Abstract
In this study, we investigated the immunoglobulin heavy (IGH) gene locus of torafugu (Takifugu rubripes) from publicly available assembly sequences and presented an annotated locus map, including the IGHV genes, pseudogenes, and IGHC genes. Three new IGHV gene families (IGHV3–IGHV5) were discovered. We observed the interspersion of IGHV1 and IGHV2 family members and that they often intermingled with each other, while other family members were further interspersed. Conservation of the promoter and recombination signal sequences (RSS) was observed in a family-specific manner. In addition to known variable region genes present on chromosome 5 (current torafugu genome assembly), we found 34 additional IGHV genes on scaffold 287 and three novel potentially functional IGHD genes on scaffold 483. In total, the variable region of the torafugu IGH locus consists of at least 48 IGHV genes, seven IGHD genes, and six IGHJ genes. IGHC genes have also been mapped in this study, with three genes encoding immunoglobulin classes: IgT, IgM, and IgD. We confirmed the expression of newly identified IGHV3 family sequences in the spleen and kidney of adult torafugu and found a favorable IGHV segment usage by IgM and IgT. Possible structural variation in the IGHδ locus was observed based on the current torafugu assembly. The complete characterization of the torafugu IGH locus will facilitate detailed studies of large-scale mechanisms associated with the recombination of the variable region genes and will offer insights into the genetic basis of the potential diversity in the antibody response observed in torafugu.
Similar content being viewed by others
References
Aparicio S et al (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301–1310. doi:10.1126/science.1072104
Bengten E, Clem LW, Miller NW, Warr GW, Wilson M (2006) Channel catfish immunoglobulins: repertoire and expression. Dev Comp Immunol 30:77–92. doi:10.1016/j.dci.2005.06.016
Brenner S, Elgar G, Sandford R, Macrae A, Venkatesh B, Aparicio S (1993) Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature 336:265–268
Brochet X, Lefranc MP, Giudicelli V (2008) IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. Nucleic Acids Res 36:W503–W508. doi:10.1093/nar/gkn316
Brodeur PH, Riblet R (1984) The immunoglobulin heavy chain variable region (Igh-V) locus in the mouse. I. One hundred Igh-V genes comprise seven families of homologous genes. Eur J Immunol 14:922–930
Cuomo CA, Mundy CL, Oettinger MA (1996) DNA sequence and structure requirements for cleavage of V(D)J recombination signal sequences. Mol Cell Biol 16:5683–5690
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 6:295–302. doi:10.1038/ni1166
Das S, Nozawa M, Klein J, Nei M (2008) Evolutionary dynamics of the immunoglobulin heavy chain variable region genes in vertebrates. Immunogenetics 60:47–55. doi:10.1007/s00251-007-0270-2
Falkner FG, Zachau HG (1984) Correct transcription of an immunoglobulin [kappa] gene requires an upstream fragment containing conserved sequence elements. Nature 310:71–74
Fillatreau S, Six A, Magadan S, Castro R, Sunyer JO, Boudinot P (2013) The astonishing diversity of Ig classes and B cell repertoires in teleost fish. Front Immunol 4:28. doi:10.3389/fimmu.2013.00028
Flajnik MF (2002) Comparative analyses of immunoglobulin genes: surprises and portents. Nat Rev Immunol 2:688–698. doi:10.1038/nri889
Flajnik MF (2005) The last flag unfurled? A new immunoglobulin isotype in fish expressed in early development. Nat Immunol 6:229–230
Flajnik MF, Kasahara M (2010) Origin and evolution of the adaptive immune system: genetic events and selective pressures. Nat Rev Genet 11:47–59. doi:10.1038/nrg2703
Gambon-Deza F, Sanchez-Espinel C, Magadan-Mompo S (2010) Presence of an unique IgT on the IGH locus in three-spined stickleback fish (Gasterosteus aculeatus) and the very recent generation of a repertoire of VH genes. Dev Comp Immunol 34:114–122. doi:10.1016/j.dci.2009.08.011
Hansen JD, Landis ED, Phillips RB (2005) Discovery of a unique Ig heavy-chain isotype (IgT) in rainbow trout: implications for a distinctive B cell developmental pathway in teleost fish. Proc Natl Acad Sci U S A 102:6919–6924. doi:10.1073/pnas.0500027102
