{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T12:13:06Z","timestamp":1776427986804,"version":"3.51.2"},"reference-count":102,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2022,12,21]],"date-time":"2022-12-21T00:00:00Z","timestamp":1671580800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31970395"],"award-info":[{"award-number":["31970395"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32270454"],"award-info":[{"award-number":["32270454"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31772478"],"award-info":[{"award-number":["31772478"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Second Tibetan Plateau Scientific Expedition and Research Program","award":["2019QZKK0501"],"award-info":[{"award-number":["2019QZKK0501"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,4,6]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The Tibetan partridge (Perdix hodgsoniae) is a widely distributed endemic species in high-altitude areas across the Tibetan Plateau where the hypoxia, lower temperature and high ultraviolet radiation are pivotal factors influencing survival. However, the underlying genetic adaptation of the Tibetan partridge to extreme environments remains uncertain due to limited genomic resources. Similarly, the phylogenetic position of Perdix within Phasianidae remains controversial due to lacking information. Consequently, we de novo assembled and annotated the whole genome of the Tibetan partridge. The genome size was 1.15 Gb with contig N50 of 3.70 Mb. A total of 202.30 Mb (17.61%) repetitive elements and 445,876 perfect microsatellites were identified. A total of 16,845 functionally annotated protein-coding genes were identified in the Tibetan partridge. Genomic phylogenetic analysis across 30 Galliformes species indicated a close relationship between Perdix and typical pheasants composed of Chrysolophus, Symaticus, Phasianus, Crossopilon, and Lophura. However, the phylogenetic relationship of (Perdix + (Chrysolophus + (Syrmaticus + other pheasants))) was different from those of (Perdix + (Syrmaticus + (Chrysolophus + other pheasants))) in previous studies. Comparative genomic results identified NFKB1 and CREBBP positively selected genes related to hypoxia with 3 and 2 Tibetan partridge-specific missense mutations, respectively. Expanded gene families were mainly associated with energy metabolism and steroid hydroxylase activity, meanwhile, contracted gene families were mainly related to immunity and olfactory perception. Our genomic data considerably contribute to the phylogeny of Perdix and the underlying adaptation strategies of the Tibetan partridge to a high-altitude environment.<\/jats:p>","DOI":"10.1093\/jhered\/esac069","type":"journal-article","created":{"date-parts":[[2022,12,22]],"date-time":"2022-12-22T10:26:23Z","timestamp":1671704783000},"page":"175-188","source":"Crossref","is-referenced-by-count":5,"title":["The draft genome of the Tibetan partridge (<i>Perdix hodgsoniae<\/i>) provides insights into its phylogenetic position and high-altitude adaptation"],"prefix":"10.1093","volume":"114","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1186-5459","authenticated-orcid":false,"given":"Chuang","family":"Zhou","sequence":"first","affiliation":[{"name":"Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University , Chengdu , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2850-7308","authenticated-orcid":false,"given":"Xiaofeng","family":"Zheng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University , Chengdu , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kaize","family":"Feng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University , Chengdu , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kexin","family":"Peng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University , Chengdu , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanni","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University , Chengdu , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guangqing","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University , Chengdu , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Meng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University , Chengdu , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0698-0754","authenticated-orcid":false,"given":"Li","family":"Zhang","sequence":"additional","affiliation":[{"name":"Chinese Institute for Brain Research, Beijing (CIBR) , Beijing , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6731-538X","authenticated-orcid":false,"given":"Bisong","family":"Yue","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University , Chengdu , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0297-2319","authenticated-orcid":false,"given":"Yongjie","family":"Wu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University , Chengdu , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,12,21]]},"reference":[{"issue":"4","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nmeth0410-248","article-title":"A method and server for predicting damaging missense mutations","volume":"7","author":"Adzhubei","year":"2010","journal-title":"Nat