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Recently, Correia et al. ([2011]) showed that tetra-, penta- and hexa nucleotide microsatellites were more informative than the di and tri nucleotide markers and specific SNPs employed for assessment of parentage and individual identification.
Class II microsatellites were more common in the BES than longer class I microsatellites.
Microsatellites were more numerous in the intergenic regions with a relative abundance of 58 No./Mb (Table 1).
In the Clementine genome, microsatellites were more numerous in non coding sequences (56% of the SSRs) than in putative coding regions (44%), as previously reported in papaya [ 20], Chinese cabbage [ 22], and Arabidopsis[ 18].
Thorough analysis of the microsatellite distribution and motif type among the 147 annotated genes revealed that the microsatellites were more frequent within the CDS regions of the kinase genes and that trinucleotides were the most abundant motif (Table S3).
In terms of the frequency of individual motifs, the results indicate that GA motif microsatellites were more common than CA motif microsatellite in the sequences of the cDNA library used for this study with implications for the common bean transcriptome.
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Genotyping with microsatellites are more labor intensive and require more detailed analysis in calling the genotypes.
First, we tested the hypothesis that longer microsatellites are more unstable and will consequently contain more IMs.
It has been suggested that short microsatellites tend to gain additional units whereas long microsatellites are more likely to lose units during a mutation event [ 39, 47].
In some species such as C. reinhardtii, Mesostigma viride and bryophytes, we found that dimer (NN) microsatellites are more common when compared to higher plants.
Two recent comparisons of sympatric parasite populations further suggested that P. vivax microsatellites are more polymorphic than those of P. falciparum [ 9, 10].
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