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ONE"},{"key":"ref43","unstructured":"Brown TA (2002) Chapter 6: Sequencing Genomes. Genomes. 2nd edition ed. Oxford: Wiley-Liss."},{"key":"ref44","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1016\/S0161-5890(02)00261-4","article-title":"Accessory proteins and the assembly of human class I MHC molecules: a molecular and structural perspective","volume":"39","author":"M Bouvier","year":"2003","journal-title":"Mol Immunol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1007\/s12042-008-9017-y","article-title":"The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates rosids","volume":"1","author":"E Lyons","year":"2008","journal-title":"Tropical Plant Biol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1146\/annurev.biophys.37.032807.125912","article-title":"Mediation, Modulation and Consequences of Membrane-Cytoskeleton Interactions","volume":"37","author":"GJ Doherty","year":"2008","journal-title":"Annu Rev Biophys"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/2047-217X-3-11","article-title":"High-coverage sequencing and annotated assemblies of the budgerigar genome","volume":"3","author":"G Ganapathy","year":"2014","journal-title":"Gigascience"},{"key":"ref48","article-title":"Genomic data from the peregrine falcon (<italic>Falco peregrinus<\/italic>)","author":"X Zhan","year":"2014","journal-title":"Gigascience"},{"key":"ref49","article-title":"Genomic data of the Ostrich (<italic>Struthio camelus australis<\/italic>)","author":"G Zhang","year":"2014","journal-title":"Gigascience"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1038\/sj.hdy.6800450","article-title":"MHC class I typing in a songbird with numerous loci and high polymorphism using motif-specific PCR and DGGE","volume":"92","author":"H Westerdahl","year":"2004","journal-title":"Heredity"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.1111\/j.1365-294X.2009.04105.x","article-title":"Diversifying selection on MHC class I in the house sparrow (<italic>Passer domesticus<\/italic>)","volume":"18","author":"C Loiseau","year":"2009","journal-title":"Mol Ecol"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1007\/s00251-009-0375-x","article-title":"Extremely high MHC class I variation in a population of a long-distance migrant, the Scarlet Rosefinch (<italic>Carpodacus erythrinus<\/italic>)","volume":"61","author":"M Promerov\u00e1","year":"2009","journal-title":"Immunogenetics"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1186\/1471-2148-10-395","article-title":"454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher","volume":"10","author":"M Zagalska-Neubauer","year":"2010","journal-title":"BMC Evol Biol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1007\/s00251-011-0532-x","article-title":"Characterization of MHC-I in the blue tit (<italic>Cyanistes caeruleus<\/italic>) reveals low levels of genetic diversity and trans-population evolution across European populations","volume":"63","author":"E Schut","year":"2011","journal-title":"Immunogenetics"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"1943","DOI":"10.1093\/molbev\/msr015","article-title":"Spectrum of MHC class II variability in Darwin Finches and Their Close Relatives","volume":"28","author":"A Sato","year":"2011","journal-title":"Mol Biol Evol"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.molimm.2012.10.030","article-title":"Antigen processing and presentation: Evolution from a bird&apos;s eye view","volume":"55","author":"J Kaufman","year":"2013","journal-title":"Mol Immunol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1007\/s00251-005-0786-2","article-title":"Chicken TAP genes differ from their human orthologues in locus organisation, size, sequence features and polymorphism","volume":"57","author":"BA Walker","year":"2005","journal-title":"Immunogenetics"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1007\/s002510050597","article-title":"Co-evolving genes in MHC haplotypes: the \u2018rule\u2019 for nonmammalian vertebrates?","volume":"50","author":"J Kaufman","year":"1999","journal-title":"Immunogenetics"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"R42","DOI":"10.1186\/gb-2009-10-4-r42","article-title":"A whole-genome assembly of the domestic cow, <italic>Bos taurus<\/italic>","volume":"10","author":"AV Zimin","year":"2009","journal-title":"Genome Biol"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.ygeno.2006.01.004","article-title":"The genomic sequence and analysis of the swine major histocompatibility complex","volume":"88","author":"C Renard","year":"2006","journal-title":"Genomics"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"bat011","DOI":"10.1093\/database\/bat011","article-title":"Sequencing and comparative analysis of the gorilla MHC genomic sequence","volume":"2013","author":"LG Wilming","year":"2013","journal-title":"Database (Oxford)"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"7708","DOI":"10.1073\/pnas.1230533100","article-title":"Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions\/deletions as the major path to genomic divergence","volume":"100","author":"T Anzai","year":"2003","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.coi.2010.10.021","article-title":"Tripartite-motif proteins and innate immune regulation","volume":"23","author":"FW McNab","year":"2011","journal-title":"Curr Opin Immunol"},{"key":"ref64","doi-asserted-by":"crossref","unstructured":"Yap MW, Stoye JP (2012) TRIM proteins and the innate immune response to viruses. In: Meroni G, editor.TRIM\/RBCC proteins. Austin, Texas: Landes Bioscience.","DOI":"10.1007\/978-1-4614-5398-7_7"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1099\/vir.0.83391-0","article-title":"Interferons and viruses: an interplay between induction, signalling, antiviral responses and virus countermeasures","volume":"89","author":"RE Randall","year":"2008","journal-title":"J Gen Virol"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/ncb1516","article-title":"Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus","volume":"9","author":"PP Kumar","year":"2007","journal-title":"Nat Cell Biol"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"7799","DOI":"10.1073\/pnas.94.15.7799","article-title":"Evolution by the birth-and-death process in multigene families of the vertebrate immune system","volume":"94","author":"M Nei","year":"1997","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"1180","DOI":"10.1093\/molbev\/msn065","article-title":"Evolutionary patterns of MHC