Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410. https://doi.org/10.1016/s0022-2836(05)80360-2

Article  CAS  PubMed  Google Scholar 

Antonacci R, Mineccia M, Lefranc MP, Ashmaoui HM, Lanave C, Piccinni B, Pesole G, Hassanane MS, Massari S, Ciccarese S (2011) Expression and genomic analyses of Camelus dromedarius T cell receptor delta (TRD) genes reveal a variable domain repertoire enlargement due to CDR3 diversification and somatic mutation. Mol Immunol 48(12–13):1384–1396. https://doi.org/10.1016/j.molimm.2011.03.011

Article  CAS  PubMed  Google Scholar 

Berens SJ, Wylie DE, Lopez OJ (1997) Use of a single VH family and long CDR3s in the variable region of cattle Ig heavy chains. Int Immunol 9(1):189–199. https://doi.org/10.1093/intimm/9.1.189

Article  CAS  PubMed  Google Scholar 

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28(1):235–242. https://doi.org/10.1093/nar/28.1.235

Article  CAS  PubMed  PubMed Central  Google Scholar 

Burke MJ, Scott JNF, Minshull TC, Gao Z, Manfield I, Savic S, Stockley PG, Calabrese AN, Boyes J (2022) A bovine antibody possessing an ultralong complementarity-determining region CDRH3 targets a highly conserved epitope in sarbecovirus spike proteins. J Biol Chem 298(12):102624. https://doi.org/10.1016/j.jbc.2022.102624

Burke MJ, Stockley PG, Boyes J (2020) Broadly neutralizing bovine antibodies: highly effective new tools against evasive pathogens? Viruses 12(4):473. https://doi.org/10.3390/v12040473

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen H, Bernstein H, Ranganathan P, Schluter S (2012) Somatic hypermutation of TCR γ V genes in the sandbar shark. Dev Comp Immunol 37(1):176–183. https://doi.org/10.1016/j.dci.2011.08.018

Article  CAS  PubMed  Google Scholar 

Chen L, Qiu Q, Jiang Y, Wang K, Lin Z, Li Z, Bibi F, Yang Y, Wang J, Nie W et al (2019) Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science 364(6446). https://doi.org/10.1126/science.aav6202

Ciccarese S, Vaccarelli G, Lefranc MP, Tasco G, Consiglio A, Casadio R, Linguiti G, Antonacci R (2014) Characteristics of the somatic hypermutation in the Camelus dromedarius T cell receptor gamma (TRG) and delta (TRD) variable domains. Dev Comp Immunol 46(2):300–313. https://doi.org/10.1016/j.dci.2014.05.001

Article  CAS  PubMed  Google Scholar 

Collins AM, Wang Y, Roskin KM, Marquis CP, Jackson KJ (2015) The mouse antibody heavy chain repertoire is germline-focused and highly variable between inbred strains. Philos Trans R Soc Lond B Biol Sci 370(1676). https://doi.org/10.1098/rstb.2014.0236

Conticello SG, Thomas CJF, Petersen-Mahrt SK, Neuberger MS (2005) Evolution of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases. Mol Biol Evol 22(2):367–377. https://doi.org/10.1093/molbev/msi026

Article  CAS  PubMed  Google Scholar 

Criscitiello M, Saltis M, Flajnik M (2006) An evolutionarily mobile antigen receptor variable region gene: doubly rearranging NAR-TcR genes in sharks. Proc Natl Acad Sci 103(13):5036–5041. https://doi.org/10.1073/pnas.0507074103

Article  CAS  PubMed  PubMed Central  Google Scholar 

Criscitiello MF (2021) Unusual T cell receptor in opossum. Science 371(6536):1308–1309. https://doi.org/10.1126/science.abg7639

Article  CAS  PubMed  Google Scholar 

Cunningham F, Allen JE, Allen J, Alvarez-Jarreta J, Amode MR, Armean Irina M, Austine-Orimoloye O, Azov Andrey G, Barnes I, Bennett R et al (2021) Ensembl 2022. Nucleic Acids Res 50(D1):D988–D995. https://doi.org/10.1093/nar/gkab1049

Article  CAS  PubMed Central  Google Scholar 

de los Rios M, Criscitiello MF, and Smider VV (2015) Structural and genetic diversity in antibody repertoires from diverse species. Curr Opin Struct Biol 33:27–41. https://doi.org/10.1016/j.sbi.2015.06.002

