Skip to main content
SpringerLink
Log in

Molecular Characterization of the Major Histocompatibility Complex Class Ia Gene in the Black-Spotted Frog, Pelophylax nigromaculata

  • Published:
Biochemical Genetics Aims and scope Submit manuscript

Abstract

The genes of the major histocompatibility complex (MHC) are attractive candidates for investigating the link between adaptive variation and individual fitness. We improved rapid amplification of cDNA ends to obtain the whole coding sequence of the MHC class Ia gene of the black-spotted frog (Pelophylax nigromaculata), the most common amphibian in China. We also used genome walking to characterize the partial introns adjacent to exon 3 of the MHC Ia gene. Based on the sequences obtained, we designed locus-specific primers to investigate the molecular polymorphisms of this species in southeast China. The MHC class Ia gene showed a high level of genetic diversity, indicating that this species retains a relatively high potential for survival, despite a population decline among frog species in general and many other amphibians.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Acevedo-Whitehouse K, Cunningham AA (2006) Is MHC enough for understanding wildlife immunogenetics? Trends Ecol Evol 21:433–438

    Article  PubMed  Google Scholar 

  • Babik W (2010) Methods for MHC genotyping in non-model vertebrates. Mol Ecol Resour 10:237–251

    Article  PubMed  CAS  Google Scholar 

  • Barribeau SM, Villinger J, Waldman B (2008) Major histocompatibility complex based resistance to a common bacterial pathogen of amphibians. PLoS One 3:e2692

    Article  PubMed  Google Scholar 

  • Beebee TJC, Griffiths RA (2005) The amphibian decline crisis: a watershed for conservation biology? Biol Conserv 125:271–285

    Article  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Bjorkman PJ, Saper MA, Samraoui B, Bennett WS, Strominger JL, Wiley DC (1987) The foreign antigen bing site and T cell recognition regions of class I histocompatibility antigens. Nat Immunol 329:512–518

    CAS  Google Scholar 

  • Bos DH, Waldman B (2006) Evolution by recombination and trans-species polymorphism in the MHC class I gene of Xenopus laevis. Mol Biol Evol 23:137–143

    Article  PubMed  CAS  Google Scholar 

  • Brito D (2008) Amphibian conservation: are we on the right track? Biol Conserv 141:2912–2917

    Article  Google Scholar 

  • Carey C, Cohen N, Rollins-Smith L (1999) Amphibian declines: an immunological perspective. Dev Comp Immunol 23:459–472

    Article  PubMed  CAS  Google Scholar 

  • Daszak P, Berger L, Cunningham AA, Hyatt AD, Green DE, Speare R (1999) Emerging infectious diseases and amphibian population declines. Emerg Infect Dis 5:735–748

    Article  PubMed  CAS  Google Scholar 

  • Edwards SV, Hedrick PW (1998) Evolution and ecology of MHC molecules: from genomics to sexual selection. Trends Ecol Evol 13:305–311

    Article  PubMed  CAS  Google Scholar 

  • Fei L, Hu S, Ye C, Huang YZ (2009) Fauna sinica: Amphibia, Anura Ranidae. Science Press, Beijing

    Google Scholar 

  • Flajnik MF, Kasahara M, Shum BP, Salter-Cid L, Taylor E, Du Pasquier L (1993) A novel type of class I gene organization in vertebrates: a large family of non-MHC-linked class I genes is expressed at the RNA level in the amphibian Xenopus. EMBO J 12:4385–4396

    PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Gonser RA, Collura RV (1996) Waste not, want not: toe-clips as a source of DNA. J Herpetol 30:445–447

    Article  Google Scholar 

  • Goyos A, Ohta Y, Guselnikov S, Robert J (2009) Novel nonclassical MHC class Ib genes associated with CD8 T cell development and thymic tumors. Mol Immunol 46:1775–1786

