Exact(2)
After completing our SMR genomic loci survey, many trends in SMR genomic arrangement were noted.
Mobile genetic elements were found to associate with all SMR homologues at a frequency of 22% within a 10 ORF radius of surveyed genomic loci (Table 2) and upon randomly expanding our genomic loci survey to a 25 ORF radius we saw an increase in mobile element detection (~34%) (data not shown).
Similar(58)
An analysis of the genetic similarity, however, revealed only five pairs of accessions with the same name as being genetically identical for the loci surveyed, indicating that only 3% of the collection is actually duplicated (P. Bat Kancat, P. Sekrit, P. Jata, P. Pulut Janggang, and P. Ubek Iyap; Fig. 2).
Simple scans for loci of unusually low diversity would incorrectly suggest selection at many of the loci surveyed: in the Canadian population, for example, nearly half of the loci sequenced are devoid of variation (Table S2).
Much of the fine-scale genetic differences in their dataset were driven by highly localized introgression signatures at one or more of the mtDNA or nuclear intron loci surveyed, including the putative mtDNA control surveyed here.
Relative to the large number of ISSR loci surveyed, the samples included in this study could not possibly contain all existing alleles within the natural population of the respective parental species.
The three microsatellite loci surveyed each had between 16 and 18 alleles.
Information about the specific loci surveyed and primers used can be found in Additional File 1.
The diversity estimates (πT and θW) displayed the same pattern independently the loci surveyed.
In contrast, the loci surveyed in our study were chosen to maximize recombination rate and minimize rate variation.
The final EDMA array (EDMA.V2) contains 414,566 probes targeting 359,738 loci, surveying 20,355 genes and 34,379 CpG islands.
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