Deiss TC, Vadnais M, Wang F, Chen PL, Torkamani A, Mwangi W, Lefranc MP, Criscitiello MF, Smider VV (2019) Immunogenetic factors driving formation of ultralong VH CDR3 in Bos taurus antibodies. Cell Mol Immunol 16:53–64. https://doi.org/10.1038/cmi.2017.117

Article  CAS  PubMed  Google Scholar 

Desmyter A, Transue TR, Ghahroudi MA, Dao Thi M-H, Poortmans F, Hamers R, Muyldermans S, Wyns L (1996) Crystal structure of a camel single-domain VH antibody fragment in complex with lysozyme. Nat Struct Mol Biol 3. https://doi.org/10.1038/nsb0996-803

Di Y, Cai S, Zheng S, Huang J, Du L, Song Y, Zhang M, Wang Z, Yu G, Ren L et al (2022) Reshaping the murine immunoglobulin heavy chain repertoire with bovine DH genes. Immunology 165(1):74–87. https://doi.org/10.1111/imm.13407

Article  CAS  PubMed  Google Scholar 

Dong J, Finn JA, Larsen PA, Smith TPL, Crowe JE (2019) Structural diversity of ultralong CDRH3s in seven bovine antibody heavy chains. Front Immunol 10. https://doi.org/10.3389/fimmu.2019.00558

Du L, Wang S, Zhu Y, Zhao H, Basit A, Yu X, Li Q, Sun X (2018) Immunoglobulin heavy chain variable region analysis in dairy goats. Immunobiology 223(11):599–607. https://doi.org/10.1016/j.imbio.2018.07.005

Article  CAS  PubMed  Google Scholar 

Dufour V, Malinge S, Nau F (1996) The sheep Ig variable region repertoire consists of a single VH family. J Immunol 156(6):2163–2170 (PMID: 8690905)

Article  CAS  PubMed  Google Scholar 

Edwards JM, Heydarchi B, Khoury G, Salazar-Quiroz NA, Gonelli CA, Wines B, Hogarth PM, Kristensen AB, Parsons MS, Purcell DFJ (2021) Enhancement of antibody-dependent cellular cytotoxicity and phagocytosis in anti-HIV-1 human-bovine chimeric broadly neutralizing antibodies. J Virol 95(13):e0021921. https://doi.org/10.1128/jvi.00219-21

Haakenson JK, Deiss TC, Warner GF, Mwangi W, Criscitiello MF, Smider VV (2019) A broad role for cysteines in bovine antibody diversity. Immunohorizons 3(10):478–487. https://doi.org/10.4049/immunohorizons.1900058

Article  CAS  PubMed  PubMed Central  Google Scholar 

Haakenson JK, Huang R, Smider VV (2018) Diversity in the cow ultralong CDR H3 antibody repertoire. Front Immunol 9. https://doi.org/10.3389/fimmu.2018.01262

Hassanin A, Ropiquet A (2004) Molecular phylogeny of the tribe Bovini (Bovidae, Bovinae) and the taxonomic status of the Kouprey, Bos sauveli Urbain 1937. Mol Phylogenet Evol 33(3):896–907. https://doi.org/10.1016/j.ympev.2004.08.009

Article  CAS  PubMed  Google Scholar 

Hernández Fernández M, Vrba ES (2005) A complete estimate of the phylogenetic relationships in Ruminantia: a dated species-level supertree of the extant ruminants. Biol Rev Camb Philos Soc 80(2):269–302. https://doi.org/10.1017/s1464793104006670

Article  PubMed  Google Scholar 

Jackson KJL (2019) Study of human antibody responses from analysis of immunoglobulin gene sequences. In Ranganathan S, Gribskov M, Nakai K, Schönbach C (eds.) Encyclopedia of Bioinformatics and Computational Biology. Academic Press, Oxford

Johnston CM, Wood AL, Bolland DJ, Corcoran AE (2006) Complete sequence assembly and characterization of the C57BL/6 mouse Ig heavy chain V region1. J Immunol 176(7):4221–4234. https://doi.org/10.4049/jimmunol.176.7.4221

Article  CAS  PubMed  Google Scholar 

Jones JM, Gellert M (2004) The taming of a transposon: V(D)J recombination and the immune system. Immunol Rev 200:233–248. https://doi.org/10.1111/j.0105-2896.2004.00168.x

Article  CAS  PubMed  Google Scholar 

Kirkham PM, Mortari F, Newton JA, Schroeder HW Jr (1992) Immunoglobulin VH clan and family identity predicts variable domain structure and may influence antigen binding. Embo J 11(2):603–609. https://doi.org/10.1002/j.1460-2075.1992.tb05092.x