Methods"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2164-15-834","article-title":"Population history and genomic signatures for high-altitude adaptation in Tibetan pigs","volume":"15","author":"Ai","year":"2014","journal-title":"BMC Genomics"},{"issue":"4","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1093\/gbe\/evw041","article-title":"Whole-genome identification, phylogeny, and evolution of the cytochrome P450 family 2 (CYP2) subfamilies in birds","volume":"8","author":"Almeida","year":"2016","journal-title":"Genome Biol Evol"},{"issue":"1654","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1098\/rspb.2008.1012","article-title":"Genome size and wing parameters in passerine birds","volume":"276","author":"Andrews","year":"2009","journal-title":"Proc R Soc B Biol Sci"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1016\/j.isci.2018.11.034","article-title":"Hypoxic and cold adaptation insights from the Himalayan Marmot Genome","volume":"11","author":"Bai","year":"2019","journal-title":"iScience"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1093\/nar\/28.1.45","article-title":"The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000","volume":"28","author":"Bairoch","year":"2000","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1101\/gr.88502","article-title":"Automated de novo identification of repeat sequence families in sequenced genomes","volume":"12","author":"Bao","year":"2002","journal-title":"Genome Res"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s13100-015-0041-9","article-title":"Repbase update, a database of repetitive elements in eukaryotic genomes","volume":"6","author":"Bao","year":"2015","journal-title":"Mobile DNA"},{"issue":"2","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"840","DOI":"10.1016\/j.ympev.2010.03.038","article-title":"The phylogenetic position and speciation dynamics of the genus Perdix (Phasianidae, Galliformes).","volume":"56","author":"Bao","year":"2010","journal-title":"Mol Phylogenet Evol"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1007\/978-1-59745-251-9_12","article-title":"Computational gene annotation in new genome assemblies using GeneID.","volume-title":"Bioinformatics for DNA sequence analysis","author":"Blanco","year":"2009"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1006\/jmbi.1997.0951","article-title":"Prediction of complete gene structures in human genomic DNA","volume":"268","author":"Burge","year":"1997","journal-title":"J Mol Biol"},{"issue":"3","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"R29","DOI":"10.1186\/gb-2013-14-3-r29","article-title":"Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude","volume":"14","author":"Cai","year":"2013","journal-title":"Genome Biol"},{"issue":"4","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1093\/oxfordjournals.molbev.a026334","article-title":"Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis","volume":"17","author":"Castresana","year":"2000","journal-title":"Mol Biol Evol"},{"issue":"14","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1357","DOI":"10.1016\/j.lfs.2006.03.051","article-title":"Atrial natriuretic peptide-dependent modulation of hypoxia-induced pulmonary vascular remodeling","volume":"79","author":"Chen","year":"2006","journal-title":"Life Sci"},{"issue":"1","key":"2023041306491415900_","first-page":"1","article-title":"Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements","volume":"21","author":"Chen","year":"2021","journal-title":"BMC Ecol Evol"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"110302","DOI":"10.1016\/j.vetimm.2021.110302","article-title":"Exonic SNP in MHC-DMB2 is associated with gene expression and humoral immunity in Japanese quails","volume":"239","author":"Chenani","year":"2021","journal-title":"Vet Immunol Immunopathol"},{"issue":"9","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"e1000475","DOI":"10.1371\/journal.pbio.1000475","article-title":"Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis","volume":"8","author":"Dalloul","year":"2010","journal-title":"PLoS Biol"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"e56259","DOI":"10.7554\/eLife.56259","article-title":"Convergent changes in muscle metabolism depend on duration of high-altitude ancestry across Andean waterfowl","volume":"9","author":"Dawson","year":"2020","journal-title":"Elife"},{"issue":"10","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1093\/bioinformatics\/btl097","article-title":"CAFE: a computational tool for the study of gene family evolution","volume":"22","author":"De Bie","year":"2006","journal-title":"Bioinformatics"},{"issue":"2","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/S1055-7903(02)00230-0","article-title":"Phylogeny of Tetraoninae and other galliform birds using mitochondrial 12S and ND2 genes.","volume":"24","author":"Dimcheff","year":"2002","journal-title":"Mol Phylogenet Evol"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40657-021-00279-0","article-title":"Coping with extremes: lowered myocardial phosphofructokinase activities and glucose content but increased fatty acids content in highland Eurasian Tree Sparrows","volume":"12","author":"Ding","year":"2021","journal-title":"Avian