First complete genome sequence in Arborophila and comparative genomics reveals the evolutionary adaptation of Hainan Partridge(Arborophila ardens)
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摘要
Background:The Hainan Partridge(Arborophila ardens,Phasianidae,Galliformes) is an endemic species of Hainan Island,China,and it is classified as globally vulnerable species.There are at least 16 species in genus Arborophila and no genome sequence is available.Methods:The whole genome of Hainan Partridge was de novo sequenced(with shotgun approach on the Illumina 2000 platform) and assembled.Results:The genome size of Arborophila ardens is about 1.05 Gb with a high N50 scaffold length of 8.28 Mb and it is the first high quality genome announced in Arborophila genus.About 9.19% of the genome was identified as repeat sequences and about 5.88 million heterozygous SNPs were detected.A total of 17,376 protein-coding genes were predicted and their functions were annotated.The genome comparison between Hainan Partridge and Red Junglefowl(Gallus gallus) demonstrated a conserved genome structure.The phylogenetic analysis indicated that the Hainan Partridge possessed a basal phylogenetic position in Phasianidae and it was most likely derived from a common ancestor approximately 36.8 million years ago(Mya).We found that the Hainan Partridge population had experienced bottleneck and its effective population decreased from about 1,040,000 individuals 1.5 Mya to about 200,000 individuals 0.2 Mya,and then recovered to about 460,000 individuals.The number of 1:1 orthologous genes that were predicted to have undergone positive selection in the Hainan Partridge was 504 and some environmental adaptation related categories,such as response to ultraviolet radiation were represented in GO distribution analysis.Conclusions:We announced the first high quality genome in Arborophila genus and it will be a valuable genomic resource for the further studies such as evolution,adaption,conservation,not only on Hainan Partridge but also on Arborophila or Phasianidae species.
Background:The Hainan Partridge(Arborophila ardens,Phasianidae,Galliformes) is an endemic species of Hainan Island,China,and it is classified as globally vulnerable species.There are at least 16 species in genus Arborophila and no genome sequence is available.Methods:The whole genome of Hainan Partridge was de novo sequenced(with shotgun approach on the Illumina 2000 platform) and assembled.Results:The genome size of Arborophila ardens is about 1.05 Gb with a high N50 scaffold length of 8.28 Mb and it is the first high quality genome announced in Arborophila genus.About 9.19% of the genome was identified as repeat sequences and about 5.88 million heterozygous SNPs were detected.A total of 17,376 protein-coding genes were predicted and their functions were annotated.The genome comparison between Hainan Partridge and Red Junglefowl(Gallus gallus) demonstrated a conserved genome structure.The phylogenetic analysis indicated that the Hainan Partridge possessed a basal phylogenetic position in Phasianidae and it was most likely derived from a common ancestor approximately 36.8 million years ago(Mya).We found that the Hainan Partridge population had experienced bottleneck and its effective population decreased from about 1,040,000 individuals 1.5 Mya to about 200,000 individuals 0.2 Mya,and then recovered to about 460,000 individuals.The number of 1:1 orthologous genes that were predicted to have undergone positive selection in the Hainan Partridge was 504 and some environmental adaptation related categories,such as response to ultraviolet radiation were represented in GO distribution analysis.Conclusions:We announced the first high quality genome in Arborophila genus and it will be a valuable genomic resource for the further studies such as evolution,adaption,conservation,not only on Hainan Partridge but also on Arborophila or Phasianidae species.
