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The neighbor-joining tree plots of the polymorphism and divergence data from the loci are available as Supplementary Material in file Results S2.
The data from the loci determined to be heterozygous (CHet; 476 loci) or homozygous (CHom; 30 loci) in Clementine (table 2) were analyzed separately.
Development of the 16 new microsatellites reported in this study was carried out as described in [ 44] and sequence data from the loci have been deposited with EMBL/GenBank Data Libraries (see Additional File 1).
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The performance of SATlotyper was tested using unphased SNP data from the locus BA213c14t7 of Solanum tuberosum.
With this list one could then systematically retrieve all data from the locus class held in SoyBase.
Based on the data from these loci, the natural populations appear to fall into five groups that Hedrick et al. (2001a) placed into two ESUs (Fig. 3).
We paired loci used in methylation analysis with gene expression data from the appropriate loci according to Entrez Gene ID.
As a proof-of-concept, sequences derived from the allelic ladders of five STR loci and data from the amelogenin locus were used as reference data sets.
Our results suggest that the phylogenetic signal provided by sequence data from the three-locus barcode may be near saturation for phylogenetic analyses of this type and that little will be improved with the addition of more loci in such investigations.
We predicted the functionality of p53 (hereafter called functionality) for each sample (see Additional file 1: Table S1) by combining data from the TP53 locus allelic state, mutation data and protein expression levels.
Based on the discovery of two putative hybrids of F. keratoplasticum (FRC S-2406 and FRC S-2509) that possess identical rDNA sequences to those of FSSC 9 [ 39], sequence data from the nine-locus MLST system were generated for three members of FSSC 9 (FRC S-2485, FRC S-2530, FRC S-2540).
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