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...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-08-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-021-07917-3 |
| _version_ | 1819066212283318272 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-21T15:58:46Z |
| format | Article |
| id | doaj.art-e43e7c8dc836414cb3bd47e8bb716656 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T15:58:46Z |
| publishDate | 2021-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-e43e7c8dc836414cb3bd47e8bb7166562022-12-21T18:58:02ZengBMCBMC Genomics1471-21642021-08-0122112010.1186/s12864-021-07917-3Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencingHenrik Christiansen0Franz M. Heindler1Bart Hellemans2Quentin Jossart3Francesca Pasotti4Henri Robert5Marie Verheye6Bruno Danis7Marc Kochzius8Frederik Leliaert9Camille Moreau10Tasnim Patel11Anton P. Van de Putte12Ann Vanreusel13Filip A. M. Volckaert14Isa Schön15Laboratory of Biodiversity and Evolutionary Genomics, KU LeuvenLaboratory of Biodiversity and Evolutionary Genomics, KU LeuvenLaboratory of Biodiversity and Evolutionary Genomics, KU LeuvenMarine Biology Group, Vrije Universiteit Brussel (VUB)Marine Biology Research Group, Ghent UniversityOD Nature, Royal Belgian Institute of Natural SciencesOD Nature, Royal Belgian Institute of Natural SciencesMarine Biology Laboratory, Université Libre de Bruxelles (ULB)Marine Biology Group, Vrije Universiteit Brussel (VUB)Marine Biology Research Group, Ghent UniversityMarine Biology Laboratory, Université Libre de Bruxelles (ULB)OD Nature, Royal Belgian Institute of Natural SciencesLaboratory of Biodiversity and Evolutionary Genomics, KU LeuvenMarine Biology Research Group, Ghent UniversityLaboratory of Biodiversity and Evolutionary Genomics, KU LeuvenOD Nature, Royal Belgian Institute of Natural SciencesAbstract 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.https://doi.org/10.1186/s12864-021-07917-3BiodiversityGenome scanGenotyping by sequencingIn silico digestionRADseqSouthern Ocean |
| spellingShingle | 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 BMC Genomics Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean |
| title | 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_short | 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 |
| topic | Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean |
| url | https://doi.org/10.1186/s12864-021-07917-3 |
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