Sequence of a Complete Chicken BG Haplotype Shows Dynamic Expansion and Contraction of Two Gene Lineages with Particular Expression Patterns

PLoS Genetics

Volumn 10, Issue 6, 2014, Pages

  Salomonsen, Jan ^a,b   Chattaway, John A ^c   Chan, Andrew C Y ^c   Parker, Aimée ^c,l   Huguet, Samuel ^c,m   Marston, Denise A ^d,n   Rogers, Sally L ^d,o   Wu, Zhiguang ^d,p   Smith, Adrian L ^d,e   Staines, Karen ^d   Butter, Colin ^d   Riegert, Patricia ^a,q   Vainio, Olli ^a,f   Nielsen, Line ^b   Kaspers, Bernd ^g   Griffin, Darren K ^h   Yang, Fengtang ⁱ   Zoorob, Rima ^j,r   Guillemot, Francois ^j,s   Auffray, Charles ^j,t   Beck, Stephan ^i,u   Skjødt, Karsten ^a,k   Kaufman, Jim ^a,c,d   more..

^a BASEL INSTITUTE FOR IMMUNOLOGY   (Switzerland)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d INSTITUTE FOR ANIMAL HEALTH   (United Kingdom)

^e UNIVERSITY OF OXFORD   (United Kingdom)

^f UNIVERSITY OF OULU   (Finland)

^g UNIVERSITY OF MUNICH   (Germany)

^h UNIVERSITY OF KENT   (United Kingdom)

ⁱ WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^j CNRS   (France)

^k UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^l INSTITUTE OF FOOD RESEARCH   (United Kingdom)

^m UNIVERSITY OF SHEFFIELD   (United Kingdom)

ⁿ VETERINARY LABORATORIES AGENCY   (United Kingdom)

^o UNIVERSITY OF GLOUCESTERSHIRE   (United Kingdom)

^p UNIVERSITY OF EDINBURGH   (United Kingdom)

^q Department of Biomedical Science University of Sheffield ^*  (France)

^r PITIÉ SALPÊTRIÈRE HOSPITAL   (France)

^s NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^t UNIVERSITÉ DE LYON   (France)

^u UNIVERSITY COLLEGE LONDON   (United Kingdom)

more..

Author keywords

[No Author keywords available]

Indexed keywords

5' UNTRANSLATED REGION; ACTIN MYOSIN INTERACTION; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BG GENE; CHICKEN; CHROMOSOME 16; CHROMOSOME 2; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE CLUSTER; GENE DELETION; GENE EXPRESSION; GENE SEQUENCE; GENETIC CODE; GENETIC LINE; HAPLOTYPE; HEMATOPOIETIC CELL; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PROMOTER REGION; REGULATOR GENE; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE; ANIMAL; BLOOD; DNA SEQUENCE; GENETICS; GENOME; MAJOR HISTOCOMPATIBILITY COMPLEX; MULTIGENE FAMILY; SEQUENCE HOMOLOGY; TANDEM REPEAT;

BLOOD GROUP ANTIGEN; BUTYROPHILIN; MEMBRANE PROTEIN;

ANIMALS; BASE SEQUENCE; BLOOD GROUP ANTIGENS; CHICKENS; GENOME; HAPLOTYPES; MAJOR HISTOCOMPATIBILITY COMPLEX; MEMBRANE GLYCOPROTEINS; MULTIGENE FAMILY; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; TANDEM REPEAT SEQUENCES;

EID: 84903489675     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004417     Document Type: Article

References (119)

