Genomic V exons from whole genome shotgun data in reptiles

Immunogenetics

Volumn 66, Issue 7-8, 2014, Pages 479-492

  Olivieri, D N ^a   Von Haeften, B ^a   Sanchez Espinel C ^b   Faro, J ^c,d,e   Gambon Deza F ^d,f  

^a UNIVERSITY OF VIGO   (Spain)

^b Area of Immunology Faculty of Biology University of Vigo ^*  (Spain)

^c UNIVERSITY OF VIGO   (Spain)

^d Instituto Biomédico de Vigo IBIV   (Spain)

^e INSTITUTO GULBENKIAN DE CIÊNCIA   (Portugal)

^f HOSPITAL DO MEIXOEIRO   (Spain)

Author keywords

Immunoglobulin (IG); Immunologic repertoire; Reptile evolution; T cell receptor (TR); Variable (V) gene

Indexed keywords

T LYMPHOCYTE RECEPTOR;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; CROCODILIAN; EXON; GENE LOCUS; GENE SEQUENCE; GENETIC VARIABILITY; GENOME; GENOMICS; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; SNAKE; TURTLE;

AVES; CROCODYLIDAE (ALL CROCODILES); MAMMALIA; REPTILIA; SERPENTES; SQUAMATA; TESTUDINES; VERTEBRATA;

AMINO ACID SEQUENCE; ANIMALS; EVOLUTION, MOLECULAR; EXONS; GENES, IMMUNOGLOBULIN; GENES, T-CELL RECEPTOR; GENETIC VARIATION; GENOME; IMMUNOGENETIC PHENOMENA; IMMUNOGLOBULIN VARIABLE REGION; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; REPTILES; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 84904258139     PISSN: 00937711     EISSN: 14321211     Source Type: Journal    
DOI: 10.1007/s00251-014-0784-3     Document Type: Article

References (49)

