Characterization of MHC class IA in the endangered southern corroboree frog

Abstract

Southern corroboree frogs (Pseudophryne corroboree) have declined to near extinction in the wild after the emergence of the amphibian chytrid fungus Batrachochytrium dendrobatidis in southeastern Australia in the 1980s. A major captive breeding and reintroduction program is underway to preserve this iconic species, but improving resistance to B. dendrobatidis would help the wild population to be self-sustaining. Using 3′ and 5′ rapid amplification of complementary DNA ends (RACE), we characterized the major histocompatibility complex (MHC) class IA locus in this species. We then used sequences generated from RACE to design primers to amplify the peptide-binding region (PBR) of this functional genetic marker. Finally, we analysed the diversity, phylogeny, and selection patterns of PBR sequences from four P. corroboree populations and compared this with other amphibian species. We found moderately high MHC class IA genetic diversity in this species and evidence of strong positive and purifying selection at sites that are associated with putative PBR pockets in other species, indicating that this gene region may be under selection for resistance to Bd. Future studies should focus on identifying alleles associated with Bd resistance in P. corroboree by performing a Bd laboratory challenge study to confirm the functional importance of our genetic findings and explore their use in artificial selection or genetic engineering to increase resistance to chytridiomycosis.

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References

  1. Aguilar A, Roemer G, Debenham S, Binns M, Garcelon D, Wayne RK (2004) High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal. Proc Natl Acad Sci U S A 101:3490–3494. doi:10.1073/pnas.0306582101

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  2. Aguilar JR-d, Westerdahl H, Puente JM-d, Tomás G, Martínez J, Merino S (2016) MHC-I provides both quantitative resistance and susceptibility to blood parasites in blue tits in the wild. J Avian Biol. doi:10.1111/jav.00830

    Google Scholar 

  3. Ashkenazi A, Dixit VM (1998) Death receptors: signaling and modulation. Science 281:1305–1308

    CAS  Article  PubMed  Google Scholar 

  4. Barribeau SM, Villinger J, Waldman B (2008) Major histocompatibility complex based resistance to a common bacterial pathogen of amphibians. PLoS One 3:e2692. doi:10.1371/journal.pone.0002692

    Article  PubMed  PubMed Central  Google Scholar 

  5. Bataille A, Cashins SD, Grogan L, Skerratt LF, Hunter D,l McFadden M, Scheele B. Brannelly LA, Macris A, Harlow PS, Bell S,  Berger L, Waldman B (2015) Susceptibility of amphibians to chytridiomycosis is associated with MHC class II conformation. Proc R Soc Lond B Biol Sci 282:20143127

  6. Bernatchez L, Landry C (2003) MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years? J Evol Biol 16:363–377

    CAS  Article  PubMed  Google Scholar 

  7. Brannelly LA, Berger L, Marrantelli G, Skerratt LF (2015) Low humidity is a failed treatment option for chytridiomycosis in the critically endangered southern corroboree frog. Wildl Res 42:44–49

    CAS  Article  Google Scholar 

  8. Brannelly LA, Webb R, Skerratt LF, Berger L (2016) Amphibians with infectious disease increase their reproductive effort: evidence for the terminal investment hypothesis. Open Biology 6. doi:10.1098/rsob.150251

  9. Brannelly LA (2016) Investigating disease ecology, pathogenesis and population persistence of frogs threatened by chytridiomycosis to improve management outcomes. Master’s Thesis, James Cook University.

  10. Delport W, Poon AF, Frost SD, Pond SLK (2010) Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26:2455–2457

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  11. Didinger C, Eimes JA, Lillie M, Waldman B (2017) Multiple major histocompatibility complex class I genes in Asian anurans: ontogeny and phylogeny. Dev Comp Immunol (in press)

  12. Ellison AR, Tunstall T, Direnzo GV, Hughey MC, Rebollar EA, Belden LK, Harris RN, Ibanez R, Lips KR, Zamudio KR (2014) More than skin deep: functional genomic basis for resistance to amphibian chytridiomycosis. Biol Evol 7:286–298

  13. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  14. Flajnik MF, Ohta Y, Greenberg AS, Salter-Cid L, Carrizosa A, Du Pasquier L, Kasahara M (1999) Two ancient allelic lineages at the single classical class I locus in the Xenopus MHC. J Immunol 163:3826–3833

    CAS  PubMed  Google Scholar 

  15. Galan M, Guivier E, Caraux G, Charbonnel N, Cosson J-F (2010) A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies. BMC Genomics 11:296

    Article  PubMed  PubMed Central  Google Scholar 

  16. Goldsby RA, Osborne BA, Kuby J. (2002) Immunology, 5th edn, WH Freeman, San Francisco 

  17. Hunter D (2012) National Recovery Plan for the southern corroboree frog Pseudophryne corroboree and northern corroboree frog Pseudophryne pengilleyi. Office of Environment and Heritage (NSW), Hurstville

