The Impact of Enzyme Selection on Conservation Genomics: A Closer Look

The urgency of addressing the current global biodiversity crisis has led to the emergence of new scientific approaches and methodologies. One of those new frontiers in the field of conservation is genomics, which has the potential to shed light on crucial knowledge about adaptation processes and evolution in organisms that do not have their genome sequenced. 

Conservation genomics studies generally involve sequencing many individuals to identify the genetic structure of populations and possible local adaptation processes. Techniques based on restriction enzymes (Reduced representation sequencing or RRS) are frequently used, which allow a small part of the genome to be sequenced without prior knowledge of it, and where it is assumed that the sequenced regions (loci) are randomly distributed throughout the genome. 

However, a recent academic study published by Ainhoa López, Carlos Carreras, Marta Pascual and Cinta Pegueroles from the Evolutionary Genetics Group, IRBio, Universitat de Barcelona, within the consolidated research group Marine Biodiversity and Evolution (MBE), has highlighted a factor that is often overlooked in these techniques: the choice of restriction enzymes. The study, titled "Evaluating Restriction Enzyme Selection for Reduced Representation Sequencing in Conservation Genomics" explores how restriction enzyme selection can affect the distribution and functional composition of genomic loci obtained using RRS. 

The researchers evaluated the distribution and functional composition of the loci obtained with the Genotyping-by-Sequencing (GBS) technique in population studies in the Mediterranean, in two species of fish, Symphodus ocellatus and Symphodus tinca, and two species of sea urchins, Paracentrotus lividus and Arbacia lixula, using the enzyme EcoT22I, and ApeKI respectively. The results indicate that there is a bias in the exonic or intronic regions depending on the restriction enzyme used (those that contain a higher percentage of cytosines and guanines in the restriction target cut more in the exonic regions), although a bias is not detected. in the functions of the sequenced loci. It should be noted that the percentage of loci that the researchers were able to map was very low (10%) despite having used as a reference the genomes of the phylogenetically closest species that are sequenced, Labrus bergylta in the case of fish and Strongylocentrotus purpuratus in the case of sea urchins. To demonstrate the effect of the enzymes on the distribution of the loci, in silico data were generated with the same enzymes for the reference genomes used. These simulations confirmed the differences in the distribution of loci caused by the enzyme in RRS. 

Restriction enzymes are the cornerstone of population genomics RRS, since they are responsible for cutting DNA fragments (loci). These results highlight the need to carefully consider the choice of restriction enzymes when using Reduced representation sequencing (RRS) techniques, as it will determine the distribution of the sequenced loci. The low percentage of loci localization in all the species studied in relation to the reference genomes used highlights the need to have high-quality annotated reference genomes of the species themselves or of phylogenetically very close species to identify candidate regions for selection in genomic conservation studies. The latter are increasingly available thanks to initiatives such as the Earth Biogenome project, which with the aim of generating reference genomes for all species offers hope of better understanding the intricate web of life on our planet. 

The implications of this research are substantial, given the current challenges of biodiversity loss and the increasing urgency to conserve vulnerable species. By shedding light on the influence of restriction enzymes on genomic outcomes, scientists can make more informed decisions when designing studies and selecting techniques for their conservation genomics research. The study by López, Carreras, Pascual and Pegueroles constitutes a valuable contribution for conservationists of today and tomorrow. 

Source: López, A., Carreras, C., Pascual, M., & Pegueroles, C. (2023). Evaluating restriction enzyme selection for reduced representation sequencing in conservation genomics. Molecular Ecology Resources.