    Article  PubMed  CAS  Google Scholar 

  • Hauswaldt JS, Stuckas H, Pfautsch S, Tiedemann R (2007) Molecular characterization of MHC class II in a nonmodel anuran species, the fire-bellied toad Bombina bombina. Immunogenetics 59:479–491

    Article  PubMed  CAS  Google Scholar 

  • Hedrick PW (1998) Balancing selection and MHC. Genetica 104:207–214

    Article  PubMed  Google Scholar 

  • Hughes AL, Yeager M (1998) Natural selection at major histocompatibility complex loci of vertebrates. Annu Rev Genet 32:415–435

    Article  PubMed  CAS  Google Scholar 

  • Jeffery KJM, Bangham CRM (2000) Do infectious diseases drive MHC diversity? Microbes Infect 2:1335–1341

    Article  PubMed  CAS  Google Scholar 

  • Kelley J, Walter L, Trowsdale J (2005) Comparative genomics of major histocompatibility complexes. Immunogenetics 56:683–695

    Article  PubMed  CAS  Google Scholar 

  • Kiemnec-Tyburczy KM, Richmond JQ, Savage AE, Lips KR, Zamudio KR (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

    Article  PubMed  CAS  Google Scholar 

  • Klein J (1986) The natural history of the major histocompatibility complex. Wiley, New York

    Google Scholar 

  • Knapp LA (2005) The ABCs of MHC. Evol Anthropol 14:28–37

    Article  Google Scholar 

  • Kobari F, Sato K, Shum BP, Tochinai S, Katagiri M, Ishibashi T, Du Pasquier L, Flajnik MF, Kasahara M (1995) Exon-intron organization of Xenopus MHC class II β chain genes. Immunogenetics 42:376–385

    Article  PubMed  CAS  Google Scholar 

  • Liu YG, Whittier RF (1995) Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from PI and YAC clones for chromosome walking. Genomics 25:674–681

    Article  PubMed  CAS  Google Scholar 

  • Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26:2462–2463

    Article  PubMed  CAS  Google Scholar 

  • Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418–426

    PubMed  CAS  Google Scholar 

  • Nonaka M, Namikawa C, Kato Y, Sasaki M, Salter-Cid L, Flajnik MF (1997) Major histocompatibility complex gene mapping in the amphibian Xenopus implies a primordial organization. Proc Natl Acad Sci USA 94:5789–5791

    Article  PubMed  CAS  Google Scholar 

  • Ohta Y, Goetz W, Hossain MZ, Nonaka M, Flajnik MF (2006) Ancestral organization of the MHC revealed in the amphibian Xenopus. J Immunol 176:3674–3685

    PubMed  CAS  Google Scholar 

  • Peakall R, Smouse PE (2006) Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Article  Google Scholar 

  • Piertney S, Oliver M (2006) The evolutionary ecology of the major histocompatibility complex. Heredity 96:7–21

    PubMed  CAS  Google Scholar 

  • Radwan J, Biedrzycka A, Babik W (2010) Does reduced MHC diversity decrease viability of vertebrate populations? Biol Conserv 143:537–544

    Article  Google Scholar 

  • Roelants K, Gower DJ, Wilkinson M, Loader SP, Biju SD, Guillaume K, Moriau L, Bossuyt F (2007) Global patterns of diversification in the history of modern amphibians. Proc Natl Acad Sci USA 104:887–892

    Article  PubMed  CAS  Google Scholar 

  • Rousset F (2008) Genepop ‘007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8:103–106

    Article  PubMed  Google Scholar 

  • Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  • Savage AE, Zamudio KR (2011) MHC genotypes associate with resistance to a frog-killing fungus. Proc Natl Acad Sci USA 108:16705–16710

    Article  PubMed  CAS  Google Scholar 

  • Shum BP, Avila D, Du Pasquier L, Kasahara M, Flajnik MF (1993) Isolation of a classical MHC class I cDNA from an amphibian. J Immunol 151:5376–5386

