Many of the large-scale genomic changes observed in our studies were also noted in previous cytogenetic studies.
However, the use of aCGH in our current study limits the results to identification of large-scale genomic changes, such as gain or loss of genes, responsible for phenotypic changes.
The adaptation of pathogenic fungi to the host environment via large-scale genomic changes is a poorly characterized phenomenon.
This method is most useful for large-scale genomic changes, rather than smaller-scale changes, such as introduction of a point mutation or a sequence encoding a tag.
The adoption of single-molecule long-read approaches such as that offered by Pacific Biosciences may also help wean us off a dependence on SNPs and reveal more large-scale genomic changes [ 6].
The dramatic large-scale genomic changes observed during temperature selection contrast sharply with ethanol selection, where after 500 generations, hybrids showed few rearrangements and no apparent loss of either parental genome.
Large-scale genomic changes, such as inversions, translocations, fusions and fissions, contribute to the reshuffling of the genomic architecture of organisms, providing new sources of variation on which natural selection can work.
This means that many homologs in the IFN and KIR clusters are out-paralogous and implies that many evolutionary events occurred in these clusters before the split of human and each other species that is, the IFN and KIR clusters have been very active in terms of large-scale genomic changes compared with the other clusters.
Syntenic depth provides a more consistent marker for large scale genomic events than changes in the copy number of individual genes which are influenced by a greater number of small scale processes (expansion and contraction of tandem arrays, transposon capture and duplication, etc).
In conclusion, large scale genomic, epigenomic and transcriptomic changes accompanied the process of hybridization in the crosses C. nankingense × T.
This indicates that the Pfam IncA domain is too specific for a large scale genomic analysis.
