Abstract
In this study, we aimed to assess the sequence diversity of major histocompatibility complex (MHC) class-II DRB gene at exon 2 in gazelles raised in Sanliurfa Province of Turkey. Twenty DNA samples isolated from gazelles (Gazella subgutturosa) were used for sequencing exon 2 of MHC class-II DRB gene. Target region was amplified by polymerase chain reaction (PCR) and their products were directly sequenced. Nine of these 20 samples yielded unambiguously readable sequences. Three of the nine samples were homozygotes and each showed different sequences. A 262-bp sequence obtained from the three homozygote samples were submitted to GenBank (accession numbers: KC309405, KC309406 and KC309407). Using an allele specific PCR, we detected 10 additional haplotypes. Among 13 haplotypes, 45 nucleotide positions were polymorphic and most of the polymorphic nucleotide positions localized at peptide-binding region (PBR). Rates of nonsynonymous substitutions were significantly higher than synonymous substitutions at PBR. Phylogenetic analysis of the haplotypes showed that 10 haplotypes of the gazelles were clustered together while three were clustered with ovine and bovine haplotypes. The results indicated that at least 13 haplotypes at exon 2 of MHC class-II DRB gene were showing high degree of nucleotide and amino acid diversity, and certain haplotypes of G. subgutturosa were more similar to haplotypes from sheep or cattle than to each other. Rates of synonymous and nonsynonymous substitutions suggested that positive selection was a driving force for diversity at this locus in G. subgutturosa.
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs12041-018-0974-0/MediaObjects/12041_2018_974_Fig1_HTML.png)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs12041-018-0974-0/MediaObjects/12041_2018_974_Fig2_HTML.png)
Similar content being viewed by others
References
Amills M., Jiménez N., Jordana J., Riccardi A., Fernandez-Arias A., Guiral J. et al. 2004 Low diversity in the major histocompatibility complex class II DRB1 gene of the Spanish ibex, Capra pyrenaica. Heredity 93, 266–272.
Ballingall K. T., Herrmann-Hoesing L., Robinson J., Marsh S. G. E. and Stear M. J. 2011 A single nomenclature and associated database for alleles at the major histocompatibility complex class II DRB1 locus of sheep. Tissue Antigens 77, 546–553.
Bärmann E. V., Rössner G. E. and Wörheide G. 2013 A revised phylogeny of Antilopini (Bovidae, Artiodactyla) using combined mitochondrial and nuclear genes. Mol. Phylogenet. Evol. 67, 484–493.
Brown J. H., Jardetzky T. S., Gorga J. C., Stern L. J., Urban R. G., Strominger J. L. et al. 1993 Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature 64, 33–39.
De S., Singh R. K. and Brahma B. 2011 Allelic diversity of major histocompatibility complex class II DRB gene in Indian cattle and buffalo. Mol. Biol. Int. 2011, 1–7.
Edwards S. V. and Hedrick P. W. 1998 Evolution and ecology of MHC molecules: from genomics to sexual selection. Trends. Ecol. Evol. 13, 305–311.
Griesinger I. 1997 Vergleichende Darstellung von DNA-Varianten im DRB-Gen des MHCs bei Schaf- und Ziegenrassen verschiedener Regionen. Ph.D. Thesis, Universität Hohenheim.
Gürler S. 2009 The following report on the reintroduction project of gazelle in Sanliurfa. Rapor No: 2009 – I, II Çevre ve Orman Bakanlığı Doğa Koruma ve Milli Parklar Genel Müdürlüğü (in Turkish).
Gürler S., Bozkaya F., Özüt D. and Durmuş M. 2015 Some morphological characteristics and neonatal weights of reintroduced gazelle (Gazella subgutturosa) in Turkey. Turk. J. Zool. 39, 458–466.
Gustafsson K. and Andersson L. 1994 Structure and polymorphism of horse MHC class II DRB genes: convergent evolution in the antigen binding site. Immunogenetics 39, 355–358.
Hall T. A. 1999 BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Res. 4, 95–98.
Hedrick P. W., Parker K. M., Gutiérrez-Espeleta G. A., Rattink A. and Lievers K. 2000 Major histocompatibility complex variation in the Arabian oryx. Evolution 54, 2145–2151.
Hughes A. L. and Nei M. 1989 Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proc. Natl. Acad. Sci. USA 86, 958–962.
Jukes T. H. and Cantor C. R. 1969 Evolution of protein molecules. In Mammalian protein metabolism (ed. H. N. Munro). Academic Press, New York.
Kankılıç T., Özüt D., Gürler Ş., Kence M., Bozkaya F. and Kence A. 2012 Rediscovery of a new mountain gazelle population and clarification of taxonomic status of the genus Gazella in Turkey using mtDNA sequencing. Folia. Zool. 61, 129–137.
Klein J., Sato A., Nagl S. and O’hUigín C. 1998 Molecular trans-species polymorphism. Ann. Rev. Ecol. Syst. 29, 1-21+cl.
Kurtz J., Kalbe M., Aeschlimann P. B., Häberli M. A., Wegner K. M., Reusch T. B. et al. 2004 Major histocompatibility complex diversity influences parasite resistance and innate immunity in sticklebacks. Proc. R. Soc. London B 271, 197–204.
Lochmiller R. L. 1996 Immunocompetence and animal population regulation. Oikos 76, 594–602.
