The Tibetan Partridge(Perdix hodgsoniae)is an endemic species distributed in high-altitude areas of 3600–5600 m on the Qinghai–Tibet Plateau.To explore how the species is adapted to the high elevation environment,we...The Tibetan Partridge(Perdix hodgsoniae)is an endemic species distributed in high-altitude areas of 3600–5600 m on the Qinghai–Tibet Plateau.To explore how the species is adapted to the high elevation environment,we as-sembled a draft genome based on both the Illumina and PacBio sequencing platforms with its population genetics and genomics analysis.In total,134.74 Gb short reads and 30.81 Gb long reads raw data were generated.The 1.05-Gb assembled genome had a contig N50 of 4.56 Mb,with 91.94%complete BUSCOs.The 17457 genes were annotated,and 11.35%of the genome was composed of repeat sequences.The phylogenetic tree showed that P.hodgsoniae was located at the basal position of the clade,including Golden Pheasant(Chrysolophus pictus),Common Pheasant(Phasianus colchicus),and Mikado Pheasant(Syrmaticus mikado).We found that 1014,2595,and 2732 of the 6641 one-to-one orthologous genes were under positive selection in P.hodgsoniae,detected using PAML,BUSTED,and aBSREL programs,respectively,of which 965 genes were common under positive selec-tion with 3 different programs.Several positively selected genes and immunity pathways relevant to high-altitude adaptation were detected.Gene family evolution showed that 99 gene families experienced significant expansion events,while 6 gene families were under contraction.The total number of olfactory receptor genes was relatively low in P.hodgsoniae.Genomic data provide an important resource for a further study on the evolutionary history of P.hodgsoniae,which provides a new insight into its high-altitude adaptation mechanisms.展开更多
The Northem Eurasia origin hypothesis is one key point in the evolutionary model. This indicates that species riginated in Northern Eurasia. Perdix, belonging to Phasianidae of Galliformes, is a valuable type of wildf...The Northem Eurasia origin hypothesis is one key point in the evolutionary model. This indicates that species riginated in Northern Eurasia. Perdix, belonging to Phasianidae of Galliformes, is a valuable type of wildfowl widely distributed Northern Eurasia and contains three species. This mini-review discusses the taxonomic status, phylogeny, and origin of Perdix. Morphological and molecular evidence suggest that the three species, P hodgsoniae, P. dauuricae and P. perdix, form a monophyletic group and they should be classified as ＂pheasant＂ rather than ＂quail.＂ The current review also shows that results were affected by the methods selected for data analysis. A taxonomic category should contain as many species as possible, have a clear system history, remain evolutionarily stable, and lack adaptive radiation. Appropriate type, number and length of genes are important as molecular markers and out-group affects the bootstrap support value. P. hodgsoniae is located at the root of the phytogenetic tree and has the phenotype of ancestral Perdix. The genus Perdix may originate in the Qinghai-Tibet Plateau and expanded into high latitude areas, towards the northern plateau. This phylogenetic and evolutionary statement differs from the Eurasian origin hypothesis.展开更多
We report for the first time the occurrence of heteroplasmy in Grey Partridge(Perdix perdix)revealed by means of two mitochondrial fragments.The possible serious biological and management implications of this exceptio...We report for the first time the occurrence of heteroplasmy in Grey Partridge(Perdix perdix)revealed by means of two mitochondrial fragments.The possible serious biological and management implications of this exception to unilateral inheritance of mtDNA were underlined.展开更多
基金The National Center for Biotechnology Information(NCBI)BioProject and BioSample accession numbers of Perdix hodgsoniae are PRJNA760267 and SAMN21212221,respectivelyThe raw reads have been deposited in the NCBI SRA database with the accession numbers SRR15900414(Illumina),SRR15900412,and SRR15900413(PacBio).
文摘The Tibetan Partridge(Perdix hodgsoniae)is an endemic species distributed in high-altitude areas of 3600–5600 m on the Qinghai–Tibet Plateau.To explore how the species is adapted to the high elevation environment,we as-sembled a draft genome based on both the Illumina and PacBio sequencing platforms with its population genetics and genomics analysis.In total,134.74 Gb short reads and 30.81 Gb long reads raw data were generated.The 1.05-Gb assembled genome had a contig N50 of 4.56 Mb,with 91.94%complete BUSCOs.The 17457 genes were annotated,and 11.35%of the genome was composed of repeat sequences.The phylogenetic tree showed that P.hodgsoniae was located at the basal position of the clade,including Golden Pheasant(Chrysolophus pictus),Common Pheasant(Phasianus colchicus),and Mikado Pheasant(Syrmaticus mikado).We found that 1014,2595,and 2732 of the 6641 one-to-one orthologous genes were under positive selection in P.hodgsoniae,detected using PAML,BUSTED,and aBSREL programs,respectively,of which 965 genes were common under positive selec-tion with 3 different programs.Several positively selected genes and immunity pathways relevant to high-altitude adaptation were detected.Gene family evolution showed that 99 gene families experienced significant expansion events,while 6 gene families were under contraction.The total number of olfactory receptor genes was relatively low in P.hodgsoniae.Genomic data provide an important resource for a further study on the evolutionary history of P.hodgsoniae,which provides a new insight into its high-altitude adaptation mechanisms.
基金supported by the National Natural Science Fundation of China(31372171)the Department of Applied Basic Research of Sichuan Province(2013JY0073)Building Plan for Scientific Research Innovation Team of Leshan Normal University
文摘The Northem Eurasia origin hypothesis is one key point in the evolutionary model. This indicates that species riginated in Northern Eurasia. Perdix, belonging to Phasianidae of Galliformes, is a valuable type of wildfowl widely distributed Northern Eurasia and contains three species. This mini-review discusses the taxonomic status, phylogeny, and origin of Perdix. Morphological and molecular evidence suggest that the three species, P hodgsoniae, P. dauuricae and P. perdix, form a monophyletic group and they should be classified as ＂pheasant＂ rather than ＂quail.＂ The current review also shows that results were affected by the methods selected for data analysis. A taxonomic category should contain as many species as possible, have a clear system history, remain evolutionarily stable, and lack adaptive radiation. Appropriate type, number and length of genes are important as molecular markers and out-group affects the bootstrap support value. P. hodgsoniae is located at the root of the phytogenetic tree and has the phenotype of ancestral Perdix. The genus Perdix may originate in the Qinghai-Tibet Plateau and expanded into high latitude areas, towards the northern plateau. This phylogenetic and evolutionary statement differs from the Eurasian origin hypothesis.
文摘We report for the first time the occurrence of heteroplasmy in Grey Partridge(Perdix perdix)revealed by means of two mitochondrial fragments.The possible serious biological and management implications of this exception to unilateral inheritance of mtDNA were underlined.
