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

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 demon...

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Bibliographic Details
Published in:Science China. Life sciences 2007-10, Vol.50 (5), p.690-699
Main Authors: Li, ShuXian, Yin, TongMing
Format: Article
Language:English
Subjects:
Animals
Chromosomes - metabolism
Chromosomes, Plant
Computational Biology
Exons
Genes, Plant
Genome, Plant
Introns
Microsatellite Repeats
Models, Statistical
Physical Chromosome Mapping
Plants - metabolism
Populus - genetics
Sequence Analysis, DNA
Software
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Summary: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 that 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.
ISSN:1006-9305
1674-7305
1862-2798
1869-1889
DOI:10.1007/s11427-007-0073-6