In silico analysis of SSRs in mitochondrial genomes of plants

OMICS. 2011 Nov;15(11):783-9. doi: 10.1089/omi.2011.0074. Epub 2011 Oct 19.


Simple sequence repeats (SSRs) or microsatellites constitute a countable portion of genomes. However, the significance of SSRs in organelle genomes has not been completely understood. The availability of organelle genome sequences allows us to understand the organization of SSRs in their genic and intergenic regions. In the current study we surveyed the patterns of SSRs in mitochondrial genomes of different taxa of plants. A total of 16 mitochondrial genomes, from algae to angiosperms, have been considered to analyze the pattern of simple sequence repeats present in them. Based on study, the mononucleotide repeats of A/T were found to be more prevalent in mitochondrial genomes over other repeat types. The dinucleotides repeats, TA/AT, were the second most numerous, whereas tri-, tetra-, and pentanucleotide repeats were in less number and present in intronic or intergenic portions only. Mononucleotide repeats prevailed in protein-coding exonic portions of all organisms. These results indicates that microsatellite pattern in mitochondrial genomes is different from nuclear genomes and also focuses on organization and diversity at SSR locuses in mitochondrial genomes. This is the novel report of microsatellite polymorphism in plant mitochondrion on whole genome level.

MeSH terms

  • DNA, Mitochondrial / chemistry
  • Genome, Mitochondrial*
  • Genome, Plant*
  • Microsatellite Repeats*
  • Mitochondria / genetics*
  • Sequence Analysis, DNA
  • Streptophyta / genetics*
  • Streptophyta / ultrastructure


  • DNA, Mitochondrial