Molecular characterization of major histocompatibility complex class I genes from the giant panda (Ailuropoda melanoleuca)

Using PacBio SMRT data for identification of class I MHC alleles in a wildlife species, Zalophus californianus (California sea lion)

High allelic polymorphism and association with disease susceptibility has made the genes encoding major histocompatibility complex (MHC) antigen presentation molecules in humans, domesticated animals, and wildlife species of wide interest to ecologists, evolutionary biologists, and health specialists. The often multifaceted polygenism and extreme polymorphism of this immunogenetic system have made it especially difficult to characterize in non-model species. Here we compare and contrast the workflows of traditional Sanger sequencing of plasmid-cloned amplicons to Pacific Biosciences SMRT circular consensus sequencing (CCS) in their ability to capture alleles of MHC class I in a wildlife species where characterization of these genes was absent. We assessed two California sea lions (Zalophus californianus), a species suffering from a high prevalence of an aggressive cancer associated with a sexually transmitted gamma herpesvirus. In this pilot study, SMRT CCS proved superior in identifying more alleles from each animal than the more laborious plasmid cloning/Sanger workflow (12:7, 10:7), and no alleles were identified with the cloning/Sanger approach that were not identified by SMRT CCS. We discuss the advantages and disadvantages of each approach including cost, allele rarefaction, and sequence fidelity.

Crystal structure of the giant panda MHC class I complex: First insights into the viral peptide presentation profile in the bear family

The viral cytotoxic T lymphocyte (CTL) epitope peptides presented by classical MHC-I molecules require the assembly of a peptide-MHC-I-β2m (pMHC-I) trimolecular complex for T cell receptor (TCR) recognition, which is the critical activation link for triggering antiviral T cell immunity. Research on T cell immunology in the Ursidae family, especially structural immunology, is still lacking. In this study, the structure of the key trimolecular complex pMHC-I, which binds a peptide from canine distemper virus, was solved for the first time using giant panda as a representative species of Ursidae. The structural characteristics of the giant panda pMHC-I complex (pAime-128), including the unique pockets in the peptide-binding groove (PBG), were analyzed in detail. Comparing the pAime-128 to others in the bear family and extending the comparison to other mammals revealed distinct features. The interaction between MHC-I and β2m, the features of pAime-128 involved in TCR docking and cluster of differentiation 8 (CD8) binding, the anchor sites in the PBG, and the CTL epitopes of potential viruses that infect pandas were clarified. Unique features of pMHC-I viral antigen presentation in the panda were revealed by solving the three-dimensional (3D) structure of pAime-128. The distinct characteristics of pAime-128 indicate an unusual event that emerged during the evolution of the MHC system in the bear family. These results provide a new platform for research on panda CTL immunity and the design of vaccines for application in the bear family.

Evolution of major histocompatibility complex class I genes in the sable Martes zibellina (Carnivora, Mustelidae)

The molecules encoded by major histocompatibility complex (MHC) genes play an essential role in the adaptive immune response among vertebrates. We investigated the molecular evolution of MHC class I genes in the sable Martes zibellina. We isolated 26 MHC class I sequences, including 12 putatively functional sequences and 14 pseudogene sequences, from 24 individuals from two geographic areas of northeast China. The number of putatively functional sequences found in a single individual ranged from one to five, which might be at least 1-3 loci. We found that both balancing selection and recombination contribute to evolution of MHC class I genes in M. zibellina. In addition, we identified a candidate nonclassical MHC class I lineage in Carnivora, which may have preceded the divergence (about 52-57 Mya) of Caniformia and Feliformia. This may contribute to further understanding of the origin and evolution of nonclassical MHC class I genes. Our study provides important immune information of MHC for M. zibellina, as well as other carnivores.