1. Doxiadis GGM, Otting N, de Groot NG, Noort R, Bontrop RE, (2000) Unprecedented polymorphism of Mhc-DRB region configurations in rhesus macaques. J Immunol 164: 3193-3199.
2. Doxiadis GGM, de Groot N, Otting N, Blokhuis JH, Bontrop RE, (2011) Genomic plasticity of the MHC class I A region in rhesus macaques: extensive haplotype diversity at the population level as revealed by microsatellites. Immunogenetics 63: 73-83.
3. Jiang W, Johnson C, Jayaraman J, Simecek N, Noble J, et al. (2012) Copy number variation leads to considerable diversity for B but not A haplotypes of the human KIR genes encoding NK cell receptors. Genome Res 22: 1845-1854.
4. Lanier LL, (2005) NK cell recognition. Annu Rev Immunol 23: 225-274.
5. Sturtevant AH, (1925) The effects of unequal crossing over at the bar locus in Drosophila. Genetics 10: 117-147.
6. Haldane JBS, (1933) The part played by recurrent mutation in evolution. Am Nat 67: 5-19.
7. Müller HJ, (1935) The origination of chromatin deficiencies as minute deletions subject to insertion elsewhere. Genetica 17: 237-252.
8. Huxley J (1942) Evolution: The modern synthesis. London: Allen and Unwin.
9. Walsh JB, (1987) Persistence of tandem arrays: implications for satellite and simple-sequence DNAs. Genetics 115: 553-567.
10. Ota T, Nei M, (1994) Divergent evolution and evolution by the birth-and-death process in the immunoglobulin VH gene family. Mol Biol Evol 11: 469-482.
11. Nei M, Gu X, Sitnikova T, (1997) Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proc Natl Acad Sci U S A 94: 7799-7806.
12. Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, et al. (2006) Copy number variation: new insights in genome diversity. Genome Res 16: 949-961.
13. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J, (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
14. Lynch M, Conery JS, (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
15. Lynch M, O'Hely M, Walsh B, Force A, (2001) The probability of preservation of a newly arisen gene duplicate. Genetics 159: 1789-1804.
16. Rooney AP, Piontkivska H, Nei M, (2002) Molecular evolution of the nontandemly repeated genes of the histone 3 multigene family. Mol Biol Evol 19: 68-75.
17. Nei M, Rooney AP, (2005) Concerted and birth-and-death evolution of multigene families. Annu Rev Genet 39: 121-152.
18. Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, et al. (2006) Copy number variation: new insights in genome diversity. Genome Res 16: 949-961.
19. Hughes T, Liberles DA, (2007) The pattern of evolution of smaller-scale gene duplicates in mammalian genomes is more consistent with neo- than subfunctionalisation. J Mol Evol 65: 574-588.
20. Traherne JA, Martin M, Ward R, Ohashi M, Pellett F, et al. (2010) Mechanisms of copy number variation and hybrid gene formation in the KIR immune gene complex. Hum Mol Genet 19: 737-751.
21. Eirín-López JM, Rebordinos L, Rooney AP, Rozas J, (2012) The birth-and-death evolution of multigene families revisited. Genome Dyn 7: 170-196.
22. Katju V, Bergthorsson U, (2013) Copy-number changes in evolution: rates, fitness effects and adaptive significance. Front Genet 4: 273.
23. Henry J, Miller MM, Pontarotti P, (1999) Structure and evolution of the extended B7 family. Immunol Today 20: 285-288.
24. Afrache H, Gouret P, Ainouche S, Pontarotti P, Olive D, (2012) The butyrophilin (BTN) gene family: from milk fat to the regulation of the immune response. Immunogenetics 64: 781-794.
25. Abeler-Dörner L, Swamy M, Williams G, Hayday AC, Bas A, (2012) Butyrophilins: an emerging family of immune regulators. Trends Immunol 33: 34-41.
