Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing.
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...
Published in: | BMC Genomics |
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Main Authors: | , , , , , , , , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2021
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Online Access: | https://hal.archives-ouvertes.fr/hal-03329042 https://doi.org/10.1186/s12864-021-07917-3 |
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English |
topic |
Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean 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] |
spellingShingle |
Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean 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] 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 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 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] |
description |
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. |
author2 |
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 Belgium (UGENT) Operational Directorate Natural Environment Royal Belgian Institute of Natural Sciences (RBINS) Laboratoire de Biologie Marine (LBM) Université libre de Bruxelles (ULB) Botanic Garden Meise Biogéosciences UMR 6282 Dijon (BGS) Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-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 |
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 |
author_facet |
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 |
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. |
publisher |
HAL CCSD |
publishDate |
2021 |
url |
https://hal.archives-ouvertes.fr/hal-03329042 https://doi.org/10.1186/s12864-021-07917-3 |
geographic |
Antarctic Southern Ocean |
geographic_facet |
Antarctic Southern Ocean |
genre |
Antarc* Antarctic Southern Ocean |
genre_facet |
Antarc* Antarctic Southern Ocean |
op_source |
EISSN: 1471-2164 BMC Genomics https://hal.archives-ouvertes.fr/hal-03329042 BMC Genomics, BioMed Central, 2021, 22 (1), pp.625. ⟨10.1186/s12864-021-07917-3⟩ https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07917-3 |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-021-07917-3 info:eu-repo/semantics/altIdentifier/pmid/34418978 hal-03329042 https://hal.archives-ouvertes.fr/hal-03329042 doi:10.1186/s12864-021-07917-3 PUBMED: 34418978 PUBMEDCENTRAL: PMC8380342 |
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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1766016445448192000 |
spelling |
ftccsdartic:oai:HAL:hal-03329042v1 2023-05-15T13:31:10+02:00 Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. 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 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 Belgium (UGENT) Operational Directorate Natural Environment Royal Belgian Institute of Natural Sciences (RBINS) Laboratoire de Biologie Marine (LBM) Université libre de Bruxelles (ULB) Botanic Garden Meise Biogéosciences UMR 6282 Dijon (BGS) Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-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). 2021-12 https://hal.archives-ouvertes.fr/hal-03329042 https://doi.org/10.1186/s12864-021-07917-3 en eng HAL CCSD BioMed Central info:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-021-07917-3 info:eu-repo/semantics/altIdentifier/pmid/34418978 hal-03329042 https://hal.archives-ouvertes.fr/hal-03329042 doi:10.1186/s12864-021-07917-3 PUBMED: 34418978 PUBMEDCENTRAL: PMC8380342 EISSN: 1471-2164 BMC Genomics https://hal.archives-ouvertes.fr/hal-03329042 BMC Genomics, BioMed Central, 2021, 22 (1), pp.625. ⟨10.1186/s12864-021-07917-3⟩ https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07917-3 Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean 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] info:eu-repo/semantics/article Journal articles 2021 ftccsdartic https://doi.org/10.1186/s12864-021-07917-3 2022-01-09T00:13:14Z 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. Article in Journal/Newspaper Antarc* Antarctic Southern Ocean Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) Antarctic Southern Ocean BMC Genomics 22 1 |