Evolution of MHC class I genes in Eurasian badgers, genus Meles (Carnivora, Mustelidae)

Because of their role in immune defense against pathogens, major histocompatibility complex (MHC) genes are useful in evolutionary studies on how wild vertebrates adapt to their environments. We investigated the molecular evolution of MHC class I (MHCI) genes in four closely related species of Eurasian badgers, genus Meles. All four species of badgers showed similarly high variation in MHCI sequences compared to other Carnivora. We identified 7-21 putatively functional MHCI sequences in each of the badger species, and 2-7 sequences per individual, indicating the existence of 1-4 loci. MHCI exon 2 and 3 sequences encoding domains α1 and α2 exhibited different clade topologies in phylogenetic networks. Non-synonymous nucleotide substitutions at codons for antigen-binding sites exceeded synonymous substitutions for domain α1 but not for domain α2, suggesting that the domains α1 and α2 likely had different evolutionary histories in these species. Positive selection and recombination seem to have shaped the variation in domain α2, whereas positive selection was dominant in shaping the variation in domain α1. In the separate phylogenetic analyses for exon 2, exon 3, and intron 2, each showed three clades of Meles alleles, with rampant trans-species polymorphism, indicative of the long-term maintenance of ancestral MHCI polymorphism by balancing selection.

The functional significance of cattle major histocompatibility complex class I genetic diversity

Current concerns about food security highlight the importance of maintaining productive and disease-resistant livestock populations. Major histocompatibility complex (MHC) class I genes have a central role in immunity. A high level of diversity in these genes allows populations to survive despite exposure to rapidly evolving pathogens. This review aims to describe the key features of MHC class I genetic diversity in cattle and to discuss their role in disease resistance. Discussion centers on data derived from the cattle genome sequence and studies addressing MHC class I gene expression and function. The impact of intensive selection on MHC diversity is also considered. A high level of complexity in MHC class I genes and functionally related gene families is revealed. This highlights the need for increased efforts to determine key genetic components that govern cattle immune responses to disease, which is increasingly important in the face of changing human and environmental demands.

Canine DLA-79 gene: an improved typing method, identification of new alleles and its role in graft rejection and graft-versus-host disease

Developing a preclinical canine model that predicts outcomes for hematopoietic cell transplantation in humans requires a model that mimics the degree of matching between human donor and recipient major histocompatibility complex (MHC) genes. The polymorphic class I and class II genes in mammals are typically located in a single chromosome as part of the MHC complex. However, a divergent class I gene in dogs, designated dog leukocyte antigen-79 (DLA-79), is located on chromosome 18 while other MHC genes are on chromosome 12. This gene is not taken into account while DLA matching for transplantation. Though divergent, this gene shares significant similarity in sequence and exon-intron architecture with other class I genes, and is transcribed. Little is known about the polymorphisms of DLA-79 and their potential role in transplantation. This study was aimed at exploring the reason for high rate of rejection seen in DLA-matched dogs given reduced intensity conditioning, in particular, the possibility that DLA-79 allele mismatches may be the cause. We found that about 82% of 407 dogs typed were homozygous for a single, reference allele. Owing to the high prevalence of a single allele, 87 of the 108 dogs (∼80%) transplanted were matched for DLA-79 with their donor. In conclusion, we have developed an efficient method to type alleles of a divergent MHC gene in dogs and identified two new alleles. We did not find any statistical correlation between DLA-79 allele disparity and graft rejection or graft-versus-host disease, among our transplant dogs.

MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus

Background

The major histocompatibility complex (MHC) genes are one of the most important genetic systems in the vertebrate immune response. The diversity of MHC genes may directly influence the survival of individuals against infectious disease. However, there has been no investigation of MHC diversity in the Asiatic black bear (Ursus thibetanus). Here, we analyzed 270-bp nucleotide sequences of the entire exon 2 region of the MHC DQB gene by using 188 samples from the Japanese black bear (Ursus thibetanus japonicus) from 12 local populations.

Results

Among 185 of 188 samples, we identified 44 MHC variants that encoded 31 different amino acid sequences (allotypes) and one putative pseudogene. The phylogenetic analysis suggests that MHC variants detected from the Japanese black bear are derived from the DQB locus. One of the 31 DQB allotypes, Urth-DQB*01, was found to be common to all local populations. Moreover, this allotype was shared between the black bear on the Asian continent and the Japanese black bear, suggesting that Urth-DQB*01 might have been maintained in the ancestral black bear population for at least 300,000 years. Our findings, from calculating the ratio of non-synonymous to synonymous substitutions, indicate that balancing selection has maintained genetic variation of peptide-binding residues at the DQB locus of the Japanese black bear. From examination of genotype frequencies among local populations, we observed a considerably lower level of observed heterozygosity than expected.

