Conservation genomic studies in non-model organisms often depend on reduced representation sequencing methods like Genotyping-by-Sequencing (GBS), using restriction enzymes to study population structure and identify candidate loci for local adaptation. Despite the increasing availability of high-quality reference genomes, their production remains costly. Thus, understanding how population genomic studies benefit from reference genomes is crucial. Here, we analysed population structure and functional characterisation using a de novo approach with subsequent mapping to the Strongylocentrotus purpuratus genome and also using the recently published Paracentrotus lividus genome. Our study underscores the reliability of de novo population genomic studies to assess population structure employing reduced representation techniques, confirming they are a critical and affordable tool for non-model organisms. Moreover, it highlights the importance of having a reference genome when going into detail in loci characterisation. However, it is important to remark that, depending on the species, functional analysis might not be highly improved, despite having a reference genome if the annotated elements lack detail on gene functions.
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