Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species ...
Abstract Background Reference genomes provide a foundational framework for evolutionary investigations, ecological analysis, and conservation science, yet uncertainties in the assembly of reference genomes are difficult to assess, and by extension rarely quantified. Reference genomes for monodontid...
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ftdatacite:10.6084/m9.figshare.c.6940518.v1 2023-12-31T10:05:17+01:00 Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species ... Bringloe, Trevor T. Parent, Geneviève J. 2023 https://dx.doi.org/10.6084/m9.figshare.c.6940518.v1 https://springernature.figshare.com/collections/Contrasting_new_and_available_reference_genomes_to_highlight_uncertainties_in_assemblies_and_areas_for_future_improvement_an_example_with_monodontid_species/6940518/1 unknown figshare https://dx.doi.org/10.6084/m9.figshare.c.6940518 Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 Genetics FOS Biological sciences article Collection 2023 ftdatacite https://doi.org/10.6084/m9.figshare.c.6940518.v110.6084/m9.figshare.c.6940518 2023-12-01T11:23:14Z Abstract Background Reference genomes provide a foundational framework for evolutionary investigations, ecological analysis, and conservation science, yet uncertainties in the assembly of reference genomes are difficult to assess, and by extension rarely quantified. Reference genomes for monodontid cetaceans span a wide spectrum of data types and analytical approaches, providing the context to derive broader insights related to discrepancies and regions of uncertainty in reference genome assembly. We generated three beluga (Delphinapterus leucas) and one narwhal (Monodon monoceros) reference genomes and contrasted these with published chromosomal scale assemblies for each species to quantify discrepancies associated with genome assemblies. Results The new reference genomes achieved chromosomal scale assembly using a combination of PacBio long reads, Illumina short reads, and Hi-C scaffolding data. For beluga, we identified discrepancies in the order and orientation of contigs in 2.2–3.7% of the total genome ... Article in Journal/Newspaper Beluga Beluga* Delphinapterus leucas Monodon monoceros narwhal* DataCite Metadata Store (German National Library of Science and Technology) |
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Genetics FOS Biological sciences |
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Genetics FOS Biological sciences Bringloe, Trevor T. Parent, Geneviève J. Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species ... |
topic_facet |
Genetics FOS Biological sciences |
description |
Abstract Background Reference genomes provide a foundational framework for evolutionary investigations, ecological analysis, and conservation science, yet uncertainties in the assembly of reference genomes are difficult to assess, and by extension rarely quantified. Reference genomes for monodontid cetaceans span a wide spectrum of data types and analytical approaches, providing the context to derive broader insights related to discrepancies and regions of uncertainty in reference genome assembly. We generated three beluga (Delphinapterus leucas) and one narwhal (Monodon monoceros) reference genomes and contrasted these with published chromosomal scale assemblies for each species to quantify discrepancies associated with genome assemblies. Results The new reference genomes achieved chromosomal scale assembly using a combination of PacBio long reads, Illumina short reads, and Hi-C scaffolding data. For beluga, we identified discrepancies in the order and orientation of contigs in 2.2–3.7% of the total genome ... |
format |
Article in Journal/Newspaper |
author |
Bringloe, Trevor T. Parent, Geneviève J. |
author_facet |
Bringloe, Trevor T. Parent, Geneviève J. |
author_sort |
Bringloe, Trevor T. |
title |
Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species ... |
title_short |
Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species ... |
title_full |
Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species ... |
title_fullStr |
Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species ... |
title_full_unstemmed |
Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species ... |
title_sort |
contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species ... |
publisher |
figshare |
publishDate |
2023 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.6940518.v1 https://springernature.figshare.com/collections/Contrasting_new_and_available_reference_genomes_to_highlight_uncertainties_in_assemblies_and_areas_for_future_improvement_an_example_with_monodontid_species/6940518/1 |
genre |
Beluga Beluga* Delphinapterus leucas Monodon monoceros narwhal* |
genre_facet |
Beluga Beluga* Delphinapterus leucas Monodon monoceros narwhal* |
op_relation |
https://dx.doi.org/10.6084/m9.figshare.c.6940518 |
op_rights |
Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 |
op_doi |
https://doi.org/10.6084/m9.figshare.c.6940518.v110.6084/m9.figshare.c.6940518 |
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1786836859514519552 |