Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing
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...
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ftunivbruxelles:oai:dipot.ulb.ac.be:2013/331395 2023-05-15T14:02:21+02:00 Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing Christiansen, Henrik Heindler, Franz Hellemans, Bart Jossart, Quentin Pasotti, Francesca Robert, Henri Verheye, Marie Danis, Bruno Kochzius, Marc Leliaert, Frederik Moreau, Camille Patel, Tasnim Van De Putte, Anton Vanreusel, Ann Volckaert, Filip Schön, Isa 2021-12 1 full-text file(s): application/pdf http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/331395 https://dipot.ulb.ac.be/dspace/bitstream/2013/331395/1/doi_315039.pdf en eng uri/info:doi/10.1186/s12864-021-07917-3 uri/info:scp/85113226892 https://dipot.ulb.ac.be/dspace/bitstream/2013/331395/1/doi_315039.pdf http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/331395 1 full-text file(s): info:eu-repo/semantics/openAccess BMC genomics, 22 (1 Biologie Biotechnologie Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean info:eu-repo/semantics/article info:ulb-repo/semantics/articlePeerReview info:ulb-repo/semantics/openurl/article 2021 ftunivbruxelles 2022-06-12T22:04:39Z 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. SCOPUS: ar.j info:eu-repo/semantics/published Article in Journal/Newspaper Antarc* Antarctic Southern Ocean DI-fusion : dépôt institutionnel de l'Université libre de Bruxelles (ULB) Antarctic Southern Ocean |
institution |
Open Polar |
collection |
DI-fusion : dépôt institutionnel de l'Université libre de Bruxelles (ULB) |
op_collection_id |
ftunivbruxelles |
language |
English |
topic |
Biologie Biotechnologie Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean |
spellingShingle |
Biologie Biotechnologie Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean Christiansen, Henrik Heindler, Franz Hellemans, Bart Jossart, Quentin Pasotti, Francesca Robert, Henri Verheye, Marie Danis, Bruno Kochzius, Marc Leliaert, Frederik Moreau, Camille Patel, Tasnim Van De Putte, Anton Vanreusel, Ann Volckaert, Filip Schön, Isa Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing |
topic_facet |
Biologie Biotechnologie Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean |
description |
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. SCOPUS: ar.j info:eu-repo/semantics/published |
format |
Article in Journal/Newspaper |
author |
Christiansen, Henrik Heindler, Franz Hellemans, Bart Jossart, Quentin Pasotti, Francesca Robert, Henri Verheye, Marie Danis, Bruno Kochzius, Marc Leliaert, Frederik Moreau, Camille Patel, Tasnim Van De Putte, Anton Vanreusel, Ann Volckaert, Filip Schön, Isa |
author_facet |
Christiansen, Henrik Heindler, Franz Hellemans, Bart Jossart, Quentin Pasotti, Francesca Robert, Henri Verheye, Marie Danis, Bruno Kochzius, Marc Leliaert, Frederik Moreau, Camille Patel, Tasnim Van De Putte, Anton Vanreusel, Ann Volckaert, Filip Schön, Isa |
author_sort |
Christiansen, Henrik |
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 |
publishDate |
2021 |
url |
http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/331395 https://dipot.ulb.ac.be/dspace/bitstream/2013/331395/1/doi_315039.pdf |
geographic |
Antarctic Southern Ocean |
geographic_facet |
Antarctic Southern Ocean |
genre |
Antarc* Antarctic Southern Ocean |
genre_facet |
Antarc* Antarctic Southern Ocean |
op_source |
BMC genomics, 22 (1 |
op_relation |
uri/info:doi/10.1186/s12864-021-07917-3 uri/info:scp/85113226892 https://dipot.ulb.ac.be/dspace/bitstream/2013/331395/1/doi_315039.pdf http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/331395 |
op_rights |
1 full-text file(s): info:eu-repo/semantics/openAccess |
_version_ |
1766272596676968448 |