Lagopus muta japonica
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| DRR192146_1.fastq.gz | Fastqsanger.gz | |||
| DRR192146_2.fastq.gz | Fastqsanger.gz | |||
| DRR192147_1.fastq.gz | Fastqsanger.gz | |||
| DRR192147_2.fastq.gz | Fastqsanger.gz |
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Project description:DNA metabarcoding was employed to identify plant-derived food resources for the Japanese rock ptarmigan (Lagopus muta japonica), which is registered as a natural living monument in Japan, in the Northern Japanese Alps in Toyama Prefecture, Japan, in July to October, 2015-2018. DNA metabarcoding using high-throughput sequencing (HTS) of rbcL and ITS2 sequences from alpine plants found in ptarmigan fecal samples collected in the study area. The obtained sequences were analyzed using a combination of a constructed local database and the National Center for Biotechnology Information (NCBI) database, revealed that a total of 53 plant taxa were food plant resources for ptarmigans. Of these plant taxa, 49 could be assigned to species (92.5%), three to genus (5.7%), and one to family (1.9%). Of the 23 plant families identified from the 105 fecal samples collected, the dominant families throughout all collection periods were Ericaceae (99.0% of 105 fecal samples), followed by Rosaceae (42.9%), Apiaceae (35.2%), and Poaceae (21.0%). In all of the fecal samples examined, the most frequently encountered plant species were Vaccinium ovalifolium var. ovalifolium (69.5%), followed by Empetrum nigrum var. japonicum (68.6%), Kalmia procumbens (42.9%), Tilingia ajanensis (34.3%) and V. uliginosum var. japonicum (34.3%). A rarefaction analysis for each collection period in the study revealed that the food plant resources found in the study area ranged from a minimum of 87.0% in July to a maximum of 97.5% in September, and that 96.4% of the food plant taxa were found throughout the study period. The findings showed that DNA metabarcoding using HTS to construct a local database of rbcL and ITS2 sequences in conjunction with rbcL and ITS2 sequences deposited at the NCBI, as well as rarefaction analysis, are well suited to identifying the dominant food plants in the diet of Japanese rock ptarmigans. In the windswept alpine dwarf shrub community found in the study area, dominant taxa in the Ericaceae family were the major food plant s for Japanese rock ptarmigans from July to October. This plant community therefore needs to be conserved in order to protect the food resources of Japanese rock ptarmigans in the region.
| S-EPMC8912148 | biostudies-literature
Project description:Lagopus muta (Rock ptarmigan) genome, bLagMut1, primary haplotype
| PRJNA836583 | ENA
Project description:Lagopus muta (Rock ptarmigan) genome, bLagMut1, alternate haplotype
| PRJNA836585 | ENA
Project 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 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).
| S-EPMC10320755 | biostudies-literature
Project description:The complete mitochondrial genome sequences of the two sister species, Scandinavian willow ptarmigan Lagopus lagopus and Icelandic rock ptarmigan Lagopus muta, were characterized using next-generation sequencing. The mitogenome for willow ptarmigan was 16,677?bp long, with base composition of 30.3% A, 30.8% C, 13.3% G and 25.6% T, with a GC content of 44.1%, while for rock ptarmigan mitogenome was 16,687?bp long, with base composition of 30.2% A, 30.6% C, 13.4% G and 25.8% T, and a GC content of 44.0%. Like other Galliformes species, the mitogenomes comprised of 13 protein-coding genes, 22 tRNA, 2 rRNA and 2 non-coding regions; and control region (D-loop). All genes except ND6 and 8 tRNA were encoded on the?+?strand. All protein-coding genes started with ATG, except for COX1, where a GTG codon was present in both willow ptarmigan and rock ptarmigan. Phylogenetic analysis of the two novel mitogenomes with other Galliformes species demonstrates close relationship within the Tetraoninae subfamily.
| S-EPMC7800188 | biostudies-literature
Project description:BackgroundThe Rock Ptarmigan Lagopus muta japonica lives in the alpine zones of central Japan, which is the southern limit of the global distribution for this species. This species is highly dependent on alpine habitats, which are considered vulnerable to rapid climate change. This study aimed to assess the impact of climate change on potential L. muta japonica habitat based on predicted changes to alpine vegetation, to identify population vulnerability under future climatic conditions for conservation planning. We developed species distribution models, which considered the structure of the alpine ecosystem by incorporating spatial hierarchy on specific environmental factors to assess the potential habitats for L. muta japonica under current and future climates. We used 24 general circulation models (GCMs) for 2081-2100 as future climate conditions.ResultsThe predicted potential habitat for L. muta japonica was similar to the actual distribution of the territories in the study area of Japan's northern Alps (36.25-36.5°N, 137.5-137.7°E). Future potential habitat for L. muta japonica was projected to decrease to 0.4% of the current potential habitat in the median of occurrence probabilities under 24 GCMs, due to a decrease in alpine vegetation communities. Some potential habitats in the central and northwestern part of the study area were predicted to be sustained in the future, depending on the GCMs.ConclusionsOur model results predicted that the potential habitats for L. muta japonica in Japan's northern Alps, which provides core habitat for this subspecies, would be vulnerable by 2081-2100. Small sustainable habitats may serve as refugia, facilitating the survival of L. muta japonica populations under future climatic conditions. Impact assessment studies of the effect of climate change on L. muta japonica habitats at a nationwide scale are urgently required to establish effective conservation planning for this species, which includes identifying candidate areas for assisted migration as an adaptive strategy.
| S-EPMC6617707 | biostudies-literature