Article  CAS  PubMed  PubMed Central  Google Scholar 

Knight KL, Becker RS (1990) Molecular basis of the allelic inheritance of rabbit immunoglobulin VH allotypes: implications for the generation of antibody diversity. Cell 60(6):963–970. https://doi.org/10.1016/0092-8674(90)90344-e

Article  CAS  PubMed  Google Scholar 

Koti M, Kataeva G, Kaushik AK (2010) Novel atypical nucleotide insertions specifically at VH-DH junction generate exceptionally long CDR3H in cattle antibodies. Mol Immunol 47. https://doi.org/10.1016/j.molimm.2010.02.014

Larimore K, McCormick MW, Robins HS, Greenberg PD (2012) Shaping of human germline IgH repertoires revealed by deep sequencing. J Immunol 189(6):3221–3230. https://doi.org/10.4049/jimmunol.1201303

Article  CAS  PubMed  Google Scholar 

Lefranc M-P (2014) Immunoglobulin and T cell receptor genes: IMGT and the birth and rise of immunoinformatics. Front Immunol 5:22–22. https://doi.org/10.3389/fimmu.2014.00022

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lefranc MP, Giudicelli V, Duroux P, Jabado-Michaloud J, Folch G, Aouinti S, Carillon E, Duvergey H, Houles A, Paysan-Lafosse T et al (2015) IMGT®, the international ImMunoGeneTics information system® 25 years on. Nucleic Acids Res 43(Database issue):D413–22. https://doi.org/10.1093/nar/gku1056

Li Z, Woo CJ, Iglesias-Ussel MD, Ronai D, Scharff MD (2004) The generation of antibody diversity through somatic hypermutation and class switch recombination. Genes Dev 18(1):1–11. https://doi.org/10.1101/gad.1161904

Article  CAS  PubMed  Google Scholar 

Liljavirta J, Ekman A, Knight JS, Pernthaner A, Iivanainen A, Niku M (2013) Activation-induced cytidine deaminase (AID) is strongly expressed in the fetal bovine ileal Peyer’s patch and spleen and is associated with expansion of the primary antibody repertoire in the absence of exogenous antigens. Mucosal Immunol 6(5):942–949. https://doi.org/10.1038/mi.2012.132

Article  CAS  PubMed  Google Scholar 

Liljavirta J, Niku M, Pessa-Morikawa T, Ekman A, Iivanainen A (2014) Expansion of the preimmune antibody repertoire by junctional diversity in Bos taurus. PLoS ONE 9(6):e99808. https://doi.org/10.1371/journal.pone.0099808

Lopez O, Perez C, Wylle D (1998) A single VH family and long CDR3s are the targets for hypermutation in bovine immunoglobulin heavy chains. Immunol Rev 162. https://doi.org/10.1111/j.1600-065X.1998.tb01429.x

Ma L, Qin T, Chu D, Cheng X, Wang J, Wang X, Wang P, Han H, Ren L, Aitken R et al (2016) Internal duplications of DH, JH, and C region genes create an unusual IgH gene locus in cattle. J Immunol 196(10):4358–4366. https://doi.org/10.4049/jimmunol.1600158

Article  CAS  PubMed  Google Scholar 

Mikocziova I, Greiff V, Sollid LM (2021) Immunoglobulin germline gene variation and its impact on human disease. Genes Immun 22(4):205–217. https://doi.org/10.1038/s41435-021-00145-5

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mitchell CD, Criscitiello MF (2020) Comparative study of cartilaginous fish divulges insights into the early evolution of primary, secondary and mucosal lymphoid tissue architecture. Fish Shellfish Immunol 107:435–443. https://doi.org/10.1016/j.fsi.2020.11.006

Article  CAS  PubMed  Google Scholar 

Morrissey KA, Wegrecki M, Praveena T, Hansen VL, Bu L, Sivaraman KK, Darko S, Douek DC, Rossjohn J, Miller RD et al (2021) The molecular assembly of the marsupial γμ T cell receptor defines a third T cell lineage. Science 371(6536):1383–1388. https://doi.org/10.1126/science.abe7070

Article  CAS  PubMed  Google Scholar 

Muyldermans S, Atarhouch T, Saldanha J, Barbosa JA, Hamers R (1994) Sequence and structure of VH domain from naturally occurring camel heavy chain immunoglobulins lacking light