Background:The Hainan Partridge(Arborophila ardens,Phasianidae,Galliformes) is an endemic species of Hainan Island,China,and it is classified as globally vulnerable species.There are at least 16 species in genus Arborophila and no genome sequence is available.Methods:The whole genome of Hainan Partridge was de novo sequenced(with shotgun approach on the Illumina 2000 platform) and assembled.Results:The genome size of Arborophila ardens is about 1.05 Gb with a high N50 scaffold length of 8.28 Mb and it is the first high quality genome announced in Arborophila genus.About 9.19% of the genome was identified as repeat sequences and about 5.88 million heterozygous SNPs were detected.A total of 17,376 protein-coding genes were predicted and their functions were annotated.The genome comparison between Hainan Partridge and Red Junglefowl(Gallus gallus) demonstrated a conserved genome structure.The phylogenetic analysis indicated that the Hainan Partridge possessed a basal phylogenetic position in Phasianidae and it was most likely derived from a common ancestor approximately 36.8 million years ago(Mya).We found that the Hainan Partridge population had experienced bottleneck and its effective population decreased from about 1,040,000 individuals 1.5 Mya to about 200,000 individuals 0.2 Mya,and then recovered to about 460,000 individuals.The number of 1:1 orthologous genes that were predicted to have undergone positive selection in the Hainan Partridge was 504 and some environmental adaptation related categories,such as response to ultraviolet radiation were represented in GO distribution analysis.Conclusions:We announced the first high quality genome in Arborophila genus and it will be a valuable genomic resource for the further studies such as evolution,adaption,conservation,not only on Hainan Partridge but also on Arborophila or Phasianidae species.
引文
Abaji C,Cousineau I,Belmaaza A.BRCA2 regulates homologous recombination in response to DNA damage:implications for genome stability and carcinogenesis.Cancer Res.2005;65:4117-25.
Altschul SF,Madden TL,Sch?ffer AA,Zhang J,Zhang Z,Miller W,Lipman DJ.Gapped BLAST and PSI-BLAST:a new generation of protein database search programs.Nucleic Acids Res.1997;25:3389-402.
Attwood TK,Croning MD,Flower DR,Lewis AP,Mabey JE,Scordis P,Selley JN,Wright W.PRINTS-S:the database formerly known as PRINTS.Nucleic Acids Res.2000;28:225-7.
Banks D,Wu M,Higa LA,Gavrilova N,Quan J,Ye T,Kobayashi R,Sun H,Zhang H.L2DTL/CDT2 and PCNA interact with p53 and regulate p53 polyubiquitination and protein stability through MDM2 and CUL4A/DDB1complexes.Cell Cycle.2006;5:1719-29.
Birney E,Clamp M,Durbin R.GeneWise and Genomewise.Genome Res.2004;14:988-95.
Boeckmann B,Bairoch A,Apweiler R,Blatter MC,Estreicher A,Gasteiger E,Martin MJ,Michoud K,O’donovan C,Phan I,Pilbout S.The SWISS-PROTprotein knowledgebase and its supplement TrEMBL in 2003.Nucleic Acids Res.2003;31:365-70.
Boetzer M,Henkel CV,Jansen HJ,Butler D,Pirovano W.Scaffolding pre-assembled contigs using SSPACE.Bioinformatics.2011;27:578-9.
Bru C,Courcelle E,Carrère S,Beausse Y,Dalmar S,Kahn D.The ProDom database of protein domain families:more emphasis on 3D.Nucleic Acids Res.2005;33:D212-5.
Burge C,Karlin S.Prediction of complete gene structures in human genomic DNA1.J Mol Biol.1997;268:78-94.
Cai Q,Qian X,Lang Y,Luo Y,Xu J,Pan S,Hui Y,Gou C,Cai Y,Hao M,Zhao J.Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude.Genome Biol.2013;14:R29.
Chang J,Chen D,Ye X,Li S-H,Liang W,Zhang Z,Li M.Coupling genetic and species distribution models to examine the response of the Hainan partridge(Arborophila ardens)to Late Quaternary climate.PLoS ONE.2012;7:e50286.
Chen D,Chang J,Li S-H,Liu Y,Liang W,Zhou F,Yao CT,Zhang Z.Was the exposed continental shelf a long-distance colonization route in the ice age?The Southeast Asia origin of Hainan and Taiwan partridges.Mol Phylogenet Evol.2015a;83:167-73.
Chen D,Liu Y,Davision WHG,Dong L,Chang J,Gao SH,Li SH,Zhang ZW.Revival of the genus Tropicoperdix Blyth 1859(Phasianidae,Aves)using multilocus sequence.Zool J Linn Soc.2015b;175:429-38.
Clements J,Schulenberg T,Iliff M,Roberson D,Fredericks B,Sullivan B,Wood C.The eBird/Clements checklist of birds of the world:v2018.2018.http://www.birds.corne ll.edu/cleme ntsch eckli st/downl oad/.Accessed 20 Sept2018.
