One of the earliest nuclease technologies involved enzymes called meganucleases, but these were less than user-friendly, explains Philippe Duchateau, chief scientific officer at Cellectis, a French genome-engineering firm that still uses the technology.
The cosmopolitan reference panel included 9 French genomes, again excluding inversions, since inverted arms were previously found to have unusually high divergence from standard arms in this population (Corbett-Detig and Hartl 2012; Pool et al. 2012).
Interestingly, three out of four pairs from Germany and a published French draft genome of a C. ulcerans isolate cluster together, as also depicted by the phylogenetic analysis using the genome-wide data.
Assays targeted five SNPs identified among the French B.Br.CNEVA genomes, one SNP specific to the A.Br.001/002 strains isolated in Doubs, and two SNPs defining the two large sub-branches 1 and 2 of the A.Br.011/009 sub-group.
Four markers that specifically define one of the newly described geographic sub-groups, as well as one additional SNP shared by all French B.Br.CNEVA genomes, were selected and incorporated into SNP discrimination HRM assays (Table 1).
They show that the Neanderthals are more closely related to the three Eurasian genomes (French, Chinese, and Papuan) than they are to the two African genomes (San and Yoruba).
To determine these thresholds, we estimated nucleotide diversity in 100-kb windows advancing in 5-kb increments for the large Rwandan (RG) sample of 27 haploid embryo genomes and the French sample of 9 haploid embryo genomes to represent sub-Saharan and cosmopolitan diversity, respectively.
PCR validations revealed that the 4 regions representing 45 kb were present in the genome of both French vaccine strains, IM1414 and IM1416, in the genomes of isolates collected in the 60's and of presently circulating isolates.
In comparison to a study of regions of differentiation among the genomes of three French dairy breeds [ 28], the coat colour (MC1R) locus on BTA18 and the region on BTA14 at 24.63 Mb (UMD3.1 position) harbouring PLAG1 which is associated with cattle stature [ 61] were identified in both studies.
RD3 (from BP1158 to BP1176) was present in the genome of the second French vaccine strain, IM1416, and of PFGE group III clinical isolates collected before 1980.
For each polymorphism, the best fitting genetic model was selected from our previous whole-genome association study in French individuals [1].