Conclusions

The low level of observed heterozygosity suggests that genetic drift reduced DQB diversity in the Japanese black bear due to a bottleneck event at the population or species level. The decline of DQB diversity might have been accelerated by the loss of rare variants that have been maintained by negative frequency-dependent selection. Nevertheless, DQB diversity of the black bear appears to be relatively high compared with some other endangered mammalian species. This result suggests that the Japanese black bears may also retain more potential resistance against pathogens than other endangered mammalian species. To prevent further decline of potential resistance against pathogens, a conservation policy for the Japanese black bear should be designed to maintain MHC rare variants in each local population.

Black and white and read all over: the past, present and future of giant panda genetics

Few species attract much more attention from the public and scientists than the giant panda (Ailuropoda melanoleuca), a popular, enigmatic but highly endangered species. The application of molecular genetics to its biology and conservation has facilitated surprising insights into the biology of giant pandas as well as the effectiveness of conservation efforts during the past decades. Here, we review the history of genetic advances in this species, from phylogeny, demographical history, genetic variation, population structure, noninvasive population census and adaptive evolution to reveal to what extent the current status of the giant panda is a reflection of its evolutionary legacy, as opposed to the influence of anthropogenic factors that have negatively impacted this species. In addition, we summarize the conservation implications of these genetic findings applied for the management of this high-profile species. Finally, on the basis of these advances and predictable future changes in genetic technology, we discuss future research directions that seem promising for giant panda biology and conservation.

Evolution of major histocompatibility complex class I and class II genes in the brown bear

BACKGROUND

Major histocompatibility complex (MHC) proteins constitute an essential component of the vertebrate immune response, and are coded by the most polymorphic of the vertebrate genes. Here, we investigated sequence variation and evolution of MHC class I and class II DRB, DQA and DQB genes in the brown bear Ursus arctos to characterise the level of polymorphism, estimate the strength of positive selection acting on them, and assess the extent of gene orthology and trans-species polymorphism in Ursidae.

RESULTS

We found 37 MHC class I, 16 MHC class II DRB, four DQB and two DQA alleles. We confirmed the expression of several loci: three MHC class I, two DRB, two DQB and one DQA. MHC class I also contained two clusters of non-expressed sequences. MHC class I and DRB allele frequencies differed between northern and southern populations of the Scandinavian brown bear. The rate of nonsynonymous substitutions (dN) exceeded the rate of synonymous substitutions (dS) at putative antigen binding sites of DRB and DQB loci and, marginally significantly, at MHC class I loci. Models of codon evolution supported positive selection at DRB and MHC class I loci. Both MHC class I and MHC class II sequences showed orthology to gene clusters found in the giant panda Ailuropoda melanoleuca.

CONCLUSIONS

Historical positive selection has acted on MHC class I, class II DRB and DQB, but not on the DQA locus. The signal of historical positive selection on the DRB locus was particularly strong, which may be a general feature of caniforms. The presence of MHC class I pseudogenes may indicate faster gene turnover in this class through the birth-and-death process. South-north population structure at MHC loci probably reflects origin of the populations from separate glacial refugia.

Natural selection on marine carnivores elaborated a diverse family of classical MHC class I genes exhibiting haplotypic gene content variation and allelic polymorphism

Pinnipeds, marine carnivores, diverged from terrestrial carnivores ~45 million years ago, before their adaptation to marine environments. This lifestyle change exposed pinnipeds to different microbiota and pathogens, with probable impact on their MHC class I genes. Investigating this question, genomic sequences were determined for 71 MHC class I variants: 27 from harbor seal and 44 from gray seal. These variants form three MHC class I gene lineages, one comprising a pseudogene. The second, a candidate nonclassical MHC class