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.

Here, we present the mitochondrial sequences of two ‘opistobranch’ heterobranchs: Runcina aurata García-Gómez, López, Luque & Cervera, 1986 and Facelina auriculata (O. F. Müller, 1776), the latter type taxon of the genus. The mitochondrial genomes were 14,282 and 14,171bp in length respectively, the two of them with a complete set of 13 CDS, 2 rRNAs, and 22 tRNAs. None of the mitogenomes showed gene reorganization, keeping the standard heterobranch mitogenomic structure. The base composition was completely distant between them, with a 25.7% GC for R. aurata, becoming the mitogenome with more AT content to the date, and 35% for F. auriculata, supposing one case of extremely rich GC content in “opistobranch” mitochondrial genomes.

Population genomic studies are increasing in the last decade, showing great potential to understand the evolutionary patterns in a great variety of organisms, mostly relying on RAD sequencing techniques to obtain reduced representations of the genomes. Among them, 2b-RAD can provide further secondary reduction to adjust study costs by using base-selective adaptors, although its impact on genotyping is unknown. Here we provide empirical comparisons on genotyping and genetic differentiation when using fully degenerate and base-selective adaptors and assess the impact of missing data. We built libraries with the two types of adaptors for the same individuals and generated independent and combined datasets with different missingness filters according to their presence (100%, 75% and 50%). Exploring locus-by-locus, we found 92% of identical genotypes between both libraries of the same individual when using loci present in 100% of the samples, which decreased to 35% when working with loci present in at least 50% of them. We show that missing data is a major source of individual genetic differentiation. The loci discordant by genotyping were in low frequency (7.67%) in all filtered files. Only 0.96% were directly attributable to base-selective adaptors, and 6.44% underestimated heterozygosity in NN libraries, of which ca. 70% had <10 reads per locus indicating that sufficient read depth should be ensured for a correct genotyping. Our work confirms that 2b-RAD libraries using base-selective adaptors are a robust tool to use in population genomics of species with large genome sizes.