Sequence Analysis of Major Histocompatibility Complex Class-II DQB1 (Patr-DQB1) Alleles in Chimpanzees by Polymerase Chain Reaction–Based Methods

Bak, Eun‐Jung; Ishii, Yoshiyuki; Omatsu, Tsutomu; Kyuwa, Shigeru; Tanoue, Tetsuya; Hayasaka, Ichirô; Yoshikawa, Yasuhiro

doi:10.1016/j.humimm.2006.04.016

Cited by 2 publications

(3 citation statements)

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“…As all PCR based methods, PCR-RFLP requires only a minute amount of DNA, and is fast and cheap. However its inherent limitation is the ability to interrogate only a fraction of sequence variation, and therefore PCR-RFLP has found only limited applications for MHC genotyping in non-model species (Wenink et al 1998;Bak et al 2006).…”

Section: Genotyping Methods Based On Interrogation Of Known Variationmentioning

confidence: 99%

Methods for MHC genotyping in non‐model vertebrates

Babik

2010

Molecular Ecology Resources

131

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Genes of the major histocompatibility complex (MHC) are considered a paradigm of adaptive evolution at the molecular level and as such are frequently investigated by evolutionary biologists and ecologists. Accurate genotyping is essential for understanding of the role that MHC variation plays in natural populations, but may be extremely challenging. Here, I discuss the DNA-based methods currently used for genotyping MHC in non-model vertebrates, as well as techniques likely to find widespread use in the future. I also highlight the aspects of MHC structure that are relevant for genotyping, and detail the challenges posed by the complex genomic organization and high sequence variation of MHC loci. Special emphasis is placed on designing appropriate PCR primers, accounting for artefacts and the problem of genotyping alleles from multiple, co-amplifying loci, a strategy which is frequently necessary due to the structure of the MHC. The suitability of typing techniques is compared in various research situations, strategies for efficient genotyping are discussed and areas of likely progress in future are identified. This review addresses the well established typing methods such as the Single Strand Conformation Polymorphism (SSCP), Denaturing Gradient Gel Electrophoresis (DGGE), Reference Strand Conformational Analysis (RSCA) and cloning of PCR products. In addition, it includes the intriguing possibility of direct amplicon sequencing followed by the computational inference of alleles and also next generation sequencing (NGS) technologies; the latter technique may, in the future, find widespread use in typing complex multilocus MHC systems.

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Section: Genotyping Methods Based On Interrogation Of Known Variationmentioning

confidence: 99%

Methods for MHC genotyping in non‐model vertebrates

Babik

2010

Molecular Ecology Resources

131

192

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“…However, contrary to Yerkes cb , this cohort may contain animals from different sub-species and/or hybrid animals (personal communication from the authors of [ 60 ]). Kuma wb , consisting of 19 wild-born individuals (of unknown origin, captured in the seventies) who were previously housed in research institutions in Japan and were further retired in the Kumamoto Primate Park, Japan [ 112 – 114 ]. Relatedness between animals is unknown.…”

Section: Methodsmentioning

confidence: 99%

“…Kuma wb , consisting of 19 wild-born individuals (of unknown origin, captured in the seventies) who were previously housed in research institutions in Japan and were further retired in the Kumamoto Primate Park, Japan [ 112 – 114 ]. Relatedness between animals is unknown.…”

Section: Methodsmentioning

confidence: 99%

Similar patterns of genetic diversity and linkage disequilibrium in Western chimpanzees (Pan troglodytes verus) and humans indicate highly conserved mechanisms of MHC molecular evolution

et al. 2020

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Background Many species are threatened with extinction as their population sizes decrease with changing environments or face novel pathogenic threats. A reduction of genetic diversity at major histocompatibility complex (MHC) genes may have dramatic effects on populations’ survival, as these genes play a key role in adaptive immunity. This might be the case for chimpanzees, the MHC genes of which reveal signatures of an ancient selective sweep likely due to a viral epidemic that reduced their population size a few million years ago. To better assess how this past event affected MHC variation in chimpanzees compared to humans, we analysed several indexes of genetic diversity and linkage disequilibrium across seven MHC genes on four cohorts of chimpanzees and we compared them to those estimated at orthologous HLA genes in a large set of human populations. Results Interestingly, the analyses uncovered similar patterns of both molecular diversity and linkage disequilibrium across the seven MHC genes in chimpanzees and humans. Indeed, in both species the greatest allelic richness and heterozygosity were found at loci A, B, C and DRB1, the greatest nucleotide diversity at loci DRB1, DQA1 and DQB1, and both significant global linkage disequilibrium and the greatest proportions of haplotypes in linkage disequilibrium were observed at pairs DQA1 ~ DQB1, DQA1 ~ DRB1, DQB1 ~ DRB1 and B ~ C. Our results also showed that, despite some differences among loci, the levels of genetic diversity and linkage disequilibrium observed in contemporary chimpanzees were globally similar to those estimated in small isolated human populations, in contrast to significant differences compared to large populations. Conclusions We conclude, first, that highly conserved mechanisms shaped the diversity of orthologous MHC genes in chimpanzees and humans. Furthermore, our findings support the hypothesis that an ancient demographic decline affecting the chimpanzee populations – like that ascribed to a viral epidemic – exerted a substantial effect on the molecular diversity of their MHC genes, albeit not more pronounced than that experienced by HLA genes in human populations that underwent rapid genetic drift during humans’ peopling history. We thus propose a model where chimpanzees’ MHC genes regenerated molecular variation through recombination/gene conversion and/or balancing selection after the selective sweep.

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Sequence Analysis of Major Histocompatibility Complex Class-II DQB1 (Patr-DQB1) Alleles in Chimpanzees by Polymerase Chain Reaction–Based Methods

Cited by 2 publications

References 42 publications

Methods for MHC genotyping in non‐model vertebrates

Methods for MHC genotyping in non‐model vertebrates

Similar patterns of genetic diversity and linkage disequilibrium in Western chimpanzees (Pan troglodytes verus) and humans indicate highly conserved mechanisms of MHC molecular evolution

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