First complete genome sequence in Arborophila and comparative genomics reveals the evolutionary adaptation of Hainan Partridge (Arborophila ardens)

Zhou, Chuang; Zheng, Shuai; Jiang, Xue; Liang, Wei; Price, Megan; Fan, Zhenxin; Yang, Meng; Yue, Bisong

doi:10.1186/s40657-018-0136-3

Cited by 2 publications

(3 citation statements)

References 51 publications

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“…CEGMA (v2.5) [7] and BUSCO (v3.1.0) [8] were employed to evaluate the genome completeness. Gene prediction and functional annotation were conducted according to our previous study [9]. The raw data is available as a Bioproject at NCBI (PRJNA419836).…”

Section: Methodsmentioning

confidence: 99%

“…To conduct comparative genomic analysis, we collected complete genomes of seven other birds from NCBI (turkey, Meleagris gallopavo , GCF_000146605.2; chicken, Gallus gallus , GCF_000002315.6; mallard, Anas platyrhynchos , GCF_003850225.1; ostrich, Struthio camelus , GCF_000698965.1; peregrine falcon, Falco peregrinus , GCF_000337955.1; zebra finch, Taeniopygia guttata , GCF_000151805.1; rock pigeon, Columba livia , GCF_000337935.1). The complete genome of Hainan partridge ( Arborophila ardens ) and Chinese monal ( Lophophorus lhuysii ) were sequenced and assembled by our lab [9,10].…”

Section: Methodsmentioning

confidence: 99%

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The Draft Genome of the Endangered Sichuan Partridge (Arborophila rufipectus) with Evolutionary Implications

Zhou

et al. 2019

Genes

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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.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The Draft Genome of the Endangered Sichuan Partridge (Arborophila rufipectus) with Evolutionary Implications

Zhou

et al. 2019

Genes

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“…Furthermore, mtDNA only reflect the matrilineal genealogy and not provide information on paternal contributions. With the fast development and F I G U R E 1 Sampling site and photographs of blood pheasant reducing cost of next-generation sequencing, an increasing number of Phasianidae species were sequenced (Cui et al, 2019;Zhou et al, 2018Zhou et al, , 2019Zhou et al, , 2020, which served as a powerful tool to infer phylogenetic relationships in the Phasianidae.…”

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The draft genome of the blood pheasant (Ithaginis cruentus): Phylogeny and high‐altitude adaptation

Zhou

Liu

Liao

et al. 2020

Ecology and Evolution

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The blood pheasant ( Ithaginis cruentus ), the only species in the genus Ithaginis , lives in an extremely inhospitable high‐altitude environment, coping with hypoxia and ultraviolet (UV) radiation. To further investigate the phylogeny of Phasianidae species based on complete genomes and understand the molecular genetic mechanisms of the high‐altitude adaptation of the blood pheasant, we de novo assembled and annotated the complete genome of the blood pheasant. The blood pheasant genome size is 1.04 Gb with scaffold N50 of 10.88 Mb. We identified 109.92 Mb (10.62%) repetitive elements, 279,037 perfect microsatellites, and 17,209 protein‐coding genes. The phylogenetic tree of Phasianidae based on whole genomes revealed three highly supported major clades with the blood pheasant included in the “erectile clade.” Comparative genomics analysis showed that many genes were positively selected in the blood pheasant, which was associated with response to hypoxia and/or UV radiation. More importantly, among these positively selected genes (PSGs) which were related to high‐altitude adaptation, sixteen PSGs had blood pheasant‐specific missense mutations. Our data and analysis lay solid foundation to the study of Phasianidae phylogeny and provided new insights into the potential adaptation mechanisms to the high altitude employed by the blood pheasant.

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First complete genome sequence in Arborophila and comparative genomics reveals the evolutionary adaptation of Hainan Partridge (Arborophila ardens)

Cited by 2 publications

References 51 publications

The Draft Genome of the Endangered Sichuan Partridge (Arborophila rufipectus) with Evolutionary Implications

The Draft Genome of the Endangered Sichuan Partridge (Arborophila rufipectus) with Evolutionary Implications

The draft genome of the blood pheasant (Ithaginis cruentus): Phylogeny and high‐altitude adaptation

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