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