Tragopan caboti strain:WYL01
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ABSTRACT:
PROVIDER: PRJNA38181 | ENA |
REPOSITORIES: ENA
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Project description:Tragopan temminckii Genome sequencing and assembly
| PRJNA1000723 | ENA
Project description:Cabot's tragopan is a pheasant-like bird found in south-east China
| PRJNA43303 | ENA
Project description:BackgroundHigh-quality genome data of birds play a significant role in the systematic study of their origin and adaptive evolution. The Temminck's tragopan (Tragopan temminckii) (Galliformes, Phasianidae), a larger pheasant, is one of the most abundant and widely distributed species of the genus Tragopan, and was defined as class II of the list of national key protected wild animals in China. The absence of a sequenced genome has restricted previous evolutionary trait studies of this taxa.ResultsThe whole genome of the Temminck's tragopan was sequenced using Illumina and PacBio platform, and then de novo assembled and annotated. The genome size was 1.06 Gb, with a contig N50 of 4.17 Mb. A total of 117.22 Mb (11.00%) repeat sequences were identified. 16,414 genes were predicted using three methods, with 16,099 (98.08%) annotated as functional genes based on five databases. In addition, comparative genome analyses were conducted across 12 Galliformes species. The results indicated that T. temminckii was the first species to branch off from the clade containing Lophura nycthemera, Phasianus colchicus, Chrysolophus pictus, Syrmaticus mikado, Perdix hodgsoniae, and Meleagris gallopavo, with a corresponding divergence time of 31.43 million years ago (MYA). Expanded gene families associated with immune response and energy metabolism were identified. Genes and pathways associated with plumage color and feather development, immune response, and energy metabolism were found in the list of positively selected genes (PSGs).ConclusionsA genome draft of the Temminck's tragopan was reported, genome feature and comparative genome analysis were described, and genes and pathways related to plumage color and feather development, immune response, and energy metabolism were identified. The genomic data of the Temminck's tragopan considerably contribute to the genome evolution and phylogeny of the genus Tragopan and the whole Galliformes species underlying ecological adaptation strategies.
| S-EPMC10702090 | biostudies-literature
Project description:Protected areas are a critical tool to conserve biodiversity in the face of the global crisis of species extinction. Here, we present the first ever management effectiveness assessment of Pakistan's Protected Areas (PAs). We link these assessments to the delivery of conservation outcomes focusing on the threatened Western Tragopan (Tragopan melanocephalus) endemic to Pakistan and India. We used two approaches, first mapping the spatial distribution of potential habitat coverage using machine learning ensemble models and second, an assessment of the management effectiveness of protected areas. Our results show that only Machiara National Park scored just above 40% (indicating relatively weak management), 22 of the PAs fell within the 25-50% quantile (indicating weak management), and 3 scored below 25% (indicating poor management). PAs within the species distributional range covered 92,387 ha which is only 2% of the total potential habitat of the Tragopan. Scoring of Planning element was insufficient both in term of the site and species. Likewise, inputs (e.g., research and monitoring program, staff numbers, staff training, current budget, security of budget, and management after process) were also inadequate. Finally, we recommend the establishment of more protected areas within the species potential habitat and inclusion of species-specific plans in Pakistan's PAs management.
| S-EPMC7999559 | biostudies-literature