Crowe TM,Bowie RC,Bloomer P,Mandiwana TG,Hedderson TA,Randi E,Pereira SL,Wakeling J.Phylogenetics,biogeography and classification of,and character evolution in,gamebirds(Aves:Galliformes):effects of character exclusion,data partitioning and missing data.Cladistics.2006;22:495-532.
del Hoyo J,Elliott A,Sargatal J,Christie DA,de Juana E.Handbook of the birds of the world alive.Barcelona:Lynx Edicions.2018.https://www.hbw.com/node/53455.Accessed 4 Sept 2018.
Finn RD,Bateman A,Clements J,Coggill P,Eberhardt RY,Eddy SR,Heger A,Hetherington K,Holm L,Mistry J,Sonnhammer EL.Pfam:the protein families database.Nucleic Acids Res.2013;42:D222-30.
Gao Y.Conservation status of endemic Galliformes on Hainan Island,China.Bird Conserv Int.1998;9:411-6.
Gough J,Chothia C.SUPERFAMILY:HMMs representing all proteins of known structure.SCOP sequence searches,alignments and genome assignments.Nucleic Acids Res.2002;30:268-72.
Haas BJ,Salzberg SL,Zhu W,Pertea M,Allen JE,Orvis J,White O,Buell CR,Wortman JR.Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments.Genome Biol.2008;9:1.
Hewitt GM.Quaternary Genetic consequences of climatic oscillations in the Quaternary.Philos Trans R Soc Lond B.2004;359:183-95.
Hunter S,Apweiler R,Attwood TK,Bairoch A,Bateman A,Binns D,Bork P,Das U,Daugherty L,Duquenne L,Finn RD.InterPro:the integrative protein signature database.Nucleic Acids Res.2008;37:D211-5.
Im J,Lawrence J,Seelig D,Nho RS.FoxM1-dependent RAD51 and BRCA2 signaling protects idiopathic pulmonary fibrosis fibroblasts from radiationinduced cell death.Cell Death Dis.2018;9:584.
IUCN.Arborophila ardens.The IUCN red list of threatened species.Version2018-1.http://www.iucnr edlis t.org.2018.Accessed 20 Jul 2018.
Kie?basa SM,Wan R,Sato K,Horton P,Frith MC.Adaptive seeds tame genomic sequence comparison.Genome Res.2011;21:487-93.
Kobayashi H,Komatsu S,Ichikawa D,Kawaguchi T,Hirajima S,Miyamae M,Okajima W,Ohashi T,Kosuga T,Konishi H,Shiozaki A.Overexpression of denticleless E3 ubiquitin protein ligase homolog(DTL)is related to poor outcome in gastric carcinoma.Oncotarget.2015;6:36615.
Letunic I,Copley RR,Schmidt S,Ciccarelli FD,Doerks T,Schultz J,Ponting CP,Bork P.SMART 4.0:towards genomic data integration.Nucleic Acids Res.2004;32:D142-4.
Liao Y,Wang W,Zhang L,Yang L.Bio-effective UV radiation intensity distribution reaching the land surface in China.Geogr Res.2007;26:821-7.
Liang W,Cai Y,Yang C.Extreme levels of hunting of birds in a remote village of Hainan Island,China.Bird Conserv Int.2013;23:45-52.
Li H,Durbin R.Inference of human population history from individual wholegenome sequences.Nature.2011;475:493.
Li L,Stoeckert CJ Jr,Roos DS.OrthoMCL:identification of ortholog groups for eukaryotic genomes.Genome Res.2003;13:2178-89.
Li J,Ng EK,Ng YP,Wong CY,Yu J,Jin H,Cheng VY,Go MY,Cheung PK,Ebert MP,Tong J.Identification of retinoic acid-regulated nuclear matrix-associated protein as a novel regulator of gastric cancer.Br J Cancer.2009;101:691.
Li R,Tian H,Li X.Climate change induced range shifts of Galliformes in China.Integr Zool.2010;5:154-63.
Liu X,He Y,Li F,Huang Q,Kato TA,Hall RP,Li C.Caspase-3 promotes genetic instability and carcinogenesis.Mol Cell.2015;58:284-96.
