title: Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera.
abstract: BACKGROUND
  Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5'UTR, ORF and 3'UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera).
  
  
  RESULTS
  Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera.
  
  
  CONCLUSIONS
  Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.
authors.forename: Sonali Sachin
authors.initials: SS
authors.lastname: Ranade
authors.forename: Yao-Cheng
authors.initials: YC
authors.lastname: Lin
authors.forename: Andrea
authors.initials: A
authors.lastname: Zuccolo
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.forename: María del Rosario
authors.initials: Mdel R
authors.lastname: García-Gil
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D020121:5' Untranslated Regions / Q000235:genetics; D032462:Cycadopsida / Q000235:genetics*; D020224:Expressed Sequence Tags; D019684:Magnoliopsida / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D014197:Trees / Q000235:genetics*
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D010940:Plant Proteins