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

Content Provider	Springer Nature : BioMed Central
Author	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
Abstract	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.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-021-07917-3.pdf
Ending Page	20
Page Count	20
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-021-07917-3
Journal	BMC Genomics
Issue Number	1
Volume Number	22
Language	English
Publisher	BioMed Central
Publisher Date	2021-08-21
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

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