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Large-scale MHC class II genotyping of a wild lemur population by next generation sequencing
- Source :
- Immunogenetics
- Publication Year :
- 2012
- Publisher :
- Springer-Verlag, 2012.
-
Abstract
- The critical role of major histocompatibility complex (MHC) genes in disease resistance, along with their putative function in sexual selection, reproduction and chemical ecology, make them an important genetic system in evolutionary ecology. Studying selective pressures acting on MHC genes in the wild nevertheless requires population-wide genotyping, which has long been challenging because of their extensive polymorphism. Here, we report on large-scale genotyping of the MHC class II loci of the grey mouse lemur (Microcebus murinus) from a wild population in western Madagascar. The second exons from MHC-DRB and -DQB of 772 and 672 individuals were sequenced, respectively, using a 454 sequencing platform, generating more than 800,000 reads. Sequence analysis, through a stepwise variant validation procedure, allowed reliable typing of more than 600 individuals. The quality of our genotyping was evaluated through three independent methods, namely genotyping the same individuals by both cloning and 454 sequencing, running duplicates, and comparing parent–offspring dyads; each displaying very high accuracy. A total of 61 (including 20 new) and 60 (including 53 new) alleles were detected at DRB and DQB genes, respectively. Both loci were non-duplicated, in tight linkage disequilibrium and in Hardy–Weinberg equilibrium, despite the fact that sequence analysis revealed clear evidence of historical selection. Our results highlight the potential of 454 sequencing technology in attempts to investigate patterns of selection shaping MHC variation in contemporary populations. The power of this approach will nevertheless be conditional upon strict quality control of the genotyping data. peerReviewed
- Subjects :
- 0106 biological sciences
Quality Control
Linkage disequilibrium
Genotyping Techniques
Sequence analysis
Population
Immunology
Genes, MHC Class II
Molecular Sequence Data
Microcebus murinus
Major histocompatibility complex
010603 evolutionary biology
01 natural sciences
DNA sequencing
Linkage Disequilibrium
Genetic diversity
03 medical and health sciences
Genetics
Madagascar
Animals
Biomedicine
Gene Function
Human Genetics
Allergology
Cell Biology
education
Genotyping
030304 developmental biology
0303 health sciences
education.field_of_study
Original Paper
Polymorphism, Genetic
biology
Base Sequence
Lemur
Next generation (454) sequencing
Exons
Sequence Analysis, DNA
Positive selection
Genetic Loci
biology.protein
Pyrosequencing
MHC
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Immunogenetics
- Accession number :
- edsair.doi.dedup.....3da48600e77c19a6ae3121fa720d9580