A chromosome-level genome assembly for the Rock Ptarmigan ( Lagopus muta)

Abstract 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 high-quality reference gen...

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Bibliographic Details
Published in:G3: Genes, Genomes, Genetics
Main Authors: Squires, Theodore E, Rödin-Mörch, Patrik, Formenti, Giulio, Tracey, Alan, Abueg, Linelle, Brajuka, Nadolina, Jarvis, Erich, Halapi, Eva C, Melsted, Páll, Höglund, Jacob, Magnússon, Kristinn Pétur
Other Authors: Mallarino, R, Icelandic Centre for Research Fund within the Icelandic Centre for Research, Jacob Höglund from the Swedish Research Council, Vetenskapsrådet, NGI/Uppsala Genome Center, Vetenskapsrådet and Science for Life Laboratory
Format: Article in Journal/Newspaper
Language:English
Published: Oxford University Press (OUP) 2023
Subjects:
Iceland
Lagopus muta
rock ptarmigan
Online Access:http://dx.doi.org/10.1093/g3journal/jkad099
https://academic.oup.com/g3journal/advance-article-pdf/doi/10.1093/g3journal/jkad099/50738631/jkad099.pdf
https://academic.oup.com/g3journal/article-pdf/13/7/jkad099/56716004/jkad099.pdf
Description
Summary:Abstract 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 high-quality 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).

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