The whole genome of Sichuan partridge will be a valuable genomic resource for answering evolutionary questions associated with this endangered species, and for the development of genetic tools for Sichuan partridge research and conservation. To help achieve the goal, we have sequenced and assembled the Sichuan partridge reference genome, and performed comparative genomics analysis. Further research is essential to clarify the environmental adaption and evolutionary history of Sichuan partridge and to elucidate functional genomic regions that underlie ecological adaptation. To date, few studies have been conducted for the investigation associated with the genetic mechanisms of the environmental adaption of the Sichuan partridge, and the whole genome of Sichuan partridge is currently not available. Owing to the habitat fragmentation of endemic birds in subtropical forest in the mountains of Southwestern China, the populations of Sichuan partridge have decreased dramatically, which has led to governmental protection of the Sichuan partridge in much of their range. It has been classified as an endangered species (IUCN 2007) and a nationally protected animal in China because of its largely restricted range, very small population size, and severely fragmented habitat ( Figure 1). The Sichuan partridge ( Arborophila rufipectus, Phasianidae, and Galliformes) is endemic to the mountains in the south-west China. Our data and findings provide valuable genomic resources not only for studying the evolutionary adaptation, but also for facilitating the long-term conservation and genetic diversity for this endangered species. Pairwise sequentially Markovian coalescent analysis revealed the recent demographic trajectory for the Sichuan partridge. Gene Ontology (GO) enrichment analysis of positively selected genes (PSGs) in Sichuan partridge showed over-represented GO functions related to environmental adaptation, such as energy metabolism and behavior. Comparisons between the Sichuan partridge genome and chicken genome revealed a conserved genome structure, and phylogenetic analysis demonstrated that Arborophila possessed a basal phylogenetic position within Phasianidae. A total of 56 olfactory receptor (OR) genes were found in Sichuan partridge, and conserved motifs were detected. About 1.94 million heterozygous single-nucleotide polymorphisms (SNPs) were detected, 17,519 protein-coding genes were predicted, and 9.29% of the genome was identified as repetitive elements. The final draft assembly consisted of approximately 1.09 Gb, and had a scaffold N50 of 4.57 Mb. To examine the evolution and genomic features of Sichuan partridge, we de novo assembled the Sichuan partridge reference genome. It has been listed in Appendix I of International Trade Convention on Endangered Wild Animal and Plant Species.The Sichuan partridge ( Arborophila rufipectus, Phasianidae, Galliformes) is distributed in south-west China, and classified as endangered grade. The eggs are dark brown yellow, with puce spots of various sizes.Ĭhinese Monal is a resident bird and endemic to China, dispersing over southeast Qinghai Province, Dingxing, Kangding, Ruchuan, Pingwu of western Sichuan Province as well as Jiaoxian, Diebu, Zouqu of Gansu Province. In artificial breeding conditions, it lays eggs in April and May, with 3 to 5 eggs per brood. Because it likes to eat culms of fritillaria, it is also named "fritillaria pheasant ". It mainly feeds on botanic radicels and corms. In winter it moves to lower mountains at an elevation of about 2,000 meters. Usually it is fond of forming into subgroups, and moving about in alpine meadows, bushes or bare rock areas at an elevation of 4,000 to 5,000 meters. The back is white, and the tail has more than 10 brown transverse bands. Body feathers of the female are dun, with approximately white fine grains. The tectices of alae has similar color with the back feathers, and the remiges are dark brown with green brims. The vertex has a tuft of gunmetal to cupreous cristae. It is pure white from back to waist, and the tail is bluish green. The upper body of the male is mostly metalescent aeruginous. It is slightly larger than the brown-tailed pheasant, with a full-length of about 76 centimeters. Its scientific name is Lophophorus Ihuysii (Latin), or Chinese Monal Pheasant (English). With the alias of fritillaria pheasant, it belongs to the Phasianidae family of Galliformes order.
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