Moreover, Karn and Laukaitis [70] previously reported evidence for substantial recent gene duplication and copy-number variation in the Abp region, especially in mouse strains with all or part of the M. m. musculus or M. m. castaneus Abp gene region.
These data reveal that substantial local gene duplications took place shortly after the whole-genome duplication event.
The next question we asked was whether these constraints have undergone substantial changes after gene duplication.
Despite coverage of the genome sequences differing between strains, we are able to identify substantial evidence of gene duplication.
Our analysis of various land plants, chlorophytes, red algae and Marchantia confirmed this hypothesis in liverworts and suggested that ancient plants had one or only a few bHLH genes and that all modern plants, including Marchantia, have bHLH proteins that are descended and radiated from these predecessors by a process that involved a substantial number of gene duplication events [ 91, 92].
In addressing the aims of this study, it has been shown that although substantial gene loss occurred after duplication, 47% of all duplicated loci had been retained as conserved paralogs.
After gene duplication, two duplicates can undergo substantial functional divergence, and it plays a major role in the evolution of new functions [40].
Among the NBS-LRR genes under subfunctionalization, most of them had positively selected sites with relative high substitution rate, consistent with previous research that subfunctionalized duplicated genes act as a transition state to neofunctionalization, which is a prolonged and substantial process during evolution of gene duplication [ 39, 53].
Most of the rest of the tree is also characterized by a substantial frequency of gene duplications and losses, and overall the family has few orthologs.
Firstly, duplicate genes maintained increased dN/ dS ratios for substantial periods of time after the gene duplication events, consistent with a relaxation of selective constraint.