1. Benton M (2005) Vertebrate Palaeontology. Blackwell, Oxford
2. Benton MJ, Donoghue PC (2007) Paleontological evidence to date the tree of life. Mol Biol Evol 24(1):26-53. doi:10.1093/molbev/msl150 (Pubitemid 46026279)
3. Bosc N, Lefranc MP (2003) The mouse (Mus musculus) T cell receptor alpha (TRA) and delta (TRD) variable genes. Dev Comp Immunol 27(6-7):465-497 (Pubitemid 36411907)
4. Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaSci 2(1):10. doi:10.1186/2047-217x-2-10
5. Cannon JP, Haire RN, Rast JP, Litman GW (2004) The phylogenetic origins of the antigen-binding receptors and somatic diversification mechanisms. Immunol Rev 200:12-22. doi:10.1111/j.0105-2896.2004.00166.x (Pubitemid 38998189)
6. Charlemagne J, Fellah JS, De Guerra A, Kerfourn F, Partula S (1998) Tcell receptors in ectothermic vertebrates. Immunol Rev 166:87-102
7. Danilova N, Amemiya CT (2009) Going adaptive: the saga of antibodies. Ann N Y Acad Sci 1168:130-155. doi:10.1111/j.1749-6632.2009.04881.x
8. deBraga M, Rieppel O (1997) Reptile phylogeny and the interrelationships of turtles. Zool J Linnean Soc 120:281-354
9. Flajnik MF, Kasahara M (2010) Origin and evolution of the adaptive immune system: genetic events and selective pressures. Nat Rev Genet 11(1):47-59. doi:10.1038/nrg2703
10. Gambon-Deza F, Sanchez Espinel C, Magadan Mompo S (2009) The immunoglobulin heavy chain locus in the reptile Anolis carolinensis. Mol Immunol 46(8 - 9):1679-1687. doi:10.1016/j.molimm.2009.02.019
11. Gambon-Deza F, Sanchez-Espinel C, Mirete-Bachiller S, Magadan-Mompo S (2012) Snakes antibodies. Dev Comp Immunol 38(1):1-9. doi:10.1016/j.dci.2012.03. 001
12. Giudicelli V, Lefranc MP (1999) Ontology for immunogenetics: the IMGT-ONTOLOGY. Bioinformatics (Oxford, England) 15(12):1047-1054 (Pubitemid 30142662)
13. Giudicelli V, Lefranc M (2012) IMGT-ONTOLOGY 2012. Front Genet 3:79. doi:10.3389/fgene.2012.00079
14. 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(Database Issue):D256-261. doi:10.1093/nar/gki010 (Pubitemid 40207873)
15. Glaberman S, Caccone A (2008) Species-specific evolution of class I MHC genes in iguanas (order: Squamata; subfamily: Iguaninae). Immunogenetics 60(7):371-382. doi:10.1007/s00251-008-0298-y
16. Glaberman S, Du Pasquier L, Caccone A (2008) Characterization of a nonclassical class I MHC gene in a reptile, the Galapagos marine iguana (Amblyrhynchus cristatus). PLoS One 3(8):e2859. doi:10.1371/journal.pone.0002859
17. Glaberman S, Moreno MA, Caccone A (2009) Characterization and evolution of MHC class II B genes in Galapagos marine iguanas (Amblyrhynchus cristatus). Dev Comp Immunol 33(8):939-947. doi:10.1016/j.dci.2009.03.003
18. Goecks J, Nekrutenko A, Taylor J (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11(8):R86. doi:10.1186/gb-2010-11-8-r86
19. Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27(2):221-224. doi:10. 1093/molbev/msp259
20. Hedges S, Kumar S (2009) The timetree of life. Oxford Univ Press, New York
21. Janes DE, Organ CL, Fujita MK, Shedlock AM, Edwards SV (2010) Genome evolution in Reptilia, the sister group of mammals. Annu Rev Genomics Hum Genet 11:239-264. doi:10.1146/annurevgenom-082509-141646
22. Lane J, Duroux P, Lefranc MP (2010) From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences. BMC Bioinforma 11:223. doi:10.1186/1471-2105-11-223
23. Laurin M (2012) Recent progress in paleontological methods for dating the Tree of Life. Front Genet 3:130. doi:10.3389/fgene.2012.00130
24. Laurin M, Girondot M (1999) Embryo retention in sarcopterygians, and the origin of the extra-embryonic membranes of the amniotic egg. Ann Sci Nat Zool 20:99-104
25. Laurin M, Reisz RR (1995) A reevaluation of early amniote phylogeny. Zool J Linnean Soc 113(2):165-223. doi:10.1111/j.1096-3642.1995.tb00932.x
26. Lefranc MP (2011) IMGT unique numbering for the variable (V), constant (C), and groove (G) domains of IG, TR, MH, IgSF, and MhSF. Cold Spring Harbor Protocols 2011(6):633-642. doi:10.1101/pdb.ip85
27. Lefranc MP (2014) Immunoglobulin and T cell receptor genes: IMGT((R)) and the birth and rise of immunoinformatics. Front Immunol 5:22. doi:10.3389/fimmu.2014.00022
28. Lefranc M, Lefranc G (2001a) The immunoglobulin factsbook. Academic, London
