Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing
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...
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ftdoajarticles:oai:doaj.org/article:e43e7c8dc836414cb3bd47e8bb716656 2023-05-15T13:46:16+02:00 Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing Henrik Christiansen Franz M. Heindler Bart Hellemans Quentin Jossart Francesca Pasotti Henri Robert Marie Verheye Bruno Danis Marc Kochzius Frederik Leliaert Camille Moreau Tasnim Patel Anton P. Van de Putte Ann Vanreusel Filip A. M. Volckaert Isa Schön 2021-08-01T00:00:00Z https://doi.org/10.1186/s12864-021-07917-3 https://doaj.org/article/e43e7c8dc836414cb3bd47e8bb716656 EN eng BMC https://doi.org/10.1186/s12864-021-07917-3 https://doaj.org/toc/1471-2164 doi:10.1186/s12864-021-07917-3 1471-2164 https://doaj.org/article/e43e7c8dc836414cb3bd47e8bb716656 BMC Genomics, Vol 22, Iss 1, Pp 1-20 (2021) Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean Biotechnology TP248.13-248.65 Genetics QH426-470 article 2021 ftdoajarticles https://doi.org/10.1186/s12864-021-07917-3 2022-12-31T12:16:19Z 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. Article in Journal/Newspaper Antarc* Antarctic Southern Ocean Directory of Open Access Journals: DOAJ Articles Antarctic Southern Ocean BMC Genomics 22 1 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean Biotechnology TP248.13-248.65 Genetics QH426-470 |
spellingShingle |
Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean Biotechnology TP248.13-248.65 Genetics QH426-470 Henrik Christiansen Franz M. Heindler Bart Hellemans Quentin Jossart Francesca Pasotti Henri Robert Marie Verheye Bruno Danis Marc Kochzius Frederik Leliaert Camille Moreau Tasnim Patel Anton P. Van de Putte Ann Vanreusel Filip A. M. Volckaert Isa Schön Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing |
topic_facet |
Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Henrik Christiansen Franz M. Heindler Bart Hellemans Quentin Jossart Francesca Pasotti Henri Robert Marie Verheye Bruno Danis Marc Kochzius Frederik Leliaert Camille Moreau Tasnim Patel Anton P. Van de Putte Ann Vanreusel Filip A. M. Volckaert Isa Schön |
author_facet |
Henrik Christiansen Franz M. Heindler Bart Hellemans Quentin Jossart Francesca Pasotti Henri Robert Marie Verheye Bruno Danis Marc Kochzius Frederik Leliaert Camille Moreau Tasnim Patel Anton P. Van de Putte Ann Vanreusel Filip A. M. Volckaert Isa Schön |
author_sort |
Henrik Christiansen |
title |
Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing |
title_short |
Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing |
title_full |
Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing |
title_fullStr |
Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing |
title_full_unstemmed |
Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing |
title_sort |
facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing |
publisher |
BMC |
publishDate |
2021 |
url |
https://doi.org/10.1186/s12864-021-07917-3 https://doaj.org/article/e43e7c8dc836414cb3bd47e8bb716656 |
geographic |
Antarctic Southern Ocean |
geographic_facet |
Antarctic Southern Ocean |
genre |
Antarc* Antarctic Southern Ocean |
genre_facet |
Antarc* Antarctic Southern Ocean |
op_source |
BMC Genomics, Vol 22, Iss 1, Pp 1-20 (2021) |
op_relation |
https://doi.org/10.1186/s12864-021-07917-3 https://doaj.org/toc/1471-2164 doi:10.1186/s12864-021-07917-3 1471-2164 https://doaj.org/article/e43e7c8dc836414cb3bd47e8bb716656 |
op_doi |
https://doi.org/10.1186/s12864-021-07917-3 |
container_title |
BMC Genomics |
container_volume |
22 |
container_issue |
1 |
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1766239644844818432 |