26. Arnett HA, Escobar SS, Viney JL, (2009) Regulation of costimulation in the era of butyrophilins. Cytokine 46: 370-375.
27. Nguyen T, Liu XK, Zhang Y, Dong C, (2006) BTNL2, a butyrophilin-like molecule that functions to inhibit T cell activation. J Immunol 176: 7354-7360.
28. Arnett HA, Escobar SS, Gonzalez-Suarez E, Budelsky AL, Steffen LA, et al. (2007) BTNL2, a butyrophilin/B7-like molecule, is a negative costimulatory molecule modulated in intestinal inflammation. J Immunol 178: 1523-1533.
29. Smith IA, Knezevic BR, Ammann JU, Rhodes DA, Aw D, et al. (2010) BTN1A1, the mammary gland butyrophilin, and BTN2A2 are both inhibitors of T cell activation. J Immunol 184: 3514-3525.
30. Yamazaki T, Goya I, Graf D, Craig S, Martin-Orozco N, et al. (2010) A butyrophilin family member critically inhibits T cell activation. J Immunol 185: 5907-5914.
31. Bas A, Swamy M, Abeler-Dörner L, Williams G, Pang DJ, et al. (2011) Butyrophilin-like 1 encodes an enterocyte protein that selectively regulates functional interactions with T lymphocytes. Proc Natl Acad Sci U S A 108: 4376-4381.
32. Harly C, Guillaume Y, Nedellec S, Peigné C-M, Mönkkönen H, et al. (2012) Key implication of CD277/butyrophilin-3 (BTN3A) in cellular stress sensing by a major human γδ T-cell subset. Blood 120: 2269-2279.
33. Palakodeti A, Sandstrom A, Sundaresan L, Harly C, Nedellec S, et al. (2012) The molecular basis for modulation of human Vγ9Vδ2 T cell responses by CD277/butyrophilin-3 (BTN3A)-specific antibodies. J Biol Chem 287: 32780-32790.
34. Vavassori S, Kumar A, Wan GS, Ramanjaneyulu GS, Cavallari M, et al. (2013) Butyrophilin 3A1 binds phosphorylated antigens and stimulates human γδ T cells. Nat Immunol 14: 908-916.
35. Valentonyte R, Hampe J, Huse K, Rosenstiel P, Albrecht M, et al. (2005) Sarcoidosis is associated with a truncating splice site mutation in BTNL2. Nat Genet 37: 357-364.
36. Szyld P, Jagiello P, Csernok E, Gross WL, Epplen JT, (2006) On the Wegener granulomatosis associated region on chromosome 6p21.3. BMC medical genetics 7: 21.
37. Spagnolo P, Sato H, Grutters JC, Renzoni EA, Marshall SE, et al. (2007) Analysis of BTNL2 genetic polymorphisms in British and Dutch patients with sarcoidosis. Tissue Antigens 70: 219-227.
38. Sato H, Spagnolo P, Silveira L, Welsh KI, du Bois RM, et al. (2007) BTNL2 allele associations with chronic beryllium disease in HLA-DPB1*Glu69-negative individuals. Tissue Antigens 70: 480-486.
39. Konno S, Takahashi D, Hizawa N, Hattori T, Takahashi A, et al. (2009) Genetic impact of a butyrophilin-like 2 (BTNL2) gene variation on specific IgE responsiveness to Dermatophagoides farinae (Der f) in Japanese. Allergol Int 58: 29-35.
40. Viken MK, Blomhoff A, Olsson M, Akselsen HE, Pociot F, et al. (2009) Reproducible association with type 1 diabetes in the extended class I region of the major histocompatibility complex. Genes Immun 10: 323-333.
41. Pathan S, Gowdy RE, Cooney R, Beckly JB, Hancock L, et al. (2009) Confirmation of the novel association at the BTNL2 locus with ulcerative colitis. Tissue Antigens 74: 322-329.
42. Hsueh K-C, Lin Y-J, Chang J-S, Wan L, Tsai F-J, (2010) BTNL2 gene polymorphisms may be associated with susceptibility to Kawasaki disease and formation of coronary artery lesions in Taiwanese children. Eur J Pediatr 169: 713-719.
43. Lian Y, Yue J, Han M, Liu J, Liu L, (2010) Analysis of the association between BTNL2 polymorphism and tuberculosis in Chinese Han population. Infect Genet Evol 10: 517-521.