Mallon D. P. and Kingswood S. C. 2001 Antelopes part 4: North Africa, the Middle East, and Asia global survey and regional action plans. SSC Antelope Specialist Group IUCN, Gland, Switzerland and Cambridge, UK.
Mainguy J., Worley K., Côté S. D. and Coltman D. W. 2007 Low MHC DRB class II diversity in the mountain goat: past bottlenecks and possible role of pathogens and parasites. Conserv. Genet. 8, 885–891.
Mikko S., Røed K., Schmutz S. and Andersson L. 1999 Monomorphism and polymorphism at Mhc DRB loci in domestic and wild ruminants. Immunol. Rev. 167, 169–178.
Murtskhvaladze M., Gurielidze Z., Kopaliani N. and Tarkhnishvili D. 2012 Gene introgression between Gazella subgutturosa and G. marica: limitations of maternal inheritance analysis for species identification with conservation purposes. Acta Theriol. 57, 383–386.
Nei M. and Gojobori T. 1986 Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418–426.
Nei M. and Kumar S. 2000 Molecular evolution and phylogenetics. Oxford University Press, New York.
O’Brien S. J. and Evermann J. F. 1988 Interactive influence of infectious disease and genetic diversity in natural populations. Trends. Ecol. Evol. 3, 254–259.
Outteridge P. M., Andersson L., Douch P. G. C., Green R. S., Gwakisa P. S., Hohenhaus M. A. et al. 1996 The PCR ty** of MHC-DRB genes in the sheep using primers for an intronic microsatellite: application to nematode parasite resistance. Immunol. Cell Biol. 74, 330–336.
Paterson S., Wilson K. and Pemberton J. M. 1998 Major histocompatibility complex variation associated with juvenile survival and parasite resistance in a large unmanaged ungulate population (Ovis aries L.). Proc. Natl. Acad. Sci. USA 95, 3714–3719.
Piertney S. B. and Oliver M. K. 2006 The evolutionary ecology of the major histocompatibility complex. Heredity 96, 7–21.
Radwan J., Kawałko A., Wojcik J. M. and Babik W. 2007 MHC-DRB3 variation in a free-living population of the European bison, Bison bonasus. Mol. Ecol. 16, 531–540.
Rebholz W. and Harley E. 1999 Phylogenetic relationships in the bovid subfamily Antilopinae based on mitochondrial DNA sequences. Mol. Phylogenet. Evol. 12, 87–94.
Schaschl H., Goodman S. J. and Suchentrunk F. 2004 Sequence analysis of the MHC class II DRB alleles in Alpine chamois (Rupicapra r. rupicapra). Dev. Comp. Immunol. 28, 265–277.
Schwaiger F. W., Buitkamp J., Weyers E. and Epplen J. T. 1993 Ty** of artiodactyl MHC-DRB genes with the help of intronic simple repeated DNA sequences. Mol. Ecol. 2, 55–59.
Spurgin L. G. and Richardson D. S. 2010 How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings. Proc. R. Soc. London B 277, 979–988.
Tamura K. and Nei M. 1993 Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512–526.
Tamura K., Peterson D., Peterson N., Stecher G., Nei M. and Kumar S. 2011 MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731–2739.
Turan N. 1977 Report on the protection and restoration of gazelle (Gazella subgutturosa) in Turkey. Turkish Department of Game-Wildlife: 7 (in Turkish).
Turan N. 1984 Türkiyenin Av ve Yaban Hayvanları Memeliler. Ankara Turkey. Ar Yayınevi (in Turkish).
Van Den Bussche R. A., Hoofer S. R. and Lochmiller R. L. 1999 Characterization of Mhc-DRB allelic diversity in white-tailed deer (Odocoileus virginianus) provides insight into Mhc-DRB allelic evolution within Cervidae. Immunogenetics 49, 429–437.
Wacher T., Wronski T., Hammond R. L., Winney B., Blacket M. J., Hundertmark K. J. et al. 2011 Phylogenetic analysis of mitochondrial DNA sequences reveals polyphyly in the goitred gazelle (Gazella subgutturosa). Conserv. Genet. 12, 827–831.
Yao G., Zhu Y., Wan Q. H. and Fang S. G. 2015 Major histocompatibility complex class II genetic variation in forest musk deer (Moschus berezovskii) in China. Anim. Genet. 46, 535–543.
Zachos F. E., Karami M., Ibenouazi Z., Hartl G. B., Eckert I. and Kirschning J. 2010 First genetic analysis of a free-living population of the threatened goitered gazelle (Gazella subgutturosa). Mam. Biol. 75, 277–282.
Acknowledgements
This study was approved by Turkish General Directorate of Nature Protection and National Parks (approval number: 30057506-430.99-194703). We thank Turkish General Directorate of Nature Protection and National Parks for their technical support.
Author information
Authors and Affiliations
Corresponding author
Additional information
Corresponding editor: Indrajit Nanda
Rights and permissions
About this article
Cite this article
Bozkaya, F., Gürler, Ş. Sequence diversity of MHC class-II DRB gene in gazelles (Gazella subgutturosa) raised in Sanliurfa of Turkey. J Genet 97, 897–903 (2018). https://doi.org/10.1007/s12041-018-0974-0
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12041-018-0974-0