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SSRs mining of Brassica species in mitochondrial genomes: Bioinformatic approaches

Abstract

Simple sequence repeats (SSRs) are ubiquitous in eukaryotic genomes and SSRs have been used extensively in plant genetic studies. Five Brassica species (B. carinata, B. juncea, B. napus, B.oleracea, and B. rapa subsp. campestris) were analyzed to understand distribution and occurrence of mitochondrial SSRs (mtSSRs) in genic and intergenic regions. A total of 1295 mtSSRs were detected with an average density of 1.03 mtSSR per kb and about 18% of mtSSRs were determined in genic region. The A/T in mononucleotides, AG/CT in dinucleotides, AAG/CCT in trinucleotides, AATG/ATTC in tetranucleotides, and ACTAG/AGTCT in pentanucleotides were predominant mtSSR motifs, while there were not any hexanucleotides in all Brassica species. The most frequent repeat types were found as trinucleotides (8.6%) followed by mononucleotides (7.2%) and tetranucleotides (1.7%), while no pentanucleotides and hexanucleotides SSRs were present, in genic regions. The most abundant genic mtSSRs were observed in B. napus (21.7%), while the least genic mtSSRs were found in B. oleracea (12.9%). Based on putative amino acid triplets in coding regions, valine amino acid (15.4%) was predominant, followed by asparagine (14.4%), and glutamine (13.5%).

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Correspondence to Ertugrul Filiz.

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Filiz, E. SSRs mining of Brassica species in mitochondrial genomes: Bioinformatic approaches. Hortic. Environ. Biotechnol. 54, 548–553 (2013). https://doi.org/10.1007/s13580-013-0026-x

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Additional key words

  • in silico analysis
  • microsatellite
  • mitochondrial SSRs