Furthermore, interpretation of genotyping data is complicated by the presence of multiple alleles that generate "double peaks" in sequencing files from PCR products, and by the potential exchange of genetic material among isolates, which may account for the non-concordance in the assignment of isolates to specific assemblages.
Based on the PCA data and because pQC is approximately 300 kb in size, it was expected that pQC-derived DNA fragments in the MGA would influence the assignment of isolates to different species or clades.
Spoligotyping, assignment of isolates to PGG, and detection of the TbD1 region, were performed according to previously described protocols [ 60, 4, 15].
Assignment of isolates to independent VDPV2 emergences and lineage groups was based on pairwise VP1 capsid region sequence differences within and between lineage groups.
In all cases, assignment of isolates to these genetic groups was consistent with their existing subspecies designations, which were based upon immunofluorescent, biochemical, and other molecular tests.
The distribution of the data by host type and by year and country of isolation is shown in Tables 1 and 2. Differences in genotype frequency between populations enable probabilistic assignment of isolates to populations, even if some sharing of genotypes occurs between those populations.
We also show that the assignment of isolates to clusters is significantly explained by both country of origin and host species, demonstrating a strong geographic component that, together with host specificity, plays a role in shaping the genomic diversity of this species complex (table 1).
A nulli-tetrasomic series of CS produced by Sears [ 37] was used for chromosome assignment of the isolated wheat cDNAs.
Assignment of our isolate to L. newyorkensis was achieved through genome sequencing and phylogenetic analyses (see below).
The assembled contigs showed an Average Nucleotide Identity (Konstantinidis and Tiedje 2005) score of 99% with L. newyorkensis genomes, supporting the assignment of our isolate to this species.