44. Yamada Y, Nishida T, Ichihara S, Sawabe M, Fuku N, et al. (2011) Association of a polymorphism of BTN2A1 with myocardial infarction in East Asian populations. Atherosclerosis 215: 145-152.
45. Orozco G, Barton A, Eyre S, Ding B, Worthington J, et al. (2011) HLA-DPB1-COL11A2 and three additional xMHC loci are independently associated with RA in a UK cohort. Genes Immun 12: 169-175.
46. Horibe H, Kato K, Oguri M, Yoshida T, Fujimaki T, et al. (2011) Association of a polymorphism of BTN2A1 with hypertension in Japanese individuals. Am J Hypertens 24: 924-929.
47. Yoshida T, Kato K, Horibe H, Oguri M, Fukuda M, et al. (2011) Association of a genetic variant of BTN2A1 with chronic kidney disease in Japanese individuals. Nephrology 16: 642-648.
48. Hiramatsu M, Oguri M, Kato K, Yoshida T, Fujimaki T, et al. (2011) Association of a polymorphism of BTN2A1 with type 2 diabetes mellitus in Japanese individuals. Diabet Med 28: 1381-1387.
49. Oguri M, Kato K, Yoshida T, Fujimaki T, Horibe H, et al. (2011) Association of a genetic variant of BTN2A1 with metabolic syndrome in East Asian populations. J Med Genet 48: 787-792.
50. Heid HW, Winter S, Bruder G, Keenan TW, Jarasch ED, (1983) Butyrophilin, an apical plasma membrane-associated glycoprotein characteristic of lactating mammary glands of diverse species. Biochim Biophys Acta 728: 228-238.
51. Stammers M, Rowen L, Rhodes D, Trowsdale J, Beck S, (2000) BTL-II: a polymorphic locus with homology to the butyrophilin gene family, located at the border of the major histocompatibility complex class II and class III regions in human and mouse. Immunogenetics 51: 373-382.
52. Rhodes DA, Stammers M, Malcherek G, Beck S, Trowsdale J, (2001) The cluster of BTN genes in the extended major histocompatibility complex. Genomics 71: 351-362.
53. Boyden LM, Lewis JM, Barbee SD, Bas A, Girardi M, et al. (2008) Skint1, the prototype of a newly identified immunoglobulin superfamily gene cluster, positively selects epidermal gammadelta T cells. Nat Genet 40: 656-662.
54. Barbee SD, Woodward MJ, Turchinovich G, Mention JJ, Lewis JM, et al. (2011) Skint-1 is a highly specific, unique selecting component for epidermal T cells. Proc Natl Acad Sci U S A 108: 3330-3335.
55. Turchinovich G, Hayday AC, (2011) Skint-1 identifies a common molecular mechanism for the development of interferon-γ-secreting versus interleukin-17-secreting γδ T cells. Immunity 35: 59-68.
56. Briles WE, McGibbon WH, Irwin MR, (1950) On multiple alleles effecting cellular antigens in the chicken. Genetics 35: 633-652.
57. Schierman LW, Nordskog AW, (1961) Relationship of blood type to histocompatibility in chickens. Science 134: 1008-1009.
58. Vilhelmová M, Miggiano VC, Pink JR, Hála K, Hartmanová J, (1977) Analysis of the alloimmune properties of a recombinant genotype in the major histocompatibility complex of the chicken. Eur J Immunol 7: 674-679.
59. Kaufman J, Skjødt K, Salomonsen J, (1991) The B-G multigene family of the chicken major histocompatibility complex. Crit Rev Immunol 11: 113-143.
60. Salomonsen J, Skjødt K, Crone M, Simonsen M, (1987) The chicken erythrocyte-specific MHC antigen. Characterization and purification of the B-G antigen by monoclonal antibodies. Immunogenetics 25: 373-382.
61. Goto R, Miyada CG, Young S, Wallace RB, Abplanalp H, et al. (1988) Isolation of a cDNA clone from the B-G subregion of the chicken histocompatibility (B) complex. Immunogenetics 27: 102-109.
62. Miller MM, Abplanalp H, Goto R, (1988) Genotyping chickens for the B-G subregion of the major histocompatibility complex using restriction fragment length polymorphisms. Immunogenetics 28: 374-379.
