Characterization of MHC class I in a long distance migratory wader, the Icelandic black-tailed godwit

High-Resolution Genotyping of Expressed Equine MHC Reveals a Highly Complex MHC Structure

The Major Histocompatibility Complex (MHC) genes play a key role in a number of biological processes, most notably in immunological responses. The MHCI and MHCII genes incorporate a complex set of highly polymorphic and polygenic series of genes, which, due to the technical limitations of previously available technologies, have only been partially characterized in non-model but economically important species such as the horse. The advent of high-throughput sequencing platforms has provided new opportunities to develop methods to generate high-resolution sequencing data on a large scale and apply them to the analysis of complex gene sets such as the MHC. In this study, we developed and applied a MiSeq-based approach for the combined analysis of the expressed MHCI and MHCII repertoires in cohorts of Thoroughbred, Icelandic, and Norwegian Fjord Horses. The approach enabled us to generate comprehensive MHCI/II data for all of the individuals (n = 168) included in the study, identifying 152 and 117 novel MHCI and MHCII sequences, respectively. There was limited overlap in MHCI and MHCII haplotypes between the Thoroughbred and the Icelandic/Norwegian Fjord horses, showcasing the variation in MHC repertoire between genetically divergent breeds, and it can be inferred that there is much more MHC diversity in the global horse population. This study provided novel insights into the structure of the expressed equine MHC repertoire and highlighted unique features of the MHC in horses.

Using de novo genome assembly and high-throughput sequencing to characterize the MHC region in a non-model bird, the Eurasian coot

Genes of the Major Histocompatibility Complex (MHC) form a key component of vertebrate adaptive immunity, as they code for molecules which bind antigens of intra- and extracellular pathogens (MHC class I and II, respectively) and present them to T cell receptors. In general, MHC genes are hyper-polymorphic and high MHC diversity is often maintained within natural populations (via balancing selection) and within individuals (via gene duplications). Because of its complex architecture with tandems of duplicated genes, characterization of MHC region in non-model vertebrate species still poses a major challenge. Here, we combined de novo genome assembly and high-throughput sequencing to characterize MHC polymorphism in a rallid bird species, the Eurasian coot Fulica atra. An analysis of genome assembly indicated high duplication rate at MHC-I, which was also supported by targeted sequencing of peptide-binding exons (at least five MHC-I loci genotyped). We found high allelic richness at both MHC-I and MHC-II, although signature of diversifying selection and recombination (gene conversion) was much stronger at MHC-II. Our results indicate that Eurasian coot retains extraordinary polymorphism at both MHC classes (when compared to other non-passerine bird species), although they may be subject to different evolutionary mechanism.

Allelic diversity and patterns of selection at the major histocompatibility complex class I and II loci in a threatened shorebird, the Snowy Plover (Charadrius nivosus)

Background

Understanding the structure and variability of adaptive loci such as the major histocompatibility complex (MHC) genes is a primary research goal for evolutionary and conservation genetics. Typically, classical MHC genes show high polymorphism and are under strong balancing selection, as their products trigger the adaptive immune response in vertebrates. Here, we assess the allelic diversity and patterns of selection for MHC class I and class II loci in a threatened shorebird with highly flexible mating and parental care behaviour, the Snowy Plover (Charadrius nivosus) across its broad geographic range.

Results

We determined the allelic and nucleotide diversity for MHC class I and class II genes using samples of 250 individuals from eight breeding population of Snowy Plovers. We found 40 alleles at MHC class I and six alleles at MHC class II, with individuals carrying two to seven different alleles (mean 3.70) at MHC class I and up to two alleles (mean 1.45) at MHC class II. Diversity was higher in the peptide-binding region, which suggests balancing selection. The MHC class I locus showed stronger signatures of both positive and negative selection than the MHC class II locus. Most alleles were present in more than one population. If present, private alleles generally occurred at very low frequencies in each population, except for the private alleles of MHC class I in one island population (Puerto Rico, lineage tenuirostris).

Conclusion

Snowy Plovers exhibited an intermediate level of diversity at the MHC, similar to that reported in other Charadriiformes. The differences found in the patterns of selection between the class I and II loci are consistent with the hypothesis that different mechanisms shape the sequence evolution of MHC class I and class II genes. The rarity of private alleles across populations is consistent with high natal and breeding dispersal and the low genetic structure previously observed at neutral genetic markers in this species.

Avian MHC Evolution in the Era of Genomics: Phase 1.0

Birds are a wonderfully diverse and accessible clade with an exceptional range of ecologies and behaviors, making the study of the avian major histocompatibility complex (MHC) of great interest. In the last 20 years, particularly with the advent of high-throughput sequencing, the avian MHC has been explored in great depth in several dimensions: its ability to explain ecological patterns in nature, such as mating preferences; its correlation with parasite resistance; and its structural evolution across the avian tree of life. Here, we review the latest pulse of avian MHC studies spurred by high-throughput sequencing. Despite high-throughput approaches to MHC studies, substantial areas remain in need of improvement with regard to our understanding of MHC structure, diversity, and evolution. Recent studies of the avian MHC have nonetheless revealed intriguing connections between MHC structure and life history traits, and highlight the advantages of long-term ecological studies for understanding the patterns of MHC variation in the wild. Given the exceptional diversity of birds, their accessibility, and the ease of sequencing their genomes, studies of avian MHC promise to improve our understanding of the many dimensions and consequences of MHC variation in nature. However, significant improvements in assembling complete MHC regions with long-read sequencing will be required for truly transformative studies.

AmpliSAS and AmpliHLA: Web Server Tools for MHC Typing of Non-Model Species and Human Using NGS Data

AmpliSAS and AmpliHLA are web server tools for automatic genotyping of MHC genes from high-throughput sequencing data. AmpliSAS is designed specifically to analyze amplicon sequencing data from non-model species and it is able to perform de-novo genotyping without any previous knowledge of the reference alleles. AmpliHLA is a human-specific version, it performs HLA typing by comparing sequenced variants against human reference alleles from the IMGT/HLA database. Here we describe four genotyping protocols: the first two use amplicon sequencing data to genotype the MHC genes of a passerine bird and human respectively; the third and fourth present the HLA typing of a human cell line starting from RNA and exome sequencing data respectively.