29. Lefranc MP, Lefranc G (2001b) The T cell receptor factsbook, 1st edn. Academic, London
30. Lefranc MP, Pommie C, Ruiz M, Giudicelli V, Foulquier E, Truong L, Thouvenin-Contet V, Lefranc G (2003) IMGTunique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev Comp Immunol 27(1):55-77 (Pubitemid 35449624)
31. Lefranc MP, Giudicelli V, Ginestoux C, Jabado-Michaloud J, Folch G, Bellahcene F, Wu Y, Gemrot E, Brochet X, Lane J, Regnier L, Ehrenmann F, Lefranc G, Duroux P (2009) IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res 37(Database Issue):D1006-1012. doi:10.1093/nar/gkn838
32. Li L, Wang T, Sun Y, Cheng G, Yang H, Wei Z, Wang P, Hu X, Ren L, Meng Q, Zhang R, Guo Y, Hammarstrom L, Li N, Zhao Y (2012) Extensive diversification of IgD-, IgY-, and truncated IgY(deltaFc)-encoding genes in the red-eared turtle (Trachemys scripta elegans). J Immunol (Baltimore, Md: 1950) 189(8):3995-4004. doi:10.4049/jimmunol.1200188
33. Magadan-Mompo S, Sanchez-Espinel C, Gambon-Deza F (2013a) IgH loci of American alligator and saltwater crocodile shed light on IgA evolution. Immunogenetics 65(7):531-541. doi:10.1007/s00251-013-0692-y
34. Magadan-Mompo S, Sanchez-Espinel C, Gambon-Deza F (2013b) Immunoglobulin genes of the turtles. Immunogenetics 65(3):227-237. doi:10.1007/s00251-012-0672- 7
35. Modesto SP, Anderson JS (2004) The phylogenetic definition of reptilia. Syst Biol 53(5):815-821. doi:10.1080/10635150490503026 (Pubitemid 39568280)
36. Narciso JE, Uy ID, Cabang AB, Chavez JF, Pablo JL, Padilla-Concepcion GP, Padlan EA (2011) Analysis of the antibody structure based on high-resolution crystallographic studies. New Biotechnol 28(5):435-447. doi:10.1016/j.nbt.2011. 03.012
37. Olivieri D, Faro J, von Haeften B, Sanchez-Espinel C, Gambon-Deza F (2013) An automated algorithm for extracting functional immunologic V-genes from genomes in jawed vertebrates. Immunogenetics 65(9):691-702. doi:10.1007/s00251-013-0715-8
38. Price MN, Dehal PS, Arkin AP (2010) FastTree 2 - approximately maximum-likelihood trees for large alignments. PLoS One 5(3):e9490. doi:10.1371/journal.pone.0009490
39. Reisz RR, Muller J (2004) Molecular timescales and the fossil record: a paleontological perspective. Trends Genetics: TIG 20(5):237-241. doi:10.1016/j.tig.2004.03.007 (Pubitemid 38510436)
40. Schroeder HW Jr, Cavacini L (2010) Structure and function of immunoglobulins. J Allergy Clin Immunol 125(2 Suppl 2):S41-52. doi:10.1016/j.jaci.2009.09.046
41. Sela-Culang I, Kunik V, Ofran Y (2013) The structural basis of antibody-antigen recognition. Front Immunol 4:302. doi:10.3389/fimmu.2013.00302
42. Sievers F, Higgins DG (2014) Clustal Omega, accurate alignment of very large numbers of sequences. MethodsMol Biol (Clifton, NJ) 1079:105-116. doi:10.1007/978-1-62703-646-7-6
43. Sun Y, Wei Z, Hammarstrom L, Zhao Y (2011) The immunoglobulin delta gene in jawed vertebrates: a comparative overview. Dev Comp Immunol 35(9):975-981. doi:10.1016/j.dci.2010.12.010
44. Sun Y, Wei Z, Li N, Zhao Y (2013) A comparative overview of immunoglobulin genes and the generation of their diversity in tetrapods. Dev Comp Immunol 39(1-2):103-109. doi:10.1016/j.dci.2012.02.008
45. 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(10):2731-2739. doi:10.1093/molbev/msr121
46. van Tuinen M, Hadly E (2004) Error in estimation of rate and time inferred from the early amniote fossil record and avian molecular clocks. J Mol Evol 59(2):267-276
47. Wei Z, Wu Q, Ren L, Hu X, Guo Y, Warr GW, Hammarstrom L, Li N, Zhao Y (2009) Expression of IgM, IgD, and IgY in a reptile, Anolis carolinensis. J Immunol (Baltimore, Md: 1950) 183(6):3858-3864. doi:10.4049/jimmunol.0803251
48. Wu Q, Wei Z, Yang Z, Wang T, Ren L, Hu X, Meng Q, Guo Y, Zhu Q, Robert J, Hammarstrom L, Li N, Zhao Y (2010) Phylogeny, genomic organization and expression of lambda and kappa immunoglobulin light chain genes in a reptile, Anolis carolinensis. Dev Comp Immunol 34(5):579-589. doi:10.1016/j.dci.2009.12. 019
49. Xu Z, Wang GL, Nie P (2009) IgM, IgD and IgY and their expression pattern in the Chinese soft-shelled turtle Pelodiscus sinensis. Mol Immunol 46(10):2124-2132. doi:10.1016/j.molimm.2009.03.028