Whole genome sequences from non-invasively collected caribou faecal samples
Abstract Conservation genomics is an important tool to manage threatened species under current biodiversity loss. Recent advances in sequencing technology mean that we can now use whole genomes to investigate demographic history, local adaptation, inbreeding, and more in unprecedented detail. Howeve...
Published in: | Conservation Genetics Resources |
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Springer Science and Business Media LLC
2021
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Online Access: | http://dx.doi.org/10.1007/s12686-021-01235-2 https://link.springer.com/content/pdf/10.1007/s12686-021-01235-2.pdf https://link.springer.com/article/10.1007/s12686-021-01235-2/fulltext.html |
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crspringernat:10.1007/s12686-021-01235-2 2023-05-15T18:04:23+02:00 Whole genome sequences from non-invasively collected caribou faecal samples Taylor, Rebecca S. Manseau, Micheline Redquest, Bridget Keobouasone, Sonesinh Gagné, Patrick Martineau, Christine Wilson, Paul J. NSERC NSERC Collaborative Research & Development (CRD) grant Manitoba Hydro Saskatchewan Power Weyerhaeuser Inc. 2021 http://dx.doi.org/10.1007/s12686-021-01235-2 https://link.springer.com/content/pdf/10.1007/s12686-021-01235-2.pdf https://link.springer.com/article/10.1007/s12686-021-01235-2/fulltext.html en eng Springer Science and Business Media LLC https://creativecommons.org/licenses/by/4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Conservation Genetics Resources ISSN 1877-7252 1877-7260 Genetics Ecology, Evolution, Behavior and Systematics journal-article 2021 crspringernat https://doi.org/10.1007/s12686-021-01235-2 2022-01-04T15:14:36Z Abstract Conservation genomics is an important tool to manage threatened species under current biodiversity loss. Recent advances in sequencing technology mean that we can now use whole genomes to investigate demographic history, local adaptation, inbreeding, and more in unprecedented detail. However, for many rare and elusive species only non-invasive samples such as faeces can be obtained, making it difficult to take advantage of whole genome data. We present a method to extract DNA from the mucosal layer of faecal samples to re-sequence high coverage whole genomes using standard laboratory techniques. We use wild collected faecal pellets collected from caribou ( Rangifer tarandus ), a species undergoing declines in many parts of its range in Canada and subject to comprehensive conservation and population monitoring measures. We compare four faecal genomes to two tissue genomes sequenced in the same run. Quality metrics were similar between faecal and tissue samples with the main difference being the alignment success of raw reads to the reference genome due to differences in low quality and endogenous DNA content, affecting overall coverage. One of our faecal genomes was only re-sequenced at low coverage (1.6 ×), however the other three obtained between 7 and 15 ×, compared to 19 and 25 × for the tissue samples. We successfully re-sequenced high-quality whole genomes from faecal DNA and are one of the first to obtain genome-wide data from wildlife faecal DNA in a non-primate species. Our work represents an important advancement for non-invasive conservation genomics. Article in Journal/Newspaper Rangifer tarandus Springer Nature (via Crossref) Canada Conservation Genetics Resources 14 1 53 68 |
institution |
Open Polar |
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Springer Nature (via Crossref) |
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crspringernat |
language |
English |
topic |
Genetics Ecology, Evolution, Behavior and Systematics |
spellingShingle |
Genetics Ecology, Evolution, Behavior and Systematics Taylor, Rebecca S. Manseau, Micheline Redquest, Bridget Keobouasone, Sonesinh Gagné, Patrick Martineau, Christine Wilson, Paul J. Whole genome sequences from non-invasively collected caribou faecal samples |
topic_facet |
Genetics Ecology, Evolution, Behavior and Systematics |
description |
Abstract Conservation genomics is an important tool to manage threatened species under current biodiversity loss. Recent advances in sequencing technology mean that we can now use whole genomes to investigate demographic history, local adaptation, inbreeding, and more in unprecedented detail. However, for many rare and elusive species only non-invasive samples such as faeces can be obtained, making it difficult to take advantage of whole genome data. We present a method to extract DNA from the mucosal layer of faecal samples to re-sequence high coverage whole genomes using standard laboratory techniques. We use wild collected faecal pellets collected from caribou ( Rangifer tarandus ), a species undergoing declines in many parts of its range in Canada and subject to comprehensive conservation and population monitoring measures. We compare four faecal genomes to two tissue genomes sequenced in the same run. Quality metrics were similar between faecal and tissue samples with the main difference being the alignment success of raw reads to the reference genome due to differences in low quality and endogenous DNA content, affecting overall coverage. One of our faecal genomes was only re-sequenced at low coverage (1.6 ×), however the other three obtained between 7 and 15 ×, compared to 19 and 25 × for the tissue samples. We successfully re-sequenced high-quality whole genomes from faecal DNA and are one of the first to obtain genome-wide data from wildlife faecal DNA in a non-primate species. Our work represents an important advancement for non-invasive conservation genomics. |
author2 |
NSERC NSERC Collaborative Research & Development (CRD) grant Manitoba Hydro Saskatchewan Power Weyerhaeuser Inc. |
format |
Article in Journal/Newspaper |
author |
Taylor, Rebecca S. Manseau, Micheline Redquest, Bridget Keobouasone, Sonesinh Gagné, Patrick Martineau, Christine Wilson, Paul J. |
author_facet |
Taylor, Rebecca S. Manseau, Micheline Redquest, Bridget Keobouasone, Sonesinh Gagné, Patrick Martineau, Christine Wilson, Paul J. |
author_sort |
Taylor, Rebecca S. |
title |
Whole genome sequences from non-invasively collected caribou faecal samples |
title_short |
Whole genome sequences from non-invasively collected caribou faecal samples |
title_full |
Whole genome sequences from non-invasively collected caribou faecal samples |
title_fullStr |
Whole genome sequences from non-invasively collected caribou faecal samples |
title_full_unstemmed |
Whole genome sequences from non-invasively collected caribou faecal samples |
title_sort |
whole genome sequences from non-invasively collected caribou faecal samples |
publisher |
Springer Science and Business Media LLC |
publishDate |
2021 |
url |
http://dx.doi.org/10.1007/s12686-021-01235-2 https://link.springer.com/content/pdf/10.1007/s12686-021-01235-2.pdf https://link.springer.com/article/10.1007/s12686-021-01235-2/fulltext.html |
geographic |
Canada |
geographic_facet |
Canada |
genre |
Rangifer tarandus |
genre_facet |
Rangifer tarandus |
op_source |
Conservation Genetics Resources ISSN 1877-7252 1877-7260 |
op_rights |
https://creativecommons.org/licenses/by/4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1007/s12686-021-01235-2 |
container_title |
Conservation Genetics Resources |
container_volume |
14 |
container_issue |
1 |
container_start_page |
53 |
op_container_end_page |
68 |
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1766175755920736256 |