Intriguingly, each of the genomes with a putative double recombination event at this position within the graphical genotypes also featured a CO between the insertion sites, which leads to the above-mentioned copy number variations and misleading genotypes.
As mentioned above, copy number in de novo assemblies is unreliable, so many of the genes were likely not really duplicated.
We constructed a DinB derivative with a tyrosine at position 13 instead of phenylalanine (pdinB(F13Y)) in the same low copy number plasmid mentioned in the above section, and introduced it by transformation into ΔdinB.
As mentioned above, changes in genome copy number resulting in polyploidy are observed for so-called giant cells of C. neoformans arising during pulmonary infection [ 25, 26].
CN2 to CN5 were transformed with different combinations of plasmids carrying gapN and UTR1 under control of the TEF1 promoter, and expressing the mentioned genes in high or low copy number (Table 1).
Interestingly, the Holstein bull (mentioned above) who had the lowest copy number in both HSFY and ZNF280BY gene families had the largest RLSC among all animals tested, strongly supporting our association results that a lower CN of the two Y-linked genes is associated with a larger testis.
As mentioned above, the genomic area of low copy number in the ICCA families corresponded to the previously described Variation_7105 (http://projects.tcag.ca/variation/)[23].
Importantly, in each genetic background mentioned above, the integrated repeats were the same length and copy number (Fig. 7B).
This adjustment not only reduces the potential bias caused by copy number alterations, but also addresses another concern mentioned in Minor comment #4 about the integration of FISH data and NGS data.
The VNTR profile of each of the analyzed M. tuberculosis was described as a set of figures of tandem repeat copy number according to this loci set order as mentioned above.