Luo K,Li L,Li Y,Wu C,Yin Y,Chen Y,Deng M,Nowsheen S,Yuan J,Lou Z.Aphosphorylation-deubiquitination cascade regulates the BRCA2-RAD51axis in homologous recombination.Genes Dev.2016;30:1-15.
Luo R,Liu B,Xie Y,Li Z,Huang W,Yuan J,He G,Chen Y,Pan Q,Liu Y,Tang J.SOAPdenovo2:an empirically improved memory-efficient short-read de novo assembler.Gigascience.2012;1:18.
Moriya Y,Itoh M,Okuda S,Yoshizawa AC,Kanehisa M.KAAS:an automatic genome annotation and pathway reconstruction server.Nucleic Acids Res.2007;35:W182-5.
Nick G,Ari L.webPRANK:a phylogeny-aware multiple sequence aligner with interactive alignment browser.BMC Bioinform.2010;11:1-7.
Parra G,Bradnam K,Korf I.CEGMA:a pipeline to accurately annotate core genes in eukaryotic genomes.Bioinformatics.2007;23:1061-7.
Posada D,Crandall KA.Modeltest:testing the model of DNA substitution.Bioinformatics(Oxford,England).1998;14:817-8.
Rao X,Yang C,Liang W.Breeding biology and novel reproductive behaviour in the Hainan partridge(Arborophila ardens).Avian Res.2017;8:34.
Shen Y,Liang L,Sun Y,Yue B,Yang X,Murphy RW,Zhang Y.A mitogenomic perspective on the ancient,rapid radiation in the Galliformes with an emphasis on the Phasianidae.BMC Evol Biol.2010;10:132.
Sigrist CJ,Cerutti L,Hulo N,Gattiker A,Falquet L,Pagni M,Bairoch A,Bucher P.PROSITE:a documented database using patterns and profiles as motif descriptors.Brief Bioinform.2002;3:265-74.
Sim?o FA,Waterhouse RM,Ioannidis P,Kriventseva EV,Zdobnov EM.BUSCO:assessing genome assembly and annotation completeness with 1:1orthologs.Bioinformatics.2015;31:3210-2.
Stamatakis A.RAxML version 8:a tool for phylogenetic analysis and postanalysis of large phylogenies.Bioinformatics.2014;30:1312-3.
Stanke M,Keller O,Gunduz I,Hayes A,Waack S,Morgenstern B.AUGUS-TUS:ab initio prediction of alternative transcripts.Nucleic Acids Res.2006;34:435-9.
Thomas PD,Kejariwal A,Campbell MJ,Mi H,Diemer K,Guo N,Ladunga I,Ulitsky-Lazareva B,Muruganujan A,Rabkin S,Vandergriff JA.PANTHER:a browsable database of gene products organized by biological function,using curated protein family and subfamily classification.Nucleic Acids Res.2003;31:334-41.
Tigano A,Sackton TB,Friesen VL.Assembly and RNA-free annotation of highly heterozygous genomes:the case of the thick-billed murre(Uria lomvia).Mol Ecol Resour.2018;18:79-90.
Warren WC,Clayton DF,Ellegren H,Arnold AP,Hillier LW,Künstner A,et al.The genome of a songbird.Nature.2010;464:757-62.
Wu CH,Nikolskaya A,Huang H,Yeh LS,Natale DA,Vinayaka CR,Hu ZZ,Mazumder R,Kumar S,Kourtesis P,Ledley RS.PIRSF:family classification system at the protein information resource.Nucleic Acids Res.2004;32:D112-4.
Xu L,He C,Shen C,Jiang T,Shi L,Sun K,Berquist SW,Feng J.Phylogeography and population genetic structure of the great leaf-nosed bat(Hipposideros armiger)in China.J Hered.2010;101:562-72.
Yang C,Zhang Y,Cai Y,Stokke BG,Liang W.Female crowing and differential responses to simulated conspecific intrusion in male and female Hainan partridge(Arborophila ardens).Zool Sci.2011;28:249-53.
Yang Z.Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci.Genetics.2002;162:1811-23.
Yang Z.PAML 4:phylogenetic analysis by maximum likelihood.Mol Biol Evol.2007;24:1586-91.
