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. 2023 Jul 5;13(7):jkad099.
doi: 10.1093/g3journal/jkad099.

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

Theodore E Squires  1   2 , Patrik Rödin-Mörch  1   2 , Giulio Formenti  3 , Alan Tracey  4 , Linelle Abueg  3 , Nadolina Brajuka  3 , Erich Jarvis  3 , Eva C Halapi  1 , Páll Melsted  5   6 , Jacob Höglund  2 , Kristinn Pétur Magnússon  1   6   7
Affiliations

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

Theodore E Squires et al. G3 (Bethesda). .

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).

Keywords: Lagopus muta; PacBio Hifi; Rock Ptarmigan; evolutionary biology; reference genome.

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Conflict of interest statement

Conflicts of interest statement The author(s) declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Species overview showing sexually dimorphic seasonal molt patterns of adult Rock Ptarmigan with white winter plumage and mottled breeding colors, alongside a range map showing the global distribution of Rock Ptarmigan above 30° north.
Fig. 2.
Fig. 2.
Hi-C contact map for the bLagMut1 genome showing long-range contacts generated using PretextView (v. 0.2.5).
Fig. 3.
Fig. 3.
A snail plot indicating the completeness of the bLagMut1 genome assembly. Summary information about scaffold statistics, BUSCO, and the Guanine-Cytosine vs Adenine-Thymine composition of various regions are included.
Fig. 4.
Fig. 4.
Outputs from Merqury showing kmer distribution according to: a) Spectra-cn plot of the bLagMut1 complete assembly, b) spectra-asm plot of the bLagMut1 complete assembly, c) spectra-cn plot of the bLagMut1 primary assembly, and d) spectra-cn plot of the bLagMut1 alternate assembly.
See this image and copyright information in PMC

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