class II <italic>B<\/italic> in owls and their implications for the understanding of avian MHC evolution","volume":"25","author":"R Burri","year":"2008","journal-title":"Mol Biol Evol"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1126\/science.278.5338.631","article-title":"A genomic perspective on protein families","volume":"278","author":"RL Tatusov","year":"1997","journal-title":"Science"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1038\/ng1579","article-title":"An adaptive radiation model for the origin of new gene functions","volume":"37","author":"MP Francino","year":"2005","journal-title":"Nature Genet"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1007\/PL00006537","article-title":"Coevolution of PERB11 (MIC) and HLA class I genes with HERV-16 and retroelements by extended genomic duplication","volume":"49","author":"JK Kulski","year":"1999","journal-title":"J Mol Evol"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"9230","DOI":"10.1073\/pnas.0500770102","article-title":"Genomic evolution of MHC class I region in primates","volume":"102","author":"K Fukami-Kobayashi","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"13282","DOI":"10.1073\/pnas.96.23.13282","article-title":"Molecular dynamics of MHC genesis unraveled by sequence analysis of the 1,796,938-bp HLA class I region","volume":"96","author":"T Shiina","year":"1999","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1159\/000079580","article-title":"A centromere-specific retroviral element associated with breaks of synteny in macropodine marsupials","volume":"107","author":"GC Ferreri","year":"2004","journal-title":"Cytogenet Genome Res"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1186\/1471-2164-10-310","article-title":"MHC-linked and un-linked class I genes in the wallaby","volume":"10","author":"HV Siddle","year":"2009","journal-title":"BMC Genomics"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1038\/nature05621","article-title":"Origin of avian genome size and structure in non-avian dinosaurs","volume":"446","author":"CL Organ","year":"2007","journal-title":"Nature"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-7-7","article-title":"OligoSpawn: a software tool for the design of overgo probes from large unigene datasets","volume":"7","author":"J Zheng","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref78","first-page":"12","article-title":"Phlebotomy techniques in crocodilians","volume":"93","author":"M Lloyd","year":"1999","journal-title":"Bull Assoc Rep Amphib Vet"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1007\/s10577-008-1266-y","article-title":"Physical map of two tammar wallaby chromosomes: a strategy for mapping in non-model mammals","volume":"16","author":"JE Deakin","year":"2008","journal-title":"Chromosome Res"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1186\/1756-0500-4-149","article-title":"Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool","volume":"4","author":"J Mariette","year":"2011","journal-title":"BMC Res Notes"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature03959","article-title":"Genome sequencing in microfabricated highdensity picolitre reactors","volume":"437","author":"M Margulies","year":"2005","journal-title":"Nature"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows-Wheeler transform","volume":"26","author":"H Li","year":"2010","journal-title":"Bioinformatics"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1101\/gr.229202. Article published online before March 2002","article-title":"BLAT\u2013the BLAST-like alignment tool","volume":"12","author":"WJ Kent","year":"2002","journal-title":"Genome Res"},{"key":"ref84","unstructured":"Kitts P (2002) Genome Assembly and Annotation Process. In: McEntyre J, Ostell Jeditors.The NCBI Handbook. Bethesda: National Center for Biotechnology Information."},{"key":"ref85","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":"C Burge","year":"1997","journal-title":"J Mol Biol"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1007\/BF00204890","article-title":"Nomenclature for the major histocompatibility complexes of different species: a proposal","volume":"31","author":"J Klein","year":"1990","journal-title":"Immunogenetics"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1007\/s002510000285","article-title":"Characterization of the MHC class I region of the Japanese puffer fish (<italic>Fugu rubripes<\/italic>)","volume":"52","author":"MS Clark","year":"2001","journal-title":"Immunogenetics"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1111\/j.1365-313X.2007.03326.x","article-title":"How to usefully compare homologous plant genes and chromosomes as DNA sequences","volume":"53","author":"E Lyons","year":"2008","journal-title":"Plant J"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1186\/1471-2148-7-214","article-title":"BEAST: Bayesian evolutionary analysis by sampling trees","volume":"7","author":"AJ Drummond","year":"2007","journal-title":"BMC Evol Biol"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/1471-2148-6-29","article-title":"Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified","volume":"6","author":"TM Keane","year":"2006","journal-title":"BMC Evol Biol"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"1596","DOI":"10.1093\/molbev\/msm092","article-title":"MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0","volume":"24","author":"K Tamura","year":"2007","journal-title":"Mol Biol Evol"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1093\/jhered\/esm056","article-title":"Comparative genomic structure of human, dog, and cat MHC: HLA, DLA, and FLA","volume":"98","author":"N Yuhki","year":"2007","journal-title":"J Hered"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1006\/smim.1994.1050","article-title":"Evolutionary conservation of MHC class I and class II molecules-different yet the same","volume":"6","author":"J Kaufman","year":"1994","journal-title":"Semin Immunol"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0114631","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,18]],"date-time":"2019-08-18T10:52:23Z","timestamp":1566125543000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0114631"}},"subtitle":[],"editor":[{"given":"Michael","family":"Schubert","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2014,12,11]]},"references-count":93,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2014,12,11]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0114631","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,12,11]]}}}