63. Miller MM, Goto R, Young S, Liu J, Hardy J, (1990) Antigens similar to major histocompatibility complex B-G are expressed in the intestinal epithelium in the chicken. Immunogenetics 32: 45-50.
64. Kaufman J, Salomonsen J, Skjødt K, Thorpe D, (1990) Size polymorphism of chicken major histocompatibility complex-encoded B-G molecules is due to length variation in the cytoplasmic heptad repeat region. Proc Natl Acad Sci U S A 87: 8277-8281.
65. Salomonsen J, Dunon D, Skjødt K, Thorpe D, Vainio O, et al. (1991) Chicken major histocompatibility complex-encoded B-G antigens are found on many cell types that are important for the immune system. Proc Natl Acad Sci U S A 88: 1359-1363.
66. Salomonsen J, Eriksson H, Skjødt K, Lundgreen T, Simonsen M, et al. (1991) The "adjuvant effect" of the polymorphic B-G antigens of the chicken major histocompatibility complex analyzed using purified molecules incorporated in liposomes. Eur J Immunol 21: 649-658.
67. Miller MM (1991) The Major Histocompatibility Complex of the Chicken. Phylogenesis of Immune Functions. Boca Raton FL: CRC Press. pp. 151-169.
68. Döhring C, Riegert P, Salomonsen J, Skjødt K, Kaufman J (1993) The extracellular Ig V-like regions of the polymorphic B-G antigens of the chicken Mhc lack structural features expected for antibody variable regions. Avian Immunology in Progress: Institut National de la Recherche Agronomique. pp. 145-152.
69. Elleder D, Stepanets V, Melder DC, Senigl F, Geryk J, et al. (2005) The receptor for the subgroup C avian sarcoma and leukosis viruses, Tvc, is related to mammalian butyrophilins, members of the immunoglobulin superfamily. J Virol 79: 10408-10419.
70. Bikle DD, Munson S, Komuves L, (1996) Zipper protein, a B-G protein with the ability to regulate actin/myosin 1 interactions in the intestinal brush border. J Biol Chem 271: 9075-9083.
71. Goto RM, Wang Y, Taylor RL, Wakenell PS, Hosomichi K, et al. (2009) BG1 has a major role in MHC-linked resistance to malignant lymphoma in the chicken. Proc Natl Acad Sci U S A 106: 16740-16745.
72. Guillemot F, Billault A, Pourquié O, Béhar G, Chaussé AM, et al. (1988) A molecular map of the chicken major histocompatibility complex: The class II beta genes are closely linked to the class I genes and the nucleolar organizer. The EMBO journal 7: 2775-2785.
73. Kaufman J, Milne S, Göbel TW, Walker BA, Jacob JP, et al. (1999) The chicken B locus is a minimal essential major histocompatibility complex. Nature 401: 923-925.
74. Miller MM, Goto R, Bernot A, Zoorob R, Auffray C, Bumstead N, Briles WE, (1994) Two Mhc class I and two Mhc class II genes map to the chicken Rfp-Y system outside the B complex. Proc Natl Acad Sci USA 91: 4397-4401.
75. Ruby T, Bed'Hom B, Wittzell H, Morin V, Oudin A, et al. (2005) Characterisation of a cluster of TRIM-B30.2 genes in the chicken MHC B locus. Immunogenetics 57: 116-128.
76. Wallny H-J, Avila D, Hunt LG, Powell TJ, Riegert P, et al. (2006) Peptide motifs of the single dominantly expressed class I molecule explain the striking MHC-determined response to Rous sarcoma virus in chickens. Proc Natl Acad Sci U S A 103: 1434-1439.
77. Shaw I, Powell TJ, Marston DA, Baker K, van Hateren A, et al. (2007) Different evolutionary histories of the two classical class I genes BF1 and BF2 illustrate drift and selection within the stable MHC haplotypes of chickens. J Immunol 178: 5744-5752.