Hendricks J et al (2010) Organization of the variable region of the immunoglobulin heavy-chain gene locus of the rat. Immunogenetics 62:479–486. doi:10.1007/s00251-010-0448-x
Jung D, Giallourakis C, Mostoslavsky R, Alt FW (2006) Mechanism and control of V(D)J recombination at the immunoglobulin heavy chain locus. Annu Rev Immunol 24:541–570. doi:10.1146/annurev.immunol.23.021704.115830
Kai W et al (2011) Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals. Genome Biol Evol 3:424–442. doi:10.1093/gbe/evr041
Kielbasa SM, Wan R, Sato K, Horton P, Frith MC (2011) Adaptive seeds tame genomic sequence comparison. Genome Res 21:487–493. doi:10.1101/gr.113985.110
Krangel MS, Carabana J, Abbarategui I, Schlimgen R, Hawwari A (2004) Enforcing order within a complex locus: current perspectives on the control of V(D)J recombination at the murine T-cell receptor α/δ locus. Immunol Rev 200:224–232
Lefranc MP (2011) IMGT, the International ImMunoGeneTics Information System. Cold Spring Harb Protoc 2011:595–603. doi:10.1101/pdb.top115
Lefranc M-P et al (2003) IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev Comp Immunol 27:55–77
Nei M (2007) The new mutation theory of phenotypic evolution. Proc Natl Acad Sci U S A 104:12235–12242. doi:10.1073/pnas.0703349104
Nei M, Rooney AP (2005) Concerted and birth-and-death evolution of multigene families. Annu Rev Genet 39:121–152
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 94:7799–7806
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
Peixoto BR, Brenner S (2000) Characterization of approximately 50 kb of the immunoglobulin VH locus of the Japanese pufferfish, Fugu rubripes. Immunogenetics 51:443–451
Ramsden AD, McBlanel JF, Gent DCV, Gellert M (1996) Distinct DNA sequence and structure requirements for the two steps of V(D)J recombination signal cleavage. EMBO (Eur Mol Biol Organ) J 15:3197–3206
Rutherford K, Parkhill J, Crook J et al (2000) Adaptive seeds tame genomic sequence comparison. Bioinformatics 16:944–945
Saha NR, Suetake H, Kikuchi K, Suzuki Y (2004) Fugu immunoglobulin D: a highly unusual gene with unprecedented duplications in its constant region. Immunogenetics 56:438–447. doi:10.1007/s00251-004-0693-y
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 42:113–124. doi:10.1016/j.molimm.2004.06.034
Savan R, Aman A, Sato K, Yamaguchi R, Sakai M (2005) Discovery of a new class of immunoglobulin heavy chain from fugu. Eur J Immunol 35:3320–3331. doi:10.1002/eji.200535248
Schatz DG, Ji Y (2011) Recombination centres and the orchestration of V(D)J recombination. Nat Rev Immunol 11:251–263. doi:10.1038/nri2941
Schroeder HW Jr, Cavacini L (2010) Structure and function of immunoglobulins. J Allergy Clin Immunol 125:S41–S52. doi:10.1016/j.jaci.2009.09.046
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. doi:10.1093/molbev/msr121
Zhang H et al (2013) Assessment of homozygosity levels in the mito-gynogenetic torafugu (Takifugu rubripes) by genome-wide SNP analyses. Aquaculture 380–383:114–119. doi:10.1016/j.aquaculture.2012.12.003
Zhang H et al (2014) Dramatic improvement in genome assembly achieved using doubled-haploid genomes. Sci Rep 4:6780. doi:10.1038/srep06780
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 39:39–62. doi:10.1016/j.dci.2012.04.001
Zimmerman AM, Moustafa FM, Romanowski KE, Steiner LA (2011) Zebrafish immunoglobulin IgD: unusual exon usage and quantitative expression profiles with IgM and IgZ/T heavy chain isotypes. Mol Immunol 48:2220–2223. doi:10.1016/j.molimm.2011.06.441
Acknowledgments
This work was supported by JSPS KAKENHI, Grant Numbers 24248034 and 25640099.
Conflict of interest
The authors have no conflict of interest to declare.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Fu, X., Zhang, H., Tan, E. et al. Characterization of the torafugu (Takifugu rubripes) immunoglobulin heavy chain gene locus. Immunogenetics 67, 179–193 (2015). https://doi.org/10.1007/s00251-014-0824-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00251-014-0824-z