Res"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1101\/gr.203201","article-title":"Systematic identification of novel protein domain families associated with nuclear functions","volume":"12","author":"Doerks","year":"2002","journal-title":"Genome Res"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40657-014-0005-7","article-title":"Nest distribution and nest habitat of the Tibetan Partridge (Perdix hodgsoniae) near Lhasa, Tibet","volume":"5","author":"Dorge","year":"2014","journal-title":"Avian Res"},{"issue":"4","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1093\/bioinformatics\/btx665","article-title":"Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design","volume":"34","author":"Du","year":"2018","journal-title":"Bioinformatics"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1186\/s13059-015-0721-2","article-title":"OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy","volume":"16","author":"Emms","year":"2015","journal-title":"Genome Biol"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol"},{"issue":"6","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1007\/s00125-013-2885-1","article-title":"Adipose tissue hypoxia induces inflammatory M1 polarity of macrophages in an HIF-1\u03b1-dependent and HIF-1\u03b1-independent manner in obese mice","volume":"56","author":"Fujisaka","year":"2013","journal-title":"Diabetologia"},{"issue":"10","key":"2023041306491415900_","first-page":"giy113","article-title":"Comparative genomics and transcriptomics of Chrysolophus provide insights into the evolution of complex plumage coloration","volume":"7","author":"Gao","year":"2018","journal-title":"GigaScience"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1858","DOI":"10.1038\/ncomms2860","article-title":"Draft genome sequence of the Tibetan antelope","volume":"4","author":"Ge","year":"2013","journal-title":"Nat Commun"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/srep29963","article-title":"Genomic analysis identified a potential novel molecular mechanism for high-altitude adaptation in sheep at the Himalayas","volume":"6","author":"Gorkhali","year":"2016","journal-title":"Sci Rep"},{"issue":"8","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1308","DOI":"10.1101\/gr.171876.113","article-title":"Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia","volume":"24","author":"Gou","year":"2014","journal-title":"Genome Res"},{"issue":"6","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1038\/s41437-018-0173-z","article-title":"Convergent evolution on the hypoxia-inducible factor (HIF) pathway genes EGLN1 and EPAS1 in high-altitude ducks","volume":"122","author":"Graham","year":"2019","journal-title":"Heredity"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"R7","DOI":"10.1186\/gb-2008-9-1-r7","article-title":"Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments","volume":"9","author":"Haas","year":"2008","journal-title":"Genome Biol"},{"issue":"3","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"e90240","DOI":"10.1371\/journal.pone.0090240","article-title":"A draft de novo genome assembly for the northern bobwhite (Colinus virginianus) reveals evidence for a rapid decline in effective population size beginning in the Late Pleistocene","volume":"9","author":"Halley","year":"2014","journal-title":"PLoS One"},{"issue":"5","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1252","DOI":"10.1073\/pnas.1423685112","article-title":"Seeing is believing: dynamic evolution of gene families","volume":"112","author":"Harris","year":"2015","journal-title":"Proc Natl Acad Sci USA"},{"issue":"10","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"2989","DOI":"10.1093\/molbev\/msaa172","article-title":"Gene loss predictably drives evolutionary adaptation.","volume":"37","author":"Helsen","year":"2020","journal-title":"Mol Biol Evol"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1038\/s41597-020-00743-4","article-title":"Highly accurate long-read HiFi sequencing data for five complex genomes","volume":"7","author":"Hon","year":"2020","journal-title":"Sci Data"},{"issue":"4","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1093\/molbev\/msv347","article-title":"Avoiding missing data biases in phylogenomic inference: an empirical study in the landfowl (Aves: Galliformes)","volume":"33","author":"Hosner","year":"2016","journal-title":"Mol Biol Evol"},{"key":"2023041306491415900_","volume-title":"The quails, partridges, and francolins of the world","author":"Johnsgard","year":"1988"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"E1460","DOI":"10.1073\/pnas.1616702114","article-title":"Dynamics of genome size evolution in birds and mammals","volume":"114","author":"Kapusta","year":"2017","journal-title":"Proc Natl Acad Sci USA"},{"issue":"4","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability.","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1006\/mpev.1998.0562","article-title":"A molecular phylogeny of the pheasants and partridges suggests that these lineages are not monophyletic.","volume":"11","author":"Kimball","year":"1999","journal-title":"Mol Phylogenet