5 Homology results between species-diverged sequences of Brassica species and A. thaliana (XLS 23 kb)

Copyright information

© The Genetics Society of Korea 2013

Authors and Affiliations

  • Lijuan Wei
    • 1
  • Meili Xiao
    • 1
  • Annaliese S. Mason
    • 2
  • Bi Ma
    • 1
  • Kun Lu
    • 1
  • Jiana Li
    • 1
  • Link Katrin
    • 1
  • Donghui Fu
    • 3
  1. 1.College of Agronomy and BiotechnologySouthwest University, Engineering Research Center of South Upland Agriculture of Ministry of EducationChongqingPeople’s Republic of China
  2. 2.Centre for Integrative Legume Research and School of Agriculture and Food SciencesThe University of QueenslandBrisbaneAustralia
  3. 3.Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy CollegeJiangxi Agricultural UniversityNanchangChina

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