title: Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda).
abstract: BACKGROUND
  Microsatellites or simple sequence repeats (SSRs) are DNA sequences consisting of 1-6 bp tandem repeat motifs present in the genome. SSRs are considered to be one of the most powerful tools in genetic studies. We carried out a comparative study of perfect SSR loci belonging to class I (≥20) and class II (≥12 and <20 bp) types located in coding regions of high confidence genes in Picea abies and Pinus taeda. SSRLocator was used to retrieve SSRs from the full length CDS of predicted genes in both species.
  
  
  RESULTS
  Trimers were the most abundant motifs in class I followed by hexamers in Picea abies, while trimers and hexamers were equally abundant in Pinus taeda class I SSRs. Hexamers were most frequent within class II SSRs followed by trimers, in both species. Although the frequency of genes containing SSRs was slightly higher in Pinus taeda, SSR counts per Mbp for class I was similar in both species (P-value = 0.22); while for class II SSRs, it was significantly higher in Picea abies (P-value = 0.00009). AT-rich motifs were higher in abundance than the GC-rich motifs, within class II SSRs in both the species (P-values = 10(-9) and 0). With reference to class I SSRs, AT-rich and GC-rich motifs were detected with equal frequency in Pinus taeda (P-value = 0.24); while in Picea abies, GC-rich motifs were detected with higher frequency than the AT-rich motifs (P-value = 0.0005).
  
  
  CONCLUSIONS
  Our study gives a comparative overview of the genome SSRs composition based on high confidence genes in the two recently sequenced and economically important conifers and, also provides information on functional molecular markers that can be applied in genetic studies in Pinus and Picea species.
authors.affiliation: Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden. Sonali.Ranade@slu.se.
authors.forename: Sonali Sachin
authors.initials: SS
authors.lastname: Ranade
authors.affiliation: Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium. yao-cheng.lin@psb.vib-ugent.be.
authors.forename: Yao-Cheng
authors.initials: YC
authors.lastname: Lin
authors.affiliation: Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium. yves.vandepeer@psb.vib-ugent.be.|Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, 0028, South Africa. yves.vandepeer@psb.vib-ugent.be.|Bioinformatics Institute Ghent, Ghent University, 9052, Ghent, Belgium. yves.vandepeer@psb.vib-ugent.be.
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.affiliation: Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden. M.Rosario.Garcia@slu.se.
authors.forename: María Rosario
authors.initials: MR
authors.lastname: García-Gil
mesh_terms: D003198:Computer Simulation; D018744:DNA, Plant / Q000032:analysis / Q000235:genetics*; D018895:Microsatellite Repeats; D059372:Nucleotide Motifs; D028222:Picea / Q000235:genetics*; D041603:Pinus taeda / Q000235:genetics*
chemical_list: D018744:DNA, Plant