Dataset Information

Sequencing of the core MHC region of black grouse (Tetrao tetrix) and comparative genomics of the galliform MHC.

ABSTRACT: BACKGROUND: The MHC, which is regarded as the most polymorphic region in the genomes of jawed vertebrates, plays a central role in the immune system by encoding various proteins involved in the immune response. The chicken MHC-B genomic region has a highly streamlined gene content compared to mammalian MHCs. Its core region includes genes encoding Class I and Class IIB molecules but is only ~92Kb in length. Sequences of other galliform MHCs show varying degrees of similarity as that of chicken. The black grouse (Tetrao tetrix) is a wild galliform bird species which is an important model in conservation genetics and ecology. We sequenced the black grouse core MHC-B region and combined this with available data from related species (chicken, turkey, gold pheasant and quail) to perform a comparative genomics study of the galliform MHC. This kind of analysis has previously been severely hampered by the lack of genomic information on avian MHC regions, and the galliformes is still the only bird lineage where such a comparison is possible. RESULTS: In this study, we present the complete genomic sequence of the MHC-B locus of black grouse, which is 88,390 bp long and contains 19 genes. It shows the same simplicity as, and almost perfect synteny with, the corresponding genomic region of chicken. We also use 454-transcriptome sequencing to verify expression in 17 of the black grouse MHC-B genes. Multiple sequence inversions of the TAPBP gene and TAP1-TAP2 gene block identify the recombination breakpoints near the BF and BLB genes. Some of the genes in the galliform MHC-B region also seem to have been affected by selective forces, as inferred from deviating phylogenetic signals and elevated rates of non-synonymous nucleotide substitutions. CONCLUSIONS: We conclude that there is large synteny between the MHC-B region of the black grouse and that of other galliform birds, but that some duplications and rearrangements have occurred within this lineage. The MHC-B sequence reported here will provide a valuable resource for future studies on the evolution of the avian MHC genes and on links between immunogenetics and ecology of black grouse.

SUBMITTER: Wang B

PROVIDER: S-EPMC3500228 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Sequencing of the core MHC region of black grouse (Tetrao tetrix) and comparative genomics of the galliform MHC.

Wang Biao B Ekblom Robert R Strand Tanja M TM Portela-Bens Silvia S Höglund Jacob J

BMC genomics 20121015

<h4>Background</h4>The MHC, which is regarded as the most polymorphic region in the genomes of jawed vertebrates, plays a central role in the immune system by encoding various proteins involved in the immune response. The chicken MHC-B genomic region has a highly streamlined gene content compared to mammalian MHCs. Its core region includes genes encoding Class I and Class IIB molecules but is only ~92Kb in length. Sequences of other galliform MHCs show varying degrees of similarity as that of ch ...[more]

PMID: 23066932

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Project description:As many other wild living species, black grouse Tetrao tetrix has to cope with anthropogenic disturbances in many habitats. Impacts of tourism and outdoor recreation on grouse species Tetraoninae have been subject to several studies in mountainous habitats in Central Europe and the United Kingdom. The geographically isolated and critically endangered black grouse population of Lower Saxony (North Germany) has been consistently monitored but beyond that poorly studied. This also applies to the key habitats of the nature reserve Lüneburg Heath (Lüneburger Heide) which, in turn, serves as a recreational area as well. In this study, the impact of tourism activity on habitat use of black grouse was investigated using data of GPS-tracked individuals. Additionally, visitor numbers on public and (usually undisturbed) closed routes were monitored using infrared light barriers. The spatio-temporal distribution of locations and the recreational activity were evaluated by linear mixed-effects models. Tagged individuals avoided the vicinity of public routes and avoiding distances were directly related to intensity of human activity. There was no seasonal change of black grouse habitat use alongside public routes. However, towards closed routes, significantly higher distances appeared during peak phases of visitor numbers (August and September), implying temporary increased disturbance levels within a key refuge area. Diurnal adaptation of habitat use was strongly dependent on the route density within the home range. Individuals used the vicinity of public trails at night and dawn but evaded these habitats during peak human activity around noon and afternoon. Recreational disturbances appeared to significantly affect the effective habitat availability for black grouse in the nature reserve. Visual cover by vegetation, however, seemed to diminish negative effects emerging from hiking trails. This provides an effective protective measure which requires minimal effort for the local conservation management.

Project description:BackgroundThe Major Histocompatibility Complex (MHC) is a cluster of genes involved in the vertebrate immune system and includes loci with an extraordinary number of alleles. Due to the complex evolution of MHC genes, alleles from different loci within the same MHC class can be very similar and therefore difficult to assign to separate loci. Consequently, single locus amplification of MHC genes is hard to carry out in species with recently duplicated genes in the same MHC class, and multiple MHC loci have to be genotyped simultaneously. Since amplified alleles have the same length, accurate genotyping is difficult. Reference Strand-Mediated Conformational Analysis (RSCA), which is increasingly used in studies of natural populations with multiple MHC genes, is a genotyping method capable to provide high resolution and accuracy in such cases.FindingsWe adapted the RSCA method to genotype multiple MHC class II B (BLB) genes in black grouse (Tetrao tetrix), a non-model galliform bird species, using a 96-Capillary Array Electrophoresis, the MegaBACE™ 1000 DNA Analysing System (GE Healthcare). In this study we used fluorescently labelled reference strands from both black grouse and hazel grouse and observed good agreement between RSCA and cloning/sequencing since 71 alleles were observed by cloning/sequencing and 76 alleles by RSCA among the 24 individuals included in the comparison. At the individual level however, there was a trend towards more alleles scored with RSCA (1-6 per individual) than cloning/sequencing (1-4 per individual). In 63% of the pair-wise comparison, the identical allele was scored in RSCA as in cloning/sequencing. Nine out of 24 individuals had the same number of alleles in RSCA as in cloning/sequencing. Our RSCA protocol allows a faster RSCA genotyping than presented in many other RSCA studies.ConclusionsIn this study, we have developed the RSCA typing method further to work on a 96-Capillary Array Electrophoresis (MegaBACE™ 1000). Our RSCA protocol can be applied to fast and reliable screening of MHC class II B diversity of black grouse populations. This will facilitate future large-scale population studies of black grouse and other galliformes species with multiple inseparable MHC loci.

Dataset Information

Sequencing of the core MHC region of black grouse (Tetrao tetrix) and comparative genomics of the galliform MHC.

Publications

Sequencing of the core MHC region of black grouse (Tetrao tetrix) and comparative genomics of the galliform MHC.

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