    Google Scholar 

  18. Hunter D, Osborne W, Smith M, McDougall K (2009) Breeding habitat use and the future management of the critically endangered southern corroboree frog. Ecol Manag Restor 10:S103–S109. doi:10.1111/j.1442-8903.2009.00461.x

  19. Hunter D, Marantelli G, McFadden M, Harlow P, Scheele B, Pietsch R (2010a) Assessment of re-introduction methods for the southern corroboree frog in the Snowy Mountains region of Australia. Global re-introduction perspectives: additional case-studies from around the globe IUCN/SSC Reintroduction Specialist Group, Abu Dhabi. 72–76

  20. Hunter DA, Speare R, Marantelli G, Mendez D, Pietsch R, Osborne W (2010b) Presence of the amphibian chytrid fungus Batrachochytrium dendrobatidis in threatened corroboree frog populations in the Australian Alps. Dis Aquat Org 92:209–216

    Article  PubMed  Google Scholar 

  21. Janeway CA, Travers P, Walport M, Capra JD (2005) Immunobiology: the immune system in health and disease, 5th edn. Garland Press, New York

    Google Scholar 

  22. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Computer applications in the biosciences: CABIOS 8:275–282

    CAS  PubMed  Google Scholar 

  23. Kagi D, Vignaux F, Ledermann B, Burkl K, Depraetere V, Nagata S, Hengartner H, Golstein P (1994) Fas and perforin pathways as major mechanisms of T cell-mediated cytotoxicity. Science 265:528–530

  24. Kiemnec-Tyburczy K, Richmond J, Savage A, Lips K, Zamudio K (2012) Genetic diversity of MHC class I loci in six non-model frogs is shaped by positive selection and gene duplication. Heredity 109:146–155

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  25. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    CAS  Article  PubMed  Google Scholar 

  26. Klein J, Figueroa F (1986) Evolution of the major histocompatibility complex. Crit Rev Immunol 6:295-386

  27. Kosakovsky Pond SL, Frost SD (2005) Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 22:1208–1222. doi:10.1093/molbev/msi105

    Article  PubMed  Google Scholar 

  28. Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD (2006) Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol 23:1891–1901. doi:10.1093/molbev/msl051

    Article  PubMed  Google Scholar 

  29. Kosch TA, Bataille A, Didinger C, Eimes JA, Rodríguez-Brenes S, Ryan MJ, Waldman B (2016) Major histocompatibility complex selection dynamics in pathogen-infected túngara frog (Physalaemus pustulosus) populations. Biol Lett 12. doi:10.1098/rsbl.2016.0345

  30. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. doi:10.1093/molbev/msw054

    PubMed Central  Google Scholar 

  31. Lees C, McFadden M, Hunter D (2013) Genetic management of southern corroboree frogs: workshop report and plan. IUCN Conservation Breeding Specialist Group, Apple Valley, MN

    Google Scholar 

  32. Lillie M, Shine R, Belov K (2014) Characterisation of major histocompatibility complex class I in the Australian cane toad, Rhinella marina. PLoS One 9:e102824

    Article  PubMed  PubMed Central  Google Scholar 

  33. Matsumura M, Fremont DH, Peterson PA, Wilson IA (1992) Emerging principles for the recognition of peptide antigens by MHC class I molecules. Science 257:927–934

    CAS  Article  PubMed  Google Scholar 

  34. McFadden M, Hobbs R, Marantelli G, Harlow P, Banks C, Hunter D (2013) Captive management and breeding of the critically endangered southern corroboree frog (Pseudophryne corroboree)(Moore 1953) at Taronga and Melbourne zoos. Amphib Reptile Conserv 5:70–87

  35. Morgan MJ, Hunter D, Pietsch R, Osborne W, Keogh JS (2008) Assessment of genetic diversity in the critically endangered Australian corroboree frogs, Pseudophryne corroboree and Pseudophryne pengilleyi, identifies four evolutionarily significant units for conservation. Mol Ecol 17:3448–3463

    PubMed  Google Scholar 

  36. Murray KA et al (2011) Assessing spatial patterns of disease risk to biodiversity: implications for the management of the amphibian pathogen, Batrachochytrium dendrobatidis. J Appl Ecol 48:163–173

    Article  Google Scholar 

  37. Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Kosakovsky Pond SL (2012) Detecting individual sites subject to episodic diversifying selection. PLoS Genet 8:e1002764. doi:10.1371/journal.pgen.1002764

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  38. Osborne W, Norman J (1991) Conservation genetics of corroboree frogs, Pseudophryne corroboree Moore (Anura, Myobatrachidae): population subdivision and genetic-divergence. Austral Zool 39:285–297

  39. Raffel TR, Rohr JR, Kiesecker JM, Hudson PJ (2006) Negative effects of changing temperature on amphibian immunity under field conditions. Funct Ecol 20:819–828. doi:10.1111/j.1365-2435.2006.01159.x

    Article  Google Scholar 

  40. Raffel TR, Romansic JM, Halstead NT, McMahon TA, Venesky MD, Rohr JR (2012) Disease and thermal acclimation in a more variable and unpredictable climate. Nat Clim Chang 3:146–151. doi:10.1038/nclimate1659