Yu J,Liu F,Yin P,Zhu X,Cheng G,Wang N,Lu A,Luan W,Zhang N,Li J,Guo K.Integrating miRNA and mRNA expression profiles in response to heat stress-induced injury in rat small intestine.Funct Integr Genomics.2011;11:203-13.
Yu X,Zheng H,Wang J,Wang W,Su B.Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup.Genomics.2006;88:745-51.
Zhang Z,Ding C,Ding P,Zheng G.The current status and a conservation strategy for species of Galliformes in China.Biodivers Sci.2003;11:414-21.
Zheng GM.Pheasants in China.Beijing:Higher Education Press;2017(in Chinese).
Altschul SF,Madden TL,Sch?ffer AA,Zhang J,Zhang Z,Miller W,Lipman DJ.Gapped BLAST and PSI-BLAST:a new generation of protein database search programs.Nucleic Acids Res.1997;25:3389-402.
Attwood TK,Croning MD,Flower DR,Lewis AP,Mabey JE,Scordis P,Selley JN,Wright W.PRINTS-S:the database formerly known as PRINTS.Nucleic Acids Res.2000;28:225-7.
Banks D,Wu M,Higa LA,Gavrilova N,Quan J,Ye T,Kobayashi R,Sun H,Zhang H.L2DTL/CDT2 and PCNA interact with p53 and regulate p53 polyubiquitination and protein stability through MDM2 and CUL4A/DDB1complexes.Cell Cycle.2006;5:1719-29.
Birney E,Clamp M,Durbin R.GeneWise and Genomewise.Genome Res.2004;14:988-95.
Boeckmann B,Bairoch A,Apweiler R,Blatter MC,Estreicher A,Gasteiger E,Martin MJ,Michoud K,O’donovan C,Phan I,Pilbout S.The SWISS-PROTprotein knowledgebase and its supplement TrEMBL in 2003.Nucleic Acids Res.2003;31:365-70.
Boetzer M,Henkel CV,Jansen HJ,Butler D,Pirovano W.Scaffolding pre-assembled contigs using SSPACE.Bioinformatics.2011;27:578-9.
Bru C,Courcelle E,Carrère S,Beausse Y,Dalmar S,Kahn D.The ProDom database of protein domain families:more emphasis on 3D.Nucleic Acids Res.2005;33:D212-5.
Burge C,Karlin S.Prediction of complete gene structures in human genomic DNA1.J Mol Biol.1997;268:78-94.
Cai Q,Qian X,Lang Y,Luo Y,Xu J,Pan S,Hui Y,Gou C,Cai Y,Hao M,Zhao J.Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude.Genome Biol.2013;14:R29.
Chang J,Chen D,Ye X,Li S-H,Liang W,Zhang Z,Li M.Coupling genetic and species distribution models to examine the response of the Hainan partridge(Arborophila ardens)to Late Quaternary climate.PLoS ONE.2012;7:e50286.
Chen D,Chang J,Li S-H,Liu Y,Liang W,Zhou F,Yao CT,Zhang Z.Was the exposed continental shelf a long-distance colonization route in the ice age?The Southeast Asia origin of Hainan and Taiwan partridges.Mol Phylogenet Evol.2015a;83:167-73.
Chen D,Liu Y,Davision WHG,Dong L,Chang J,Gao SH,Li SH,Zhang ZW.Revival of the genus Tropicoperdix Blyth 1859(Phasianidae,Aves)using multilocus sequence.Zool J Linn Soc.2015b;175:429-38.
Clements J,Schulenberg T,Iliff M,Roberson D,Fredericks B,Sullivan B,Wood C.The eBird/Clements checklist of birds of the world:v2018.2018.http://www.birds.corne ll.edu/cleme ntsch eckli st/downl oad/.Accessed 20 Sept2018.
Crowe TM,Bowie RC,Bloomer P,Mandiwana TG,Hedderson TA,Randi E,Pereira SL,Wakeling J.Phylogenetics,biogeography and classification of,and character evolution in,gamebirds(Aves:Galliformes):effects of character exclusion,data partitioning and missing data.Cladistics.2006;22:495-532.
del Hoyo J,Elliott A,Sargatal J,Christie DA,de Juana E.Handbook of the birds of the world alive.Barcelona:Lynx Edicions.2018.https://www.hbw.com/node/53455.Accessed 4 Sept 2018.
