Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing.

• Published in: BMC Genomics
• Main Authors: Christiansen, Henrik, Heindler, Franz M., Hellemans, Bart, Jossart, Quentin, Pasotti, Francesca, Robert, Henri, Verheye, Marie, Danis, Bruno, Kochzius, Marc, Leliaert, Frederik, Moreau, Camille, Patel, Tasnim, van de Putte, Anton P., Vanreusel, Ann, Volckaert, Filip A.M., Schön, Isa
• Other Authors: Laboratory of Biodiversity and Evolutionary Genomics, Catholic University of Leuven = Katholieke Universiteit Leuven (KU Leuven), Marine Biology Group, Vrije Universiteit Brussel Bruxelles (VUB), Marine Biology Research Group, Universiteit Gent = Ghent University (UGENT), Operational Directorate Natural Environment, Institut Royal des Sciences Naturelles de Belgique = Royal Belgian Institute of Natural Sciences (IRSNB / RBINS), Laboratoire de Biologie Marine (LBM), Université libre de Bruxelles (ULB), Meise Botanic Garden Belgium (Plantentuin), Biogéosciences UMR 6282 (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Funded by the Belgian Science Policy Office (BELSPO, Contract no. BR/132/A1/vERSO) and contribution no. 8 of the RECTO project (BELSPO, Contract no. BR/154/A1/ RECTO), BELSPO, by the Scientific Research Network “Eco-evolutionary dynamics in natural and anthropogenic communities” (grant W0.037.10 N), and the European Marine Biological Resource Center (EMBRC) Belgium, both funded by the Research Foundation – Flanders (FWO), by an individual grant from the former Flemish Agency for Innovation by Science and Technology, now managed through Flanders Innovation & Entrepreneurship (VLAIO, grant no. 141328).
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2021
• Subjects: Genotyping by sequencing; In silico digestion; RADseq; Southern Ocean; Biodiversity; Genome scan; MESH: Animals; MESH: Genome; MESH: Genomics; MESH: Humans; MESH: Metagenomics; MESH: Research Design; MESH: Sequence Analysis; DNA; [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]; Antarctic; Antarc*
• Online Access: https://hal.science/hal-03329042; https://doi.org/10.1186/s12864-021-07917-3

20 pages International audience Background Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. Results In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Conclusions Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.