A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta)
The Rock Ptarmigan (Lagopus muta) is a cold-adapted, largely sedentary, game bird with a Holarctic distribution. The species represents an important example of an organism likely to be affected by ongoing climatic shifts across a disparate range. We provide here a highquality reference genome and mi...
Published in: | G3: Genes, Genomes, Genetics |
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Language: | English |
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Uppsala universitet, Zooekologi
2023
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Online Access: | http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-512755 https://doi.org/10.1093/g3journal/jkad099 |
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ftuppsalauniv:oai:DiVA.org:uu-512755 2024-02-11T10:05:10+01:00 A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta) Squires, Theodore E. Rödin Mörch, Patrik Formenti, Giulio Tracey, Alan Abueg, Linelle Brajuka, Nadolina Jarvis, Erich Halapi, Eva C. Melsted, Pall Höglund, Jacob Magnusson, Kristinn Petur 2023 application/pdf http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-512755 https://doi.org/10.1093/g3journal/jkad099 eng eng Uppsala universitet, Zooekologi Univ Akureyri, Fac Nat Resource Sci, Borgir vio Noroursloo, IS-600 Akureyri, Iceland. Rockefeller Univ, Ctr Genom & Syst Biol, 1230 York Ave, New York, NY 10065 USA. Wellcome Sanger Inst, Wellcome Genome Campus, Hinxton CB10 1SA, Cambs, England. Univ Iceland, Dept Comp Sci, Saemundargata 2, IS-102 Reykjavik, Iceland.;Univ Iceland, Biomed Ctr, Med Pk,Vatnsmyrarvegur 16, IS-101 Reykjavik, Iceland. Univ Akureyri, Fac Nat Resource Sci, Borgir vio Noroursloo, IS-600 Akureyri, Iceland.;Univ Iceland, Biomed Ctr, Med Pk,Vatnsmyrarvegur 16, IS-101 Reykjavik, Iceland.;Iceland Inst Nat Hist, Borgir vio Noroursloo, IS-600 Akureyri, Iceland. G3 : Genes, Genomes, Genetics, 2023, 13:7, orcid:0000-0001-6737-1488 orcid:0000-0002-5840-779x orcid:0000-0003-4528-6826 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-512755 doi:10.1093/g3journal/jkad099 PMID 37141262 ISI:000997472900001 info:eu-repo/semantics/openAccess Rock Ptarmigan Lagopus muta reference genome PacBio Hifi evolutionary biology Evolutionsbiologi Article in journal info:eu-repo/semantics/article text 2023 ftuppsalauniv https://doi.org/10.1093/g3journal/jkad099 2024-01-17T23:33:44Z The Rock Ptarmigan (Lagopus muta) is a cold-adapted, largely sedentary, game bird with a Holarctic distribution. The species represents an important example of an organism likely to be affected by ongoing climatic shifts across a disparate range. We provide here a highquality reference genome and mitogenome for the Rock Ptarmigan assembled from PacBio HiFi and Hi-C sequencing of a female bird from Iceland. The total size of the genome is 1.03 Gb with a scaffold N50 of 71.23 Mb and a contig N50 of 17.91 Mb. The final scaffolds represent all 40 predicted chromosomes, and the mitochondria with a BUSCO score of 98.6%. Gene annotation resulted in 16,078 protein-coding genes out of a total 19,831 predicted (81.08% excluding pseudogenes). The genome included 21.07% repeat sequences, and the average length of genes, exons, and introns were 33605, 394, and 4265 bp, respectively. The availability of a new reference-quality genome will contribute to understanding the Rock Ptarmigan's unique evolutionary history, vulnerability to climate change, and demographic trajectories around the globe while serving as a benchmark for species in the family Phasianidae (order Galliformes). Article in Journal/Newspaper Iceland Lagopus muta rock ptarmigan Uppsala University: Publications (DiVA) G3: Genes, Genomes, Genetics 13 7 |
institution |
Open Polar |
collection |
Uppsala University: Publications (DiVA) |
op_collection_id |
ftuppsalauniv |
language |
English |
topic |
Rock Ptarmigan Lagopus muta reference genome PacBio Hifi evolutionary biology Evolutionsbiologi |
spellingShingle |
Rock Ptarmigan Lagopus muta reference genome PacBio Hifi evolutionary biology Evolutionsbiologi Squires, Theodore E. Rödin Mörch, Patrik Formenti, Giulio Tracey, Alan Abueg, Linelle Brajuka, Nadolina Jarvis, Erich Halapi, Eva C. Melsted, Pall Höglund, Jacob Magnusson, Kristinn Petur A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta) |
topic_facet |
Rock Ptarmigan Lagopus muta reference genome PacBio Hifi evolutionary biology Evolutionsbiologi |
description |
The Rock Ptarmigan (Lagopus muta) is a cold-adapted, largely sedentary, game bird with a Holarctic distribution. The species represents an important example of an organism likely to be affected by ongoing climatic shifts across a disparate range. We provide here a highquality reference genome and mitogenome for the Rock Ptarmigan assembled from PacBio HiFi and Hi-C sequencing of a female bird from Iceland. The total size of the genome is 1.03 Gb with a scaffold N50 of 71.23 Mb and a contig N50 of 17.91 Mb. The final scaffolds represent all 40 predicted chromosomes, and the mitochondria with a BUSCO score of 98.6%. Gene annotation resulted in 16,078 protein-coding genes out of a total 19,831 predicted (81.08% excluding pseudogenes). The genome included 21.07% repeat sequences, and the average length of genes, exons, and introns were 33605, 394, and 4265 bp, respectively. The availability of a new reference-quality genome will contribute to understanding the Rock Ptarmigan's unique evolutionary history, vulnerability to climate change, and demographic trajectories around the globe while serving as a benchmark for species in the family Phasianidae (order Galliformes). |
format |
Article in Journal/Newspaper |
author |
Squires, Theodore E. Rödin Mörch, Patrik Formenti, Giulio Tracey, Alan Abueg, Linelle Brajuka, Nadolina Jarvis, Erich Halapi, Eva C. Melsted, Pall Höglund, Jacob Magnusson, Kristinn Petur |
author_facet |
Squires, Theodore E. Rödin Mörch, Patrik Formenti, Giulio Tracey, Alan Abueg, Linelle Brajuka, Nadolina Jarvis, Erich Halapi, Eva C. Melsted, Pall Höglund, Jacob Magnusson, Kristinn Petur |
author_sort |
Squires, Theodore E. |
title |
A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta) |
title_short |
A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta) |
title_full |
A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta) |
title_fullStr |
A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta) |
title_full_unstemmed |
A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta) |
title_sort |
chromosome-level genome assembly for the rock ptarmigan (lagopus muta) |
publisher |
Uppsala universitet, Zooekologi |
publishDate |
2023 |
url |
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-512755 https://doi.org/10.1093/g3journal/jkad099 |
genre |
Iceland Lagopus muta rock ptarmigan |
genre_facet |
Iceland Lagopus muta rock ptarmigan |
op_relation |
G3 : Genes, Genomes, Genetics, 2023, 13:7, orcid:0000-0001-6737-1488 orcid:0000-0002-5840-779x orcid:0000-0003-4528-6826 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-512755 doi:10.1093/g3journal/jkad099 PMID 37141262 ISI:000997472900001 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1093/g3journal/jkad099 |
container_title |
G3: Genes, Genomes, Genetics |
container_volume |
13 |
container_issue |
7 |
_version_ |
1790602049203732480 |