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LITERATURE CITED

  • Amemiya CT, Ohta Y, Litman RT, et al. 1993. VH gene organization in a relict species, the coelacanth Latimeria chalumnae: evolutionary implications. Proc Natl Acad Sci USA 90:66616665.
  • Amemiya CT, Alfoldi J, Lee AP, et al. 2013. The African coelacanth genome provides insights into tetrapod evolution. Nature 496:311316.
  • Anderson MK, Strong SJ, Litman RT, et al. 1999. A long form of the skate IgX gene exhibits a striking resemblance to the new shark IgW and IgNARC genes. Immunogenetics 49:5667.
  • Andersson E, Matsunaga T. 1995. Evolution of immunoglobulin heavy chain variable region genes: a VH family can last for 150–200 million years or longer. Immunogenetics 41:1828.
  • Ansari-Lari MA, Muzny DM, Lu J, et al. 1996. A gene-rich cluster between the CD4 and triosephosphate isomerase genes at human chromosome 12p13. Genome Res 6:314326.
  • Araki K, Suetake H, Kikuchi K, Suzuki Y. 2005. Characterization and expression analysis of CD3varepsilon and CD3gamma/delta in fugu, Takifugu rubripes. Immunogenetics 57:158163.
  • Barreto VM, Pan-Hammarstrom Q, Zhao Y, et al. 2005. AID from bony fish catalyzes class switch recombination. J Exp Med 202:733738.
  • Bengten E, Leanderson T, Pilstrom L. 1992. Immunoglobulin heavy chain cDNA from the teleost Atlantic cod (Gadus morhua L.): nucleotide sequences of secretory and membrane form show an unusual splicing pattern. Eur J Immunol 22:294.
  • Bernot A, Auffray C. 1991. Primary structure and ontogeny of an avian CD3 transcript. Proc Natl Acad Sci USA 88:25502554.
  • Betz UA, Mayer WE, Klein J. 1994. Major histocompatibility complex class I genes of the coelacanth Latimeria chalumnae. Proc Natl Acad Sci USA 91:1106511069.
  • Boudinot P, Zou J, Ota T, et al. 2014. A tetrapod-like repertoire of innate immune receptors and effectors for coelacanths: an emphasis on antiviral immunity. J Exp Zool Part B Mol Dev Evol 322B:415437.
  • Brinkmann H, Venkatesh B, Brenner S, Meyer A. 2004. Nuclear protein-coding genes support lungfish and not the coelacanth as the closest living relatives of land vertebrates. Proc Natl Acad Sci USA 101:49004905.
  • Burge C, Karlin S. 1997. Prediction of complete gene structures in human genomic DNA. J Mol Biol 268:7894.
  • Campanella JJ, Bitincka L, Smalley J. 2003. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. BMC Bioinformatics 4:29.
  • Cramer CA, Bonatto SL, Reis RE. 2011. Molecular phylogeny of the Neoplecostominae and Hypoptopomatinae (Siluriformes: Loricariidae) using multiple genes. Mol Phylogenet Evol 59:4352.
  • Criscitiello MF, Flajnik MF. 2007. Four primordial immunoglobulin light chain isotypes, including lambda and kappa, identified in the most primitive living jawed vertebrates. Eur J Immunol 37:26832694.
  • Criscitiello MF, Ohta Y, Saltis M, McKinney EC, Flajnik MF. 2010. Evolutionarily conserved TCR binding sites, identification of T cells in primary lymphoid tissues, and surprising trans-rearrangements in nurse shark. J Immunol 184:69506960.
  • Criscitiello MF, Saltis M, Flajnik MF. 2006. An evolutionarily mobile antigen receptor variable region gene: doubly rearranging NAR-TcR genes in sharks. Proc Natl Acad Sci USA 103:50365041.
  • Crow KD, Smith CD, Cheng JF, Wagner GP, Amemiya CT. 2012. An independent genome duplication inferred from Hox paralogs in the American paddlefish—a representative basal ray-finned fish and important comparative reference. Genome Biol Evol 4:937953.
  • Danilova N, Bussmann J, Jekosch K, Steiner LA. 2005. The immunoglobulin heavy-chain locus in zebrafish: identification and expression of a previously unknown isotype, immunoglobulin Z. Nat Immunol 6:295302.
  • Danke J, Miyake T, Powers T, et al. 2004. Genome resource for the Indonesian coelacanth, Latimeria menadoensis. J Exp Zool A Comp Exp Biol 301:228234.
  • Das S, Hirano M, Tako R, McCallister C, Nikolaidis N. 2012. Evolutionary genomics of immunoglobulin-encoding Loci in vertebrates. Curr Genomics 13:95102.
