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Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing
Christiansen, H.; Heindler, F.M.; Hellemans, B.; Jossart, Q.; Pasotti, F.; Robert, H.; Verheye, M.; Danis, B.; Kochzius, M.; Leliaert, F.; Moreau, C.; Patel, T.; Van de Putte, A.P.; Vanreusel, A.; Volckaert, F.A.M.; Schön, I. (2021). Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. BMC Genom. 22(1): 625. https://dx.doi.org/10.1186/s12864-021-07917-3
In: BMC Genomics. BioMed Central: London. ISSN 1471-2164, more
Peer reviewed article  

Available in  Authors 

Keyword
    Marine/Coastal
Author keywords
    Biodiversity; Genome scan; Genotyping by sequencing; In silico digestion; RADseq; Southern Ocean

Authors  Top 
  • Patel, T., more
  • Van de Putte, A.P., more
  • Vanreusel, A., more
  • Volckaert, F.A.M., more
  • Schön, I., more

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.


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