    PubMed  CAS  Google Scholar 

  • Sommer S (2005) The importance of immune gene variability (MHC) in evolutionary ecology and conservation. Front Zool 2:16

    Article  PubMed  Google Scholar 

  • Spurgin LG, Richardson DS (2010) How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings. Proc Biol Sci 277:979–988

    Article  PubMed  CAS  Google Scholar 

  • Stuart SN, Chanson JS, Cox NA, Young BE, Rodrigues AS, Fischman DL, Waller RW (2004) Status and trends of amphibian declines and extinctions worldwide. Science 306:1783–1786

    Article  PubMed  CAS  Google Scholar 

  • Sunnucks P, Wilson ACC, Beheregaray LB, Zenger K, French J, Taylor AC (2000) SSCP is not so difficult: the application and utility of single-stranded conformation polymorphism in evolutionary biology and molecular ecology. Mol Ecol 9:1699–1710

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Terauchi R, Kahl G (2000) Rapid isolation of promoter sequences by TAIL-PCR: the 5′-flanking regions of Pal and Pgi genes from yams (Dioscorea). Mol Gen Genet 263:554–560

    Article  PubMed  CAS  Google Scholar 

  • Trowsdale J (2011) The MHC, disease and selection. Immunol Lett 137:1–8

    Article  PubMed  CAS  Google Scholar 

  • van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538

    Article  Google Scholar 

  • Wake DB, Vredenburg VT (2008) Are we in the midst of the sixth mass extinction? A view from the world of amphibians. Proc Natl Acad Sci USA 105:11466–11473

    Article  PubMed  CAS  Google Scholar 

  • Wan QH, Zhang P, Ni XW, Wu HL, Chen YY, Kuang YY, Ge YF, Fang SG (2011) A novel HURRAH protocol reveals high numbers of monomorphic MHC class II loci and two asymmetric multi-locus haplotypes in Père David’s deer. PLoS One 6:e14518

    Article  PubMed  CAS  Google Scholar 

  • Wegner K, Reusch T, Kalbe M (2003) Multiple parasites are driving major histocompatibility complex polymorphism in the wild. J Evol Biol 16:224–232

    Article  PubMed  CAS  Google Scholar 

  • Xie F, Liu HN, Stuart SN, Chanson JS, Cox NA, Fischman DL (2006) The overview of amphibians protection in China. Sci China C Life Sci 36:570–581

    Google Scholar 

  • Xu K, Zhu DZ, Wei Y, Schloegel LM, Chen XF, Wang XL (2010) Broad distribution of Ranavirus in free-ranging Rana dybowskii in Heilongjiang, China. EcoHealth 7:18–23

    Article  PubMed  Google Scholar 

  • Zhang RZ (2011) Zoogeography of China. Science Press, Beijing

    Google Scholar 

Download references

Acknowledgments

This work was supported by a grant from the National Natural Science Foundation of China (No. 31170349) and by the Fundamental Research Funds for the Central Universities of the People’s Republic of China.

Author information

Authors and Affiliations

  1. Key Laboratory of Conservation Biology for Endangered Wildlife, Ministry of Education and State Conservation Center for Gene Resources of Endangered Wildlife, and College of Life Sciences, Zhejiang University, Zijingang Campus, 388 Yu Hang Tang Road, Hangzhou, 310058, China

    Jie Gong, Qi-Peng Sun, Fei Xue, Sheng-Guo Fang & Qiu-Hong Wan

Authors
  1. Jie Gong
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Qi-Peng Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Fei Xue
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sheng-Guo Fang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Qiu-Hong Wan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Qiu-Hong Wan.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gong, J., Sun, QP., Xue, F. et al. Molecular Characterization of the Major Histocompatibility Complex Class Ia Gene in the Black-Spotted Frog, Pelophylax nigromaculata . Biochem Genet 51, 876–888 (2013). https://doi.org/10.1007/s10528-013-9614-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10528-013-9614-9

Keywords

Search

Navigation