  • Dzialo RC, Cooper MD. 1997. An amphibian CD3 homologue of the mammalian CD3 gamma and delta genes. Eur J Immunol 27:16401647.
  • Edholm ES, Wilson M, Sahoo M, et al. 2009. Identification of Igsigma and Iglambda in channel catfish, Ictalurus punctatus, and Iglambda in Atlantic cod, Gadus morhua. Immunogenetics 61:353370.
  • Edholm ES, Wilson M, Bengten E. 2011. Immunoglobulin light (IgL) chains in ectothermic vertebrates. Dev Comp Immunol 35:906915.
  • Fanning LJ, Connor AM, Wu GE. 1996. Development of the immunoglobulin repertoire. Clin Immunol Immunopathol 79:114.
  • Fjell CD, Bosdet I, Schein JE, Jones SJ, Marra MA. 2003. Internet Contig Explorer (iCE)-a tool for visualizing clone fingerprint maps. Genome Res 13:12441249.
  • Flajnik MF. 2002. Comparative analyses of immunoglobulin genes: surprises and portents. Nat Rev Immunol 2:688698.
  • Flajnik MF, Du Pasquier LD. 2008. Evolution of the immune system. In: Paul WE, editor. Fundamental immunology. Philadelphia, PA: Lippincott Williams & Wilkins, Wolters Kluwer. p 56124.
  • Fugmann SD, Messier C, Novack LA, Cameron RA, Rast JP. 2006. An ancient evolutionary origin of the Rag1/2 gene locus. Proc Natl Acad Sci USA 103:37283733.
  • Gambon-Deza F, Sanchez-Espinel C, Mirete-Bachiller S, Magadan-Mompo S. 2012. Snakes antibodies. Dev Comp Immunol 38:19.
  • Ghaffari SH, Lobb CJ. 1991. Heavy chain variable region gene families evolved early in phylogeny. Ig complexity in fish. J Immunol 146:10371046.
  • Giudicelli V, Chaume D, Lefranc MP. 2005. IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res 33:D256D261.
  • Gordon D, Abajian C, Green P. 1998. Consed: a graphical tool for sequence finishing. Genome Res 8:195202.
  • Hansen JD, Kaattari SL. 1996. The recombination activating gene 2 (RAG2) of the rainbow trout Oncorhynchus mykiss. Immunogenetics 44:203211.
  • Hansen J, Leong JA, Kaattari S. 1994. Complete nucleotide sequence of a rainbow trout cDNA encoding a membrane-bound form of immunoglobulin heavy chain. Mol Immunol 31:499501.
  • Harding FA, Amemiya CT, Litman RT, Cohen N, Litman GW. 1990. Two distinct immunoglobulin heavy chain isotypes in a primitive, cartilaginous fish, Raja erinacea. Nucleic Acids Res 18:63696376.
  • Heufler C, Koch F, Stanzl U, et al. 1996. Interleukin-12 is produced by dendritic cells and mediates T helper 1 development as well as interferon-gamma production by T helper 1 cells. Eur J Immunol 26:659668.
  • Hikima J, Jung TS, Aoki T. 2011. Immunoglobulin genes and their transcriptional control in teleosts. Dev Comp Immunol 35:924936.
  • Hinds-Frey KR, Nishikata H, Litman RT, Litman GW. 1993. Somatic variation precedes extensive diversification of germline sequences and combinatorial joining in the evolution of immunoglobulin heavy chain diversity. J Exp Med 178:815824.
  • Hsu E, Criscitiello MF. 2006. Diverse immunoglobulin light chain organizations in fish retain potential to revise B cell receptor specificities. J Immunol 177:24522462.
  • Huang B, Yachou A, Fleury S, Hendrickson WA, Sekaly RP. 1997. Analysis of the contact sites on the CD4 molecule with class II MHC molecule: co-ligand versus co-receptor function. J Immunol 158:216225.
  • Ichikawa HT, Sowden MP, Torelli AT, et al. 2006. Structural phylogenetic analysis of activation-induced deaminase function. J Immunol 177:355361.
  • Kasahara M. 1997. New insights into the genomic organization and origin of the major histocompatibility complex: role of chromosomal (genome) duplication in the emergence of the adaptive immune system. Hereditas 127:5965.
  • Kataoka T, Kawakami T, Takahashi N, Honjo T. 1980. Rearrangement of immunoglobulin gamma 1-chain gene and mechanism for heavy-chain class switch. Proc Natl Acad Sci USA 77:919923.
