Map and analysis of microsatellites in the genome of Populus: The first sequenced perennial plant

Environmental Sciences Division, Oak Ridge National Laboratory, TN, USA We mapped and analyzed the microsatellites throughout 284295605 base pairs of the unambiguously assembled sequence scaffolds along 19 chromosomes of the haploid poplar genome. Totally, we found 150985 SSRs with repeat unit lengths between 2 and 5 bp. The established microsatellite physical map demonstrated tr at SSRs were distributed relatively evenly across the genome of Populus. On average, These SSRs occurred every 1883 bp within the poplar genome and the SSR densities in intergenic regions, introns, exons and UTRs were 85.4%, 10.7%, 2.7% and 1.2%, respectively. We took di-, tri-, tetra-and pentamers as the four classes of repeat units and found that the density of each class of SSRs decreased with the repeat unit lengths except for the tetranucleotide repeats. It was noteworthy that the length diversification of microsatellite sequences was negatively correlated with their repeat unit length and the SSRs with shorter repeat units gained repeats faster than the SSRs with longer repeat units. We also found that the GC content of poplar sequence significantly correlated with densities of SSRs with uneven repeat unit lengths (tri-and penta-), but had no significant correlation with densities of SSRs with even repeat unit lengths (di-and tetra-). In poplar genome, there were evidences that the occurrence of different microsatellites was under selection and the GC content in SSR sequences was found to significantly relate to the functional importance of microsatellites.

We mapped and analyzed the microsatellites throughout 284295605 base pairs ofthe unambiguously assembled sequence scaffolds along 19 chromosomes of the haploid poplargenome.Totally,we found 150985 SSRs with repeat unit lengths between 2 and 5 bp.The establishedmicrosatellite physical map demonstrated tr at SSRs were distributed relatively evenly across thegenome of Populus.On average,These SSRs occurred every 1883 bp within the poplar genome and the SSRdensities in intergenic regions,introns,exons and UTRs were 85.4%,10.7%,2.7% and1.2%,respectively.We took di-,tri-,tetra-and pentamers as the four classes of repeat units and foundthat the density of each class of SSRs decreased with the repeat unit lengths except for thetetranucleotide repeats.It was noteworthy that the length diversification of microsatellitesequences was negatively correlated with their repeat unit length and the SSRs with shorter repeatunits gained repeats faster than the SSRs with longer repeat units.We also found that the GC contentof poplar sequence significantly correlated with densities of SSRs with uneven repeat unit lengths(tri-and penta-),but had no significant correlation with densities of SSRs with even repeat unitlengths (di-and tetra-).In poplar genome,there were evidences that the occurrence of differentmicrosatellites was under selection and the GC content in SSR sequences was found to significantlyrelate to the functional importance of microsatellites.