    Article  Google Scholar 

  41. Richards-Zawacki CL (2010) Thermoregulatory behaviour affects prevalence of chytrid fungal infection in a wild population of Panamanian golden frogs. Proc R Soc B 277:519–528. doi:10.1098/rspb.2009.1656

  42. Richmond JQ, Savage AE, Zamudio KR, Rosenblum EB (2009) Toward immunogenetic studies of amphibian chytridiomycosis: linking innate and acquired immunity. Bioscience 59:311–320. doi:10.1525/bio.2009.59.4.9

    Article  Google Scholar 

  43. Roilides E, Dimitriadou-Georgiadou A, Sein T, Kadiltsoglou I, Walsh TJ (1998) Tumor necrosis factor alpha enhances antifungal activities of polymorphonuclear and mononuclear phagocytes against Aspergillus fumigatus. Infect Immun 66:5999–6003

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Savage AE, Zamudio KR (2011) MHC genotypes associate with resistance to a frog-killing fungus. Proc Natl Acad Sci U S A 108:16705–16710. doi:10.1073/pnas.1106893108

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  45. Savage AE, Zamudio KR (2016) Adaptive tolerance to a pathogenic fungus drives major histocompatibility complex evolution in natural amphibian populations. Proc R Soc B 283. doi:10.1098/rspb.2015.3115

  46. Scheele BC, Hunter DA, Brannelly LA, Skerratt LF, Driscoll DA (2016) Reservoir-host amplification of disease impact in an endangered amphibian. Conserv Biol. doi:10.1111/cobi.12830

  47. Scheele BC, Hunter DA, Grogan LF, Berger L, Kolby JE, McFadden MS, Marantelli G, Skerratt LF, Driscoll DA (2014) Interventions for Reducing Extinction Risk in Chytridiomycosis‐Threatened Amphibians. Conserv Biol 28:1195–1205. doi:10.1111/cobi.12322

  48. Scheffler K, Martin DP, Seoighe C (2006) Robust inference of positive selection from recombining coding sequences. Bioinformatics 22:2493–2499. doi:10.1093/bioinformatics/btl427

    CAS  Article  PubMed  Google Scholar 

  49. Scotto-Lavino E, Du G, Frohman MA (2006a) 3′ end cDNA amplification using classic RACE. Nat Protoc 1:2742–2745. doi:10.1038/nprot.2006.481

    CAS  Article  PubMed  Google Scholar 

  50. Scotto-Lavino E, Du G, Frohman MA (2006b) 5′ end cDNA amplification using classic RACE. Nat Protoc 1:2555–2562. doi:10.1038/nprot.2006.480

    CAS  Article  PubMed  Google Scholar 

  51. Stevens DA, Brummer E, Clemons Karl V (2006) Interferon-γ as an antifungal. J Infect Dis 194:S33–S37. doi:10.1086/505357

    CAS  Article  PubMed  Google Scholar 

  52. Teacher AGF, Garner TWJ, Nichols RA (2009) Evidence for directional selection at a novel major histocompatibility class I marker in wild common frogs (Rana temporaria) exposed to a viral pathogen (Ranavirus). PLoS One 4:e4616. doi:10.1371/journal.pone.0004616

    Article  PubMed  PubMed Central  Google Scholar 

  53. Wang Y, Qiu M, Yang J, Zhao X, Wang Y, Zhu Q, Liu Y (2014) Sequence variations of the MHC class I gene exon 2 and exon 3 between infected and uninfected chickens challenged with Marek’s disease virus. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 21:103–109. doi:10.1016/j.meegid.2013.10.020

    CAS  Article  PubMed  Google Scholar 

  54. Zhang C, Anderson A, DeLisi C (1998) Structural principles that govern the peptide-binding motifs of class I MHC molecules1. J Mol Biol 281:929–947. doi:10.1006/jmbi.1998.1982

    CAS  Article  PubMed  Google Scholar 

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Acknowledgements

We thank Gerry Marantelli of the Amphibian Research Centre for providing the P. corroboree used in this study. Funding was provided by the Australian Research Council grants LP110200240 and FT100100375, the National Research Foundation of Korea grant 2015R1D1A1A01057282 (to B.W.) funded by the government of the Republic of Korea (MOE), the Taronga Conservation Society, and the New South Wales Office of Environment and Heritage.

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Correspondence to Tiffany A. Kosch.

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The authors declare that they have no conflict of interest. Ethical approval was granted by James Cook University for this study under application A1875, entitled “Innate and adaptive immune mechanisms against amphibian chytrid fungus and non-chemotherapeutic treatment methods”.

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Kosch, T.A., Eimes, J.A., Didinger, C. et al. Characterization of MHC class IA in the endangered southern corroboree frog. Immunogenetics 69, 165–174 (2017). https://doi.org/10.1007/s00251-016-0965-3

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Keywords

  • Major histocompatibility complex
  • Pseudophryne corroboree
  • Batrachochytrium dendrobatidis
  • Genetic variation
  • Chytrid fungus
  • Amphibian declines