Rapid identification of major histocompatibility complex class I haplotypes using deep sequencing in an endangered Old World monkey

详细信息    查看全文

• 作者：Noah D. Simons ; Maria Jose Ruiz-Lopez ; Colin A. Chapman…
• 关键词：Major histocompatibility complex ; Next generation sequencing ; Primates ; Immunogenetics ; Red colobus
• 刊名：Conservation Genetics Resources
• 出版年：2016
• 出版时间：March 2016
• 年：2016
• 卷：8
• 期：1
• 页码：23-26
• 全文大小：727 KB
• 参考文献：Brearley G, Rhodes J, Bradley A, Baxter G, Seabrook L, Lunney D, Liu Y, McAlpine C (2013) Wildlife disease prevalence in human-modified landscapes. Biol Rev 88:427–442CrossRef PubMed
  Dodt M, Roehr JT, Ahmed R, Dieterich C (2012) FLEXBAR-flexible barcode and adapter processing for next-generation sequencing platforms. Biology 1(3):895–905CrossRef PubMed PubMedCentral
  Grubb P, Butynski TM, Oates JF, Bearder SK, Disotell TR, Groves CP, Struhsaker TT (2003) Assessment of the diversity of African primates. Int J Primatol 24:1301–1357CrossRef
  Karl JA, Heimbruch KE, Vriezen CE, Mironczuk CJ, Dudley DM, Wiseman RW, O’Connor DH (2014) Survey of major histocompatibility complex class II diversity in pig-tailed macaques. Immunogenetics 66(11):613–623CrossRef PubMed PubMedCentral
  Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25CrossRef PubMed PubMedCentral
  Magoc T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27(21):2957–2963CrossRef PubMed PubMedCentral
  Oates J, Davies G (1994) Colobine monkeys: their ecology, behaviour and evolution. Cambridge University Press, Cambridge, p 415
  Sommer S, Courtiol A, Mazzoni CJ (2013) MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout. BMC Genom 14(1):542CrossRef
  Struhsaker TT (2005) Conservation of red colobus and their habitats. Int J Primatol 26:525–538CrossRef
  Ting N (2008) Molecular systematics of red colobus monkeys (Procolobus [Piliocolobus]): understanding the evolution of an endangered primate. Ph.D. Dissertation. City University of New York Graduate Center
  Zagalska-Neubauer M, Babik W, Stuglik M, Gustafsson L, Cichoń M, Radwan J (2010) 454 sequencing reveals extreme complexity of the class II major histocompatibility complex in the collared flycatcher. BMC Evol Biol 10(1):395CrossRef PubMed PubMedCentral
  
• 作者单位：Noah D. Simons (1)
  Maria Jose Ruiz-Lopez (2)
  Colin A. Chapman (3)
  Tony L. Goldberg (4) (6)
  Julie A. Karl (6)
  Roger W. Wiseman (6)
  Patrick S. Bohn (6)
  David H. O’Connor (5) (6)
  Nelson Ting (1) (2)
  
  1. Department of Anthropology, University of Oregon, Eugene, OR, 97405, USA
  2. Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97405, USA
  3. Department of Anthropology, McGill School of Environment, Montreal, QC, H3A 2T7, Canada
  4. Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53725, USA
  6. Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
  5. Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53715, USA
  
• 刊物主题：Conservation Biology/Ecology; Plant Sciences; Animal Anatomy / Morphology / Histology; Evolutionary Biology;
• 出版者：Springer Netherlands
• ISSN：1877-7260

文摘

Immunogenetic data from wild primate populations have been difficult to obtain, due to logistic and methodological constraints. We applied a well-characterized deep sequencing method for MHC I typing, developed for macaques, to a population of wild red colobus to assess the feasibility of identifying MHC I-A/B haplotypes. Ten individuals produced sufficient data from blood and tissue samples to assign haplotypes. Eighty-two sequences were classified as red colobus MHC I alleles distributed across six MHC I loci. Individuals averaged ~13 k reads across six MHC I loci, with 83 % of all alleles representing either MHC I-A or MHC I-B loci. This study not only represents an important advance in the identification and genotyping of MHC in the endangered red colobus but also shows the potential for using this approach in other endangered wild primates.