Abstract
The Sichuan partridge (Arborophila rufipectus, Phasianidae, Galliformes) is distributed in south-west China, and classified as endangered grade. To examine the evolution and genomic features of Sichuan partridge, we de novo assembled the Sichuan partridge reference genome. The final draft assembly consisted of approximately 1.09 Gb, and had a scaffold N50 of 4.57 Mb. 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. A total of 56 olfactory receptor (OR) genes were found in Sichuan partridge, and conserved motifs were detected. 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. 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. Pairwise sequentially Markovian coalescent analysis revealed the recent demographic trajectory for the Sichuan partridge. 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.
Highlights
The Sichuan partridge (Arborophila rufipectus, Phasianidae, and Galliformes) is endemic to the mountains in the south-west China [1]
A total of 296.74 Gb (~272-fold coverage) of high-quality reads were generated for the Sichuan
K-mer analysis, the genome size of Sichuan partridge was estimated to be 1.09 Gb, which was similar to other thereported genome avian size ofgenomes
Summary
The Sichuan partridge (Arborophila rufipectus, Phasianidae, and Galliformes) is endemic to the mountains in the south-west China [1]. 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) [2,3]. 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 [4], which has led to governmental protection of the Sichuan partridge in much of their range.
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