  • Koskinen R, Salomonsen J, Tregaskes CA, et al. 2002. The chicken CD4 gene has remained conserved in evolution. Immunogenetics 54:520525.
  • Kumar S, Nei M, Dudley J, Tamura K. 2008. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9:299306.
  • Lin J, Weiss A. 2001. T cell receptor signalling. J Cell Sci 114:243244.
  • Longerich S, Orelli BJ, Martin RW, Bishop DK, Storb U. 2008. Brca1 in immunoglobulin gene conversion and somatic hypermutation. DNA Repair (Amst) 7:253266.
  • Lundqvist ML, Middleton DL, Radford C, Warr GW, Magor KE. 2006. Immunoglobulins of the non-galliform birds: antibody expression and repertoire in the duck. Dev Comp Immunol 30:93100.
  • Magadan-Mompo S, Zimmerman AM, Sanchez-Espinel C, Gambon-Deza F. 2013. Immunoglobulin light chains in medaka (Oryzias latipes). Immunogenetics 65:387396.
  • Malmstrom M, Jentoft S, Gregers TF, Jakobsen KS. 2013. Unraveling the evolution of the Atlantic cod's (Gadus morhua L.) alternative immune strategy. PLoS ONE 8:e74004.
  • Moore KW, de Waal MR, Coffman RL, O'Garra A. 2001. Interleukin-10 and the interleukin-10 receptor. Annu Rev Immunol 19:683765.
  • Moore LJ, Somamoto T, Lie KK, Dijkstra JM, Hordvik I. 2005. Characterisation of salmon and trout CD8alpha and CD8beta. Mol Immunol 42:12251234.
  • Nagarajan UM, O'Connell C, Rank RG. 2004. Molecular characterization of guinea - pig (Cavia porcellus) CD8alpha and CD8beta cDNA. Tissue Antigens 63:184189.
  • Nikaido M, Noguchi H, Nishihara H, et al. 2013. Coelacanth genomes reveal signatures for evolutionary transition from water to land. Genome Res 23:17401748.
  • Okkenhaug K, Bilancio A, Emery JL, Vanhaesebroeck B. 2004. Phosphoinositide 3-kinase in T cell activation and survival. Biochem Soc Trans 32:332335.
  • Ota T, Nei M. 1994. Divergent evolution and evolution by the birth-and-death process in the immunoglobulin VH gene family. Mol Biol Evol 11:469482.
  • Ota T, Rast JP, Litman GW, Amemiya CT. 2003a. Lineage-restricted retention of a primitive immunoglobulin heavy chain isotype within the Dipnoi reveals an evolutionary paradox. Proc Natl Acad Sci USA 100:25012506.
  • Ota T, Rast JP, Litman GW, Amemiya CT. 2003b. Lineage-restricted retention of a primitive immunoglobulin heavy chain isotype within the Dipnoi reveals an evolutionary paradox. Proc Natl Acad Sci USA 100:25012506.
  • Pallavicini A, Canapa A, Barucca M, et al. 2013. Analysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis. BMC Genomics 14:538.
  • Park CI, Hirono I, Aoki T. 2005. Molecular characterization of the Japanese flounder, Paralichthys olivaceus, CD3epsilon and evolution of the CD3 cluster. Dev Comp Immunol 29:123133.
  • Parra ZE, Miller RD. 2012. Comparative analysis of the chicken TCRalpha/delta locus. Immunogenetics 64:641645.
  • Parra ZE, Baker ML, Schwarz RS, et al. 2007. A unique T cell receptor discovered in marsupials. Proc Natl Acad Sci USA 104:97769781.
  • Parra ZE, Baker ML, Lopez AM, et al. 2009. TCR mu recombination and transcription relative to the conventional TCR during postnatal development in opossums. J Immunol 182:154163.
  • Parra ZE, Ohta Y, Criscitiello MF, Flajnik MF, Miller RD. 2010. The dynamic TCRdelta: TCRdelta chains in the amphibian Xenopus tropicalis utilize antibody-like V genes. Eur J Immunol 40:23192329.
  • Parra ZE, Lillie M, Miller RD. 2012. A model for the evolution of the mammalian t-cell receptor alpha/delta and mu loci based on evidence from the duckbill Platypus. Mol Biol Evol 29:32053214.
  • Rast JP, Anderson MK, Litman GW. 1989. The structure and organization of immunoglobulin genes in lower vertebrates. In: Honjo T, Alt FW, Rabbitts TH, editors. Immunoglobulin genes. London, UK: Academic Press. p 315341.
