Genome architecture impacts on reduced representation population genomics

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.