Finn RD,Bateman A,Clements J,Coggill P,Eberhardt RY,Eddy SR,Heger A,Hetherington K,Holm L,Mistry J,Sonnhammer EL.Pfam:the protein families database.Nucleic Acids Res.2013;42:D222-30.
Gao Y.Conservation status of endemic Galliformes on Hainan Island,China.Bird Conserv Int.1998;9:411-6.
Gough J,Chothia C.SUPERFAMILY:HMMs representing all proteins of known structure.SCOP sequence searches,alignments and genome assignments.Nucleic Acids Res.2002;30:268-72.
Haas BJ,Salzberg SL,Zhu W,Pertea M,Allen JE,Orvis J,White O,Buell CR,Wortman JR.Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments.Genome Biol.2008;9:1.
Hewitt GM.Quaternary Genetic consequences of climatic oscillations in the Quaternary.Philos Trans R Soc Lond B.2004;359:183-95.
Hunter S,Apweiler R,Attwood TK,Bairoch A,Bateman A,Binns D,Bork P,Das U,Daugherty L,Duquenne L,Finn RD.InterPro:the integrative protein signature database.Nucleic Acids Res.2008;37:D211-5.
Im J,Lawrence J,Seelig D,Nho RS.FoxM1-dependent RAD51 and BRCA2 signaling protects idiopathic pulmonary fibrosis fibroblasts from radiationinduced cell death.Cell Death Dis.2018;9:584.
IUCN.Arborophila ardens.The IUCN red list of threatened species.Version2018-1.http://www.iucnr edlis t.org.2018.Accessed 20 Jul 2018.
Kie?basa SM,Wan R,Sato K,Horton P,Frith MC.Adaptive seeds tame genomic sequence comparison.Genome Res.2011;21:487-93.
Kobayashi H,Komatsu S,Ichikawa D,Kawaguchi T,Hirajima S,Miyamae M,Okajima W,Ohashi T,Kosuga T,Konishi H,Shiozaki A.Overexpression of denticleless E3 ubiquitin protein ligase homolog(DTL)is related to poor outcome in gastric carcinoma.Oncotarget.2015;6:36615.
Letunic I,Copley RR,Schmidt S,Ciccarelli FD,Doerks T,Schultz J,Ponting CP,Bork P.SMART 4.0:towards genomic data integration.Nucleic Acids Res.2004;32:D142-4.
Liao Y,Wang W,Zhang L,Yang L.Bio-effective UV radiation intensity distribution reaching the land surface in China.Geogr Res.2007;26:821-7.
Liang W,Cai Y,Yang C.Extreme levels of hunting of birds in a remote village of Hainan Island,China.Bird Conserv Int.2013;23:45-52.
Li H,Durbin R.Inference of human population history from individual wholegenome sequences.Nature.2011;475:493.
Li L,Stoeckert CJ Jr,Roos DS.OrthoMCL:identification of ortholog groups for eukaryotic genomes.Genome Res.2003;13:2178-89.
Li J,Ng EK,Ng YP,Wong CY,Yu J,Jin H,Cheng VY,Go MY,Cheung PK,Ebert MP,Tong J.Identification of retinoic acid-regulated nuclear matrix-associated protein as a novel regulator of gastric cancer.Br J Cancer.2009;101:691.
Li R,Tian H,Li X.Climate change induced range shifts of Galliformes in China.Integr Zool.2010;5:154-63.
Liu X,He Y,Li F,Huang Q,Kato TA,Hall RP,Li C.Caspase-3 promotes genetic instability and carcinogenesis.Mol Cell.2015;58:284-96.
Luo K,Li L,Li Y,Wu C,Yin Y,Chen Y,Deng M,Nowsheen S,Yuan J,Lou Z.Aphosphorylation-deubiquitination cascade regulates the BRCA2-RAD51axis in homologous recombination.Genes Dev.2016;30:1-15.
Luo R,Liu B,Xie Y,Li Z,Huang W,Yuan J,He G,Chen Y,Pan Q,Liu Y,Tang J.SOAPdenovo2:an empirically improved memory-efficient short-read de novo assembler.Gigascience.2012;1:18.
