Map and analysis of microsatellites in the genome of <Emphasis Type="Italic">Populus</Emphasis>: The first sequenced perennial plant |
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Authors: | Li ShuXian Yin TongMing |
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Institution: | 1.College of Environment and Forest Resources,Nanjing Forestry University,Nanjing,China;2.Environmental Sciences Division,Oak Ridge National Laboratory,USA |
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Abstract: | 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. |
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Keywords: | poplar genome microsatellite length diversification GC-content genie and nongenic regions |
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