78. Kaufman J, Salomonsen J, Skjødt K, (1989) B-G cDNA clones have multiple small repeats and hybridize to both chicken MHC regions. Immunogenetics 30: 440-451.
79. International Chicken Genome Sequencing Consortium, (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.
80. Miller MM, Goto R, Abplanalp H, (1984) Analysis of the B-G antigens of the chicken MHC by two-dimensional gel electrophoresis. Immunogenetics 20: 373-385.
81. Shiina T, Briles WE, Goto RM, Hosomichi K, Yanagiya K, et al. (2007) Extended gene map reveals tripartite motif, C-type lectin, and Ig superfamily type genes within a subregion of the chicken MHC-B affecting infectious disease. J Immunol 178: 7162-7172.
82. Miller MM, Goto R, Young S, Chirivella J, Hawke D, et al. (1991) Immunoglobulin variable-region-like domains of diverse sequence within the major histocompatibility complex of the chicken. Proc Natl Acad Sci U S A 88: 4377-4381.
83. Hosomichi K, Miller MM, Goto RM, Wang Y, Suzuki S, et al. (2008) Contribution of mutation, recombination, and gene conversion to chicken MHC-B haplotype diversity. J Immunol 181: 3393-3399.
84. Shiina T, Ota M, Shimizu S, Katsuyama Y, Hashimoto N, et al. (2006) Rapid evolution of majorhistocompatibility complex class I genes in primates generates new disease alleles in humans via hitchhiking diversity. Genetics 173: 1555-1570.
85. van Oosterhout, (2009) A new theory of MHC evolution: beyond selection on the immune genes.Proc Biol Sci. 276: 657-665.
86. Amadou C, (1999) Evolution of the Mhc class I region: The framework hypothesis. Immunogenetics 49: 362-367.
87. Miller MM, Goto R, Briles WE, (1988) Biochemical confirmation of recombination within the B-G subregion of the chicken major histocompatibility complex. Immunogenetics 27: 127-132.
88. Wilson MJ, Torkar M, Haude A, Milne S, Jones T, et al. (2000) Plasticity in the organization and sequences of human KIR/ILT gene families. Proc Natl Acad Sci U S A 97: 4778-4783.
89. Canavez F, Young NT, Guethlein LA, Rajalingam R, Khakoo SI, et al. (2001) Comparison of chimpanzee and human leukocyte Ig-like receptor genes reveals framework and rapidly evolving genes. J Immunol 167: 5786-5794.
90. Abi-Rached L, Parham P, (2005) Natural selection drives recurrent formation of activating killer cell immunoglobulin-like receptor and Ly49 from inhibitory homologues. J Exp Med 201: 1319-1332.
91. Maniatis T, Fritsch E, Sambrook J (1982) Molecular Cloning. A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
92. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: Vol-3: A Laboratory Manual: Appendixes: CSH Laboratory Press.
93. Riegert P, Andersen R, Bumstead N, Döhring C, Dominguez-Steglich M, et al. (1996) The chicken beta 2-microglobulin gene is located on a non-major histocompatibility complex microchromosome: a small, G+C-rich gene with X and Y boxes in the promoter. Proc Natl Acad Sci U S A 93: 1243-1248.
94. Salomonsen J, Marston D, Avila D, Bumstead N, Johansson B, et al. (2003) The properties of the single chicken MHC classical class II alpha chain (B-LA) gene indicate an ancient origin for the DR/E-like isotype of class II molecules. Immunogenetics 55: 605-614.
95. Peck R, Murthy KK, Vainio O, (1982) Expression of B-L (Ia-like) antigens on macrophages from chicken lymphoid organs. J Immunol 129: 4-5.
96. Mast J, Goddeeris BM, Peeters K, Vandesande F, Berghman LR, (1998) Characterisation of chicken monocytes, macrophages and interdigitating cells by the monoclonal antibody KUL01. Vet Immunol Immunopathol 61: 343-357.
97. Weining KC, Schultz U, Münster U, Kaspers B, Staeheli P, (1996) Biological properties of recombinant chicken interferon-gamma. Eur J Immunol 26: 2440-2447.