Moriya Y,Itoh M,Okuda S,Yoshizawa AC,Kanehisa M.KAAS:an automatic genome annotation and pathway reconstruction server.Nucleic Acids Res.2007;35:W182-5.
Nick G,Ari L.webPRANK:a phylogeny-aware multiple sequence aligner with interactive alignment browser.BMC Bioinform.2010;11:1-7.
Parra G,Bradnam K,Korf I.CEGMA:a pipeline to accurately annotate core genes in eukaryotic genomes.Bioinformatics.2007;23:1061-7.
Posada D,Crandall KA.Modeltest:testing the model of DNA substitution.Bioinformatics(Oxford,England).1998;14:817-8.
Rao X,Yang C,Liang W.Breeding biology and novel reproductive behaviour in the Hainan partridge(Arborophila ardens).Avian Res.2017;8:34.
Shen Y,Liang L,Sun Y,Yue B,Yang X,Murphy RW,Zhang Y.A mitogenomic perspective on the ancient,rapid radiation in the Galliformes with an emphasis on the Phasianidae.BMC Evol Biol.2010;10:132.
Sigrist CJ,Cerutti L,Hulo N,Gattiker A,Falquet L,Pagni M,Bairoch A,Bucher P.PROSITE:a documented database using patterns and profiles as motif descriptors.Brief Bioinform.2002;3:265-74.
Sim?o FA,Waterhouse RM,Ioannidis P,Kriventseva EV,Zdobnov EM.BUSCO:assessing genome assembly and annotation completeness with 1:1orthologs.Bioinformatics.2015;31:3210-2.
Stamatakis A.RAxML version 8:a tool for phylogenetic analysis and postanalysis of large phylogenies.Bioinformatics.2014;30:1312-3.
Stanke M,Keller O,Gunduz I,Hayes A,Waack S,Morgenstern B.AUGUS-TUS:ab initio prediction of alternative transcripts.Nucleic Acids Res.2006;34:435-9.
Thomas PD,Kejariwal A,Campbell MJ,Mi H,Diemer K,Guo N,Ladunga I,Ulitsky-Lazareva B,Muruganujan A,Rabkin S,Vandergriff JA.PANTHER:a browsable database of gene products organized by biological function,using curated protein family and subfamily classification.Nucleic Acids Res.2003;31:334-41.
Tigano A,Sackton TB,Friesen VL.Assembly and RNA-free annotation of highly heterozygous genomes:the case of the thick-billed murre(Uria lomvia).Mol Ecol Resour.2018;18:79-90.
Warren WC,Clayton DF,Ellegren H,Arnold AP,Hillier LW,Künstner A,et al.The genome of a songbird.Nature.2010;464:757-62.
Wu CH,Nikolskaya A,Huang H,Yeh LS,Natale DA,Vinayaka CR,Hu ZZ,Mazumder R,Kumar S,Kourtesis P,Ledley RS.PIRSF:family classification system at the protein information resource.Nucleic Acids Res.2004;32:D112-4.
Xu L,He C,Shen C,Jiang T,Shi L,Sun K,Berquist SW,Feng J.Phylogeography and population genetic structure of the great leaf-nosed bat(Hipposideros armiger)in China.J Hered.2010;101:562-72.
Yang C,Zhang Y,Cai Y,Stokke BG,Liang W.Female crowing and differential responses to simulated conspecific intrusion in male and female Hainan partridge(Arborophila ardens).Zool Sci.2011;28:249-53.
Yang Z.Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci.Genetics.2002;162:1811-23.
Yang Z.PAML 4:phylogenetic analysis by maximum likelihood.Mol Biol Evol.2007;24:1586-91.
Yu J,Liu F,Yin P,Zhu X,Cheng G,Wang N,Lu A,Luan W,Zhang N,Li J,Guo K.Integrating miRNA and mRNA expression profiles in response to heat stress-induced injury in rat small intestine.Funct Integr Genomics.2011;11:203-13.
Yu X,Zheng H,Wang J,Wang W,Su B.Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup.Genomics.2006;88:745-51.
Zhang Z,Ding C,Ding P,Zheng G.The current status and a conservation strategy for species of Galliformes in China.Biodivers Sci.2003;11:414-21.
Zheng GM.Pheasants in China.Beijing:Higher Education Press;2017(in Chinese).