Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs
Abstract Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone...
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crwiley:10.1111/1755-0998.13524 2024-09-09T19:26:56+00:00 Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs O’Grady, Christopher James Dhandapani, Vignesh Colbourne, John K. Frisch, Dagmar H2020 Marie Skłodowska-Curie Actions NERC Biomolecular Analysis Facility 2021 http://dx.doi.org/10.1111/1755-0998.13524 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13524 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13524 en eng Wiley http://creativecommons.org/licenses/by/4.0/ Molecular Ecology Resources volume 22, issue 3, page 946-961 ISSN 1755-098X 1755-0998 journal-article 2021 crwiley https://doi.org/10.1111/1755-0998.13524 2024-08-15T04:20:17Z Abstract Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia , a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimized workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10 and 300 years old. Resulting genome coverage breadth in most samples was ~70%, including those from >100‐year‐old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with single nucleotide polymorphisms in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by‐product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300 years). The mitochondrial DNA provides an additional source for evolutionary studies of these populations. We provide an optimized workflow for WGA followed by whole genome sequencing including steps to minimize exogenous DNA. Article in Journal/Newspaper Arctic Wiley Online Library Arctic Arctic Lake ENVELOPE(-130.826,-130.826,57.231,57.231) Molecular Ecology Resources 22 3 946 961 |
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Wiley Online Library |
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crwiley |
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English |
description |
Abstract Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia , a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimized workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10 and 300 years old. Resulting genome coverage breadth in most samples was ~70%, including those from >100‐year‐old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with single nucleotide polymorphisms in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by‐product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300 years). The mitochondrial DNA provides an additional source for evolutionary studies of these populations. We provide an optimized workflow for WGA followed by whole genome sequencing including steps to minimize exogenous DNA. |
author2 |
H2020 Marie Skłodowska-Curie Actions NERC Biomolecular Analysis Facility |
format |
Article in Journal/Newspaper |
author |
O’Grady, Christopher James Dhandapani, Vignesh Colbourne, John K. Frisch, Dagmar |
spellingShingle |
O’Grady, Christopher James Dhandapani, Vignesh Colbourne, John K. Frisch, Dagmar Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs |
author_facet |
O’Grady, Christopher James Dhandapani, Vignesh Colbourne, John K. Frisch, Dagmar |
author_sort |
O’Grady, Christopher James |
title |
Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs |
title_short |
Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs |
title_full |
Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs |
title_fullStr |
Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs |
title_full_unstemmed |
Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs |
title_sort |
refining the evolutionary time machine: an assessment of whole genome amplification using single historical daphnia eggs |
publisher |
Wiley |
publishDate |
2021 |
url |
http://dx.doi.org/10.1111/1755-0998.13524 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13524 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13524 |
long_lat |
ENVELOPE(-130.826,-130.826,57.231,57.231) |
geographic |
Arctic Arctic Lake |
geographic_facet |
Arctic Arctic Lake |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Molecular Ecology Resources volume 22, issue 3, page 946-961 ISSN 1755-098X 1755-0998 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1111/1755-0998.13524 |
container_title |
Molecular Ecology Resources |
container_volume |
22 |
container_issue |
3 |
container_start_page |
946 |
op_container_end_page |
961 |
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1809896460245794816 |