The complete mitochondrial genome of the Japanese rock ptarmigan (<i>Lagopus muta japonica</i> Clark, 1907)

Yonezawa, Takahiro; Nishibori, Masahide

doi:10.1080/23802359.2020.1746207

Cited by 3 publications

(5 citation statements)

References 6 publications

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“…The mitochondrial DNA was described with all 13 expected protein coding regions and analyzed for accuracy through comparative analysis. With our addition, there are now four extant mitochondrial genomes published for the Rock Ptarmigan; Two from Iceland, one from Japan, and one from Siberia (Sveinsdóttir and Magnússon, 2017; Yonezawa and Nishibori, 2020; Wang et. al., 2017).…”

Section: Resultsmentioning

confidence: 99%

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A Chromosome-Level Genome Assembly for the Rock Ptarmigan (Lagopus muta)

Morch

Squires

Formenti

et al. 2023

Preprint

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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 Ptarmigans unique evolutionary history, vulnerability to climate change, and demographic trajectories around the globe. As a wild relative of domesticated Galliformes, findings of avicultural importance may also be revealed.

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Section: Resultsmentioning

confidence: 99%

“…The mitochondrial genome was assembled separately from both raw reads and contigs using MitoHifi (v. 2.2; Uliano-Silva et. al., 2021) with automatic alignment to the Japanese Rock Ptarmigan ( L. muta japonica; Yonezawa and Nishibori, 2020) via built-in features from the MitoFinder dependency (v. 1.4.1; Allio et. al., 2020).…”

Section: Methodsmentioning

confidence: 99%

A Chromosome-Level Genome Assembly for the Rock Ptarmigan (Lagopus muta)

Morch

Squires

Formenti

et al. 2023

Preprint

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show abstract

“…The mitochondrial DNA was described with all 13 expected protein-coding regions and analyzed for accuracy through comparative analysis. With our addition, there are now four extant mitochondrial genomes published for the Rock Ptarmigan; two from Iceland, one from Japan, and one from Siberia ( Sveinsdóttir and Magnússon 2017 ; Wang et al 2017 ; Yonezawa and Nishibori 2020 ). Using the ClustalW package embedded in BioEdit ( Thompson et al 1994 ; Hall 1999 ), we found a total of 24 bases divergent from the previously published Icelandic Rock Ptarmigan mitogenome in a manual review.…”

Section: Resultsmentioning

confidence: 99%

“…The mitochondrial genome was assembled separately from both raw reads and contigs using MitoHifi (v. 2.2; Uliano-Silva et al 2021 ) with automatic alignment to the Japanese Rock Ptarmigan ( L. muta japonica ; Yonezawa and Nishibori 2020 ) via built-in features from the MitoFinder dependency (v. 1.4.1; Allio et al 2020 ).…”

Section: Methodsmentioning

confidence: 99%

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

Squires

Rödin‐Mörch

Formenti

et al. 2023

G3: Genes, Genomes, Genetics

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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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“…These updated phylogenies provide new insights into the origins and history of domestication. With the aim of addressing these questions for Tosa-Jidori, we selected one sample (Tosa 2; 921 strain) for determination of the complete mitogenome sequence as described by other researchers using different bird species (Japanese quail [ 16 ]; chickens [ 17 , 19 , 23 ]; rock ptarmigans [ 24 ]).…”

Section: Resultsmentioning

confidence: 99%

Complete mitochondrial genome sequence of Tosa-Jidori sheds light on the origin and evolution of Japanese native chickens

2021

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14 15 ORCID 16 Sayed A.-M. Osman: https://orcid.org/0000-0001-6925-9414 ABSTRACT 27 Objective: In Japan, approximately 50 breeds of indigenous domestic chicken, called Japanese native 28 chickens (JNCs), have been developed. JNCs gradually became established based on three major 29 original groups, "Jidori", "Shoukoku" and "Shamo". Tosa-Jidori is a breed of Jidori, and archival 30 records as well as its morphologically primitive characters suggest an ancient origin. Although Jidori 31 is thought to have been introduced from East Asia, a previous study based on mitochondrial D-loop s 32 equences demonstrated that Tosa-Jidori belongs to haplogroup D, which is abundant in Southeast Asia 33 but rare in other regions, and a Southeast Asian origin for Tosa-Jidori was therefore suggested. The 34 relatively small size of the D-loop region offers limited resolution in comparison with mitogenome 35 phylogeny. This study was conducted to determine the phylogenetic position of the Tosa-Jidori breed 36 based on complete mitochondrial D-loop and mitogenome sequences, and to clarify its 37 evolutionary relationships, possible maternal origin and routes of introduction into Japan.38 Methods: Maximum parsimony trees were based on 133 chickens, and consisted of 86 mitogenome 39 sequences as well as 47 D-loop sequences.40Results: This is the first report of the complete mitogenome not only for the Tosa-Jidori breed, but 41 also for a member of one of the three major original groups of JNCs. Our phylogenetic analysis based 42 on D-loop and mitogenome sequences suggests that Tosa-Jidori individuals characterized in this study 43 belong to the haplogroup D as well as the sub-haplogroup E1. 44 Conclusion: \The sub-haplogroup E1 is relatively common in East Asia, and so although the 45 Southeast Asian origin hypothesis cannot be rejected, East Asia is another possible origin of Tosa-46 Jidori. This study highlights the complicated origin and breeding history of Tosa-Jidori and other JNC 47 breeds.48 49 A c c e p t e d A r t i c l e 53 Given the unique geographical location of Japan in the East Asian peripheral region, with 54 water surrounding it on all sides, Japanese native chicken (JNC) breeds of Gallus gallus have been 55 profoundly influenced by continental breeds, but at the same time, they have developed indigenously. 56 There are approximately 50 breeds of Japanese native chickens [1]. Until 1867, most of them were 57 developed for their special plumage, crowing and cockfighting, while subsequently, from the end of 58 the 19th century to the early stages of the 20th century, some new breeds were created to produce eggs 59 and/or meat. 60 Most of today's JNC breeds were established from members of three major original groups or 61 breeds: "Jidori", "Shoukoku", and "Shamo" [2]. Jidori does not specify a breed, but is a generic name 62 used for various local primitive chickens whose ancestors are thought to have been introduced to 63 Japan in the Yayoi period (300 BC-300 AD) via Korea. The Jidori group includes the three well-64 kn...

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The complete mitochondrial genome of the Japanese rock ptarmigan (Lagopus muta japonica Clark, 1907)

Cited by 3 publications

References 6 publications

A Chromosome-Level Genome Assembly for the Rock Ptarmigan (Lagopus muta)

A Chromosome-Level Genome Assembly for the Rock Ptarmigan (Lagopus muta)

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

Complete mitochondrial genome sequence of Tosa-Jidori sheds light on the origin and evolution of Japanese native chickens

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