Evol"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"107091","DOI":"10.1016\/j.ympev.2021.107091","article-title":"A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths.","volume":"158","author":"Kimball","year":"2021","journal-title":"Mol Phylogenet Evol"},{"issue":"3","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1007\/s00405-007-0446-2","article-title":"Changes of pressure and humidity affect olfactory function","volume":"265","author":"Kuehn","year":"2008","journal-title":"Eur Arch Otorhinolaryngol"},{"issue":"7","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1812","DOI":"10.1093\/molbev\/msx116","article-title":"TimeTree: a resource for timelines, timetrees, and divergence times.","volume":"34","author":"Kumar","year":"2017","journal-title":"Mol Biol Evol"},{"issue":"2","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"e0172211","DOI":"10.1371\/journal.pone.0172211","article-title":"A non-synonymous SNP with the allele frequency correlated with the altitude may contribute to the hypoxia adaptation of Tibetan chicken","volume":"12","author":"Li","year":"2017","journal-title":"PLoS One"},{"issue":"12","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1038\/ng.2811","article-title":"Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars","volume":"45","author":"Li","year":"2013","journal-title":"Nat Genet"},{"issue":"2","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/j.molcel.2011.02.026","article-title":"SHPRH and HLTF act in a damage-specific manner to coordinate different forms of postreplication repair and prevent mutagenesis","volume":"42","author":"Lin","year":"2011","journal-title":"Mol Cell"},{"issue":"20","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"6494","DOI":"10.1093\/nar\/gki937","article-title":"Gene identification in novel eukaryotic genomes by self-training algorithm","volume":"33","author":"Lomsadze","year":"2005","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12915-020-0743-4","article-title":"The quail genome: insights into social behaviour, seasonal biology and infectious disease response","volume":"18","author":"Morris","year":"2020","journal-title":"BMC Biol"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/gene.2012.49","article-title":"Transcriptome characterization of immune suppression from battlefield-like stress.","volume":"14","author":"Muhie","year":"2013","journal-title":"Genes Immunity"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/978-1-59745-515-2_5","article-title":"InterPro and InterProScan: tools for protein sequence classification and comparison","volume":"396","author":"Mulder","year":"2007","journal-title":"Methods Mol Biol"},{"issue":"9","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1667","DOI":"10.1096\/fj.00-0757fje","article-title":"Vascular endothelial growth factor induces cyclooxygenase-dependent proliferation of endothelial cells via the VEGF-2 receptor","volume":"15","author":"Murphy","year":"2001","journal-title":"FASEB J"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"key":"2023041306491415900_","article-title":"Olfactory receptor genes: evolution","author":"Niimura","year":"2014","journal-title":"eLS"},{"issue":"9270","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1016\/S0140-6736(00)04904-7","article-title":"An overview of the immune system","volume":"357","author":"Parkin","year":"2001","journal-title":"Lancet"},{"issue":"2","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1016\/j.ympev.2005.07.007","article-title":"A molecular timescale for galliform birds accounting for uncertainty in time estimates and heterogeneity of rates of DNA substitutions across lineages and sites.","volume":"38","author":"Pereira","year":"2006","journal-title":"Mol Phylogenet Evol"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"712","DOI":"10.3389\/fphys.2021.676782","article-title":"Hypoxia and inflammation: insights from high-altitude physiology","volume":"12","author":"Pham","year":"2021","journal-title":"Front Physiol"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"i351","DOI":"10.1093\/bioinformatics\/bti1018","article-title":"De novo identification of repeat families in large genomes","volume":"21","author":"Price","year":"2005","journal-title":"Bioinformatics"},{"issue":"8","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1038\/ng.2343","article-title":"The yak genome and adaptation to life at high altitude","volume":"44","author":"Qiu","year":"2012","journal-title":"Nat Genet"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/ncomms3071","article-title":"Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau","volume":"4","author":"Qu","year":"2013","journal-title":"Nat Commun"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1146\/annurev.pathmechdis.3.121806.151456","article-title":"The inflammatory response to cell death.","volume":"3","author":"Rock","year":"2008","journal-title":"Annu Rev Pathol Mech Dis"},{"issue":"24","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"2350","DOI":"10.1016\/j.cub.2012.10.043","article-title":"Increase in carbohydrate utilization in high-altitude Andean mice","volume":"22","author":"Schippers","year":"2012","journal-title":"Curr Biol"},{"issue":"8","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1962","DOI":"10.1093\/molbev\/msv076","article-title":"Adaptive