  • Rast JP, Amemiya CT, Litman RT, Strong SJ, Litman GW. 1998. Distinct patterns of IgH structure and organization in a divergent lineage of chrondrichthyan fishes. Immunogenetics 47:234245.
  • Reyes-Cerpa S, Maisey K, Reyes-Lopez F, et al. 2012. Fish cytokines and immune response. In: Türker H, editor. New advances and contributions to fish biology. Rijeka, Croatia: Intech. p 357.
  • Reynaud CA, Dahan A, Anquez V, Weill JC. 1989 Somatic hyperconversion diversifies the single Vh gene of the chicken with a high incidence in the D region Cell 59:171183.
  • Roman T, Andersson E, Bengten E, et al. 1996. Unified nomenclature of Ig VH genes in rainbow trout (Oncorhynchus mykiss): definition of eleven VH families. Immunogenetics 43:325326.
  • Ropars A, Bautz AM, Dournon C. 2002. Sequencing and expression of the CD3 gamma/delta mRNA in Pleurodeles waltl (urodele amphibian). Immunogenetics 54:130138.
  • Rumfelt LL, Lohr RL, Dooley H, Flajnik MF. 2004. Diversity and repertoire of IgW and IgM VH families in the newborn nurse shark. BMC Immunol 5:8.
  • Saha NR, Suetake H, Kikuchi K, Suzuki Y. 2004. Fugu immunoglobulin D: a highly unusual gene with unprecedented duplications in its constant region. Immunogenetics 56:438447.
  • Saha NR, Suetake H, Suzuki Y. 2005. Analysis and characterization of the expression of the secretory and membrane forms of IgM heavy chains in the pufferfish, Takifugu rubripes. Mol Immunol 42:113124.
  • Saraiva M, Christensen JR, Veldhoen M, et al. 2009. Interleukin-10 production by Th1 cells requires interleukin-12-induced STAT4 transcription factor and ERK MAP kinase activation by high antigen dose. Immunity 31:209219.
  • Savan R, Sakai M. 2006. Genomics of fish cytokines. Comp Biochem Physiol Part D Genomics Proteomics 1:89101.
  • Star B, Nederbragt AJ, Jentoft S, et al. 2011. The genome sequence of Atlantic cod reveals a unique immune system. Nature 477:207210.
  • Stavnezer J, Amemiya CT. 2004. Evolution of isotype switching. Semin Immunol 16:257275.
  • Suetake H, Araki K, Akatsu K, et al. 2007. Genomic organization and expression of CD8alpha and CD8beta genes in fugu Takifugu rubripes. Fish Shellfish Immunol 23:11071118.
  • Sun Y, Liu Z, Ren L, et al. 2012. Immunoglobulin genes and diversity: what we have learned from domestic animals. J Anim Sci Biotechnol 3:18.
  • Tomlinson IM, Walter G, Marks JD, Llewelyn MB, Winter G. 1992. The repertoire of human germline VH sequences reveals about fifty groups of VH segments with different hypervariable loops. J Mol Biol 227:776798.
  • Turchin A, Hsu E. 1996. The generation of antibody diversity in the turtle. J Immunol 156:37973805.
  • Tutter A, Brodeur P, Shlomchik M, Riblet R. 1991. Structure, map position, and evolution of two newly diverged mouse Ig VH gene families. J Immunol 147:32153223.
  • Wakae K, Magor BG, Saunders H, et al. 2006. Evolution of class switch recombination function in fish activation-induced cytidine deaminase, AID. Int Immunol 18:4147.
  • Wang X, Parra ZE, Miller RD. 2011. Platypus TCRmu provides insight into the origins and evolution of a uniquely mammalian TCR locus. J Immunol 187:52465254.
  • Warr GW, Middleton DL, Miller NW, Clem LW, Wilson MR. 1991. An additional family of VH sequences in the channel catfish. Eur J Immunogenet 18:393397.
  • Wen Y, Shao JZ, Xiang LX, Fang W. 2006. Cloning, characterization and expression analysis of two Tetraodon nigroviridis interleukin-16 isoform genes. Comp Biochem Physiol B Biochem Mol Biol 144:159166.
  • Willett CE, Cherry JJ, Steiner LA. 1997. Characterization and expression of the recombination activating genes (rag1 and rag2) of zebrafish. Immunogenetics 45:394404.
  • Wu H, Kwong PD, Hendrickson WA. 1997. Dimeric association and segmental variability in the structure of human CD4. Nature 387:527530.
  • Zhu LY, Nie L, Zhu G, Xiang LX, Shao JZ. 2013. Advances in research of fish immune-relevant genes: a comparative overview of innate and adaptive immunity in teleosts. Dev Comp Immunol 39:3962.