Genomic architecture is a key evolutionary trait for living organisms.
Due to multiple complex adaptive and neutral forces which impose
evolutionary pressures on genomes, there is a huge disparity of genomic
features. However, existing genome architecture studies are taxon
biased, and thus a wider picture should be obtained by expanding the
taxonomic scope. Moreover, the extent to which genomic architecture
determines the typology of loci recovered in reduced representation
sequencing techniques with digestion enzymes is largely unexplored.
Here, we observed that whereas plants mostly increase their genome size
by expanding their intergenic regions, animals expand both intergenic
and intronic regions, although the expansion patterns differ between
deuterostomes and protostomes. We found positive correlations between
the percentage of loci obtained with in-silico digestion using
2b-enzymes mapping in introns, exons and intergenic categories and the
percentage of these regions in the genome. However, exonic regions
showed a significant enrichment regardless of the enzyme used. Moreover,
the percentage of loci retained after secondary reductions varied with
selective-adaptors and genome GC content. In summary, we show that
genome architecture has an impact on the markers obtained in reduced
representation sequencing that should be considered in conservation
genomics for correct wildlife management.