modifications of muscle phenotype in high-altitude deer mice are associated with evolved changes in gene regulation","volume":"32","author":"Scott","year":"2015","journal-title":"Mol Biol Evol"},{"issue":"5","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"e62415","DOI":"10.1371\/journal.pone.0062415","article-title":"A multi-platform draft de novo genome assembly and comparative analysis for the Scarlet Macaw (Ara macao)","volume":"8","author":"Seabury","year":"2013","journal-title":"PLoS One"},{"key":"2023041306491415900_","article-title":"Association of Toll-like receptor 2, 4, and 9 gene polymorphism with high altitude induced thrombosis patients in Indian population.","author":"Sharma","year":"2019","journal-title":"Insights Clin Cell Immunol"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-018-03667-1","article-title":"A genomics approach reveals insights into the importance of gene losses for mammalian adaptations","volume":"9","author":"Sharma","year":"2018","journal-title":"Nat Commun"},{"issue":"11","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"8352","DOI":"10.1074\/jbc.M109.041129","article-title":"Ultraviolet radiation stress triggers the down-regulation of essential replication factor Mcm10","volume":"285","author":"Sharma","year":"2010","journal-title":"J Biol Chem"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2148-10-132","article-title":"A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae","volume":"10","author":"Shen","year":"2010","journal-title":"BMC Evol Biol"},{"issue":"19","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"key":"2023041306491415900_","author":"Smit","year":"2018"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","DOI":"10.1016\/j.jbc.2021.100461","article-title":"High-altitude deer mouse hypoxia-inducible factor-2\u03b1 shows defective interaction with CREB-binding protein","volume":"296","author":"Song","year":"2021","journal-title":"J Biol Chem"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"2316","DOI":"10.1182\/blood-2018-99-117463","article-title":"Novel form of alternative splicing of NFKB1. Its role in polycythemia and adaptation to high altitude in Andean Aymara","volume":"132","author":"Song","year":"2018","journal-title":"Blood"},{"issue":"9","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"issue":"5","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1093\/bioinformatics\/btn013","article-title":"Using native and syntenically mapped cDNA alignments to improve de novo gene finding.","volume":"24","author":"Stanke","year":"2008","journal-title":"Bioinformatics"},{"issue":"3","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1093\/jhered\/esp105","article-title":"Evidence for adaptive evolution of olfactory receptor genes in 9 bird species","volume":"101","author":"Steiger","year":"2010","journal-title":"J Hered"},{"issue":"33","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"10425","DOI":"10.1073\/pnas.1507486112","article-title":"Endothelin receptor B, a candidate gene from human studies at high altitude, improves cardiac tolerance to hypoxia in genetically engineered heterozygote mice","volume":"112","author":"Stobdan","year":"2015","journal-title":"Proc Natl Acad Sci USA"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"W609","DOI":"10.1093\/nar\/gkl315","article-title":"PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments","volume":"34","author":"Suyama","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi0410s25","article-title":"Using RepeatMasker to identify repetitive elements in genomic sequences.","author":"Tarailo-Graovac","year":"2009","journal-title":"Curr Protoc Bioinformatics"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"S10","DOI":"10.1016\/S0923-1811(99)00073-0","article-title":"The role of cytokines in UV-induced systemic immune suppression","volume":"23","author":"Ullrich","year":"2000","journal-title":"J Dermatol Sci"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/j.ympev.2017.01.006","article-title":"Historical relationships of three enigmatic phasianid genera (Aves: Galliformes) inferred using phylogenomic and mitogenomic data","volume":"109","author":"Wang","year":"2017","journal-title":"Mol Phylogenet Evol"},{"issue":"5","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"e64312","DOI":"10.1371\/journal.pone.0064312","article-title":"Assessing phylogenetic relationships among Galliformes: a multigene phylogeny with expanded taxon sampling in Phasianidae","volume":"8","author":"Wang","year":"2013","journal-title":"PLoS One"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1111\/jbi.12782","article-title":"Ancestral range reconstruction of Galliformes: the effects of topology and taxon sampling","volume":"44","author":"Wang","year":"2017","journal-title":"J Biogeogr"},{"issue":"7","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1880","DOI":"10.1093\/molbev\/msv071","article-title":"Genomic analyses reveal potential independent adaptation to high altitude in Tibetan chickens.","volume":"32","author":"Wang","year":"2015","journal-title":"Mol Biol Evol"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"e8914","DOI":"10.7717\/peerj.8914","article-title":"First