98. Ding M, Zhang M, Wong JL, Rogers NE, Ignarro LJ, et al. (1998) Antisense knockdown of inducible nitric oxide synthase inhibits induction of experimental autoimmune encephalomyelitis in SJL/J mice. J Immunol 160: 2560-2564.
99. Wu Z, Rothwell L, Young JR, Kaufman J, Butter C, et al. (2010) Generation and characterization of chicken bone marrow-derived dendritic cells. Immunology 129: 133-145.
100. Goodman T, Lefrançois L, (1988) Expression of the gamma-delta T-cell receptor on intestinal CD8+ intraepithelial lymphocytes. Nature 333: 855-858.
101. Salomonsen J, Sørensen MR, Marston DA, Rogers SL, Collen T, et al. (2005) Two CD1 genes map to the chicken MHC, indicating that CD1 genes are ancient and likely to have been present in the primordial MHC. Proc Natl Acad Sci U S A 102: 8668-8673.
102. Linna TJ, Frommel D, Good RA, (1972) Effects of early cyclophosphamide treatment on the development of lymphoid organs and immunological functions in the chickens. Int Arch Allergy Appl Immunol 42: 20-39.
103. Kaufman J, Andersen R, Avila D, Engberg J, Lambris J, et al. (1992) Different features of the MHC class I heterodimer have evolved at different rates. Chicken B-F and beta 2-microglobulin sequences reveal invariant surface residues. J Immunol 148: 1532-1546.
104. Ronquist F, Huelsenbeck JP, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
105. Swofford DL (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
106. Shimodaira H, Hasegawa M, (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17: 1246-1247.
107. Huson DH, (1998) SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14: 68-73.
108. Huson DH, Bryant D, (2006) Application of Phylogenetic Networks in Evolutionary Studies. Mol Biol Evol 23: 254-267.
109. Bruen T, Phillipe H, Bryant D, (2006) A quick and robust statistical test to detect the presence of recombination. Genetics 172: 2665-2681.
110. Castresana J, (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molec Biol Evol 17: 540-552.
111. Talavera G, Castresana J, (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systemat Biol 56: 564-577.
112. Zamani N, Russell P, Lantz H, Hoeppner MP, Meadows JRS, et al. (2013) Unsupervised genome-wide recognition of local relationship patterns. BMC genomics 14: 347.
113. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
114. Marmor MD, Benatar T, Ratcliffe MJ, (1993) Retroviral transformation in vitro of chicken T cells expressing either alpha/beta or gamma/delta T cell receptors by reticuloendotheliosis virus strain T. J Exp Med 177: 647-656.
115. Maccubbin D, Schierman L, (1986) MHC-restricted cytotoxic response of chicken T cells: expression, augmentation, and clonal characterization. J Immunol 136: 12-16.
116. Walker BA, Hunt LG, Sowa AK, Skjødt K, Göbel TW,et al The dominantly expressed class I molecule of the chicken MHC is explained by coevolution with the polymorphic peptide transporter (TAP) genes. Proc Natl Acad Sci U S A 108: 8396-8401.
117. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, et al. (2007) Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome. Science 318: 420-426.
118. Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, et al. (2008) Copy number variation and evolution in humans and chimpanzees. Genome Res 18: 1698-1710.
119. Yang F, Müller S, Just R, Ferguson-Smith MA, Wienberg J, (1997) Comparative chromosome painting in mammals: human and the Indian muntjac (Muntiacus muntjak vaginalis). Genomics 39: 396-401.