de novo whole genome sequencing and assembly of the bar-headed goose","volume":"8","author":"Wang","year":"2020","journal-title":"PeerJ"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1534\/g3.116.035923","article-title":"A new chicken genome assembly provides insight into avian genome structure.","volume":"7","author":"Warren","year":"2017","journal-title":"G3"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1007\/978-3-030-16477-5_5","article-title":"Repetitive DNA: the dark matter of avian genomics.","volume-title":"Avian genomics in ecology and evolution","author":"Weissensteiner","year":"2019"},{"issue":"1","key":"2023041306491415900_","first-page":"93","article-title":"A mini-review of advances in the study of the evolution of Perdix species.","volume":"40","author":"Wen","year":"2015","journal-title":"Zool Syst"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1016\/S1096-4959(01)00540-1","article-title":"Arctic spring: hormone\u2013behavior interactions in a severe environment.","volume":"132","author":"Wingfield","year":"2002","journal-title":"Comp Biochem Physiol B Biochem Mol Biol"},{"key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"W316","DOI":"10.1093\/nar\/gkr483","article-title":"KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases","volume":"39","author":"Xie","year":"2011","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"e1009270","DOI":"10.1371\/journal.pgen.1009270","article-title":"Physiological and genetic convergence supports hypoxia resistance in high-altitude songbirds","volume":"16","author":"Xiong","year":"2020","journal-title":"PLoS Genet"},{"issue":"8","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: phylogenetic analysis by maximum likelihood.","volume":"24","author":"Yang","year":"2007","journal-title":"Mol Biol Evol"},{"issue":"16","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"4189","DOI":"10.1073\/pnas.1617042114","article-title":"Genetic signatures of high-altitude adaptation in Tibetans","volume":"114","author":"Yang","year":"2017","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"13674","DOI":"10.1038\/srep13674","article-title":"Increased expression of surface CD44 in hypoxia-DCs skews helper T cells toward a Th2 polarization","volume":"5","author":"Yang","year":"2015","journal-title":"Sci Rep"},{"issue":"4","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"748","DOI":"10.5603\/FM.a2020.0011","article-title":"Expression and distribution of HIF-1\u03b1, HIF-2\u03b1, VEGF, VEGFR-2 and HIMF in the kidneys of Tibetan sheep, plain sheep and goat","volume":"79","author":"Yang","year":"2020","journal-title":"Folia Morphol"},{"issue":"3","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1007\/BF02817645","article-title":"Microorganisms in a high altitude glacier ice in Tibet","volume":"47","author":"Zhang","year":"2002","journal-title":"Folia Microbiol"},{"issue":"1","key":"2023041306491415900_","first-page":"1","article-title":"Comparative transcriptomic and proteomic analyses provide insights into functional genes for hypoxic adaptation in embryos of Tibetan chickens","volume":"10","author":"Zhang","year":"2020","journal-title":"Sci Rep"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1007\/s00438-019-01601-8","article-title":"Genome-wide analysis sheds light on the high-altitude adaptation of the buff-throated partridge (Tetraophasis szechenyii).","volume":"295","author":"Zhou","year":"2020","journal-title":"Mol Genet Genomics"},{"issue":"1","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"2249","DOI":"10.1038\/s41598-019-38680-x","article-title":"Comparative genomics sheds light on the predatory lifestyle of accipitrids and owls","volume":"9","author":"Zhou","year":"2019","journal-title":"Sci Rep"},{"issue":"9","key":"2023041306491415900_","doi-asserted-by":"crossref","first-page":"677","DOI":"10.3390\/genes10090677","article-title":"The draft genome of the endangered sichuan partridge (Arborophila rufipectus) with evolutionary implications","volume":"10","author":"Zhou","year":"2019","journal-title":"Genes"}],"container-title":["Journal of Heredity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jhered\/advance-article-pdf\/doi\/10.1093\/jhered\/esac069\/49384354\/esac069.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jhered\/article-pdf\/114\/2\/175\/49872321\/esac069.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jhered\/article-pdf\/114\/2\/175\/49872321\/esac069.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,3]],"date-time":"2023-12-03T09:40:12Z","timestamp":1701596412000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jhered\/article\/114\/2\/175\/6955807"}},"subtitle":[],"editor":[{"given":"William","family":"Murphy","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2022,12,21]]},"references-count":102,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2022,12,21]]},"published-print":{"date-parts":[[2023,4,6]]}},"URL":"https:\/\/doi.org\/10.1093\/jhered\/esac069","relation":{},"ISSN":["0022-1503","1465-7333"],"issn-type":[{"value":"0022-1503","type":"print"},{"value":"1465-7333","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,3,1]]},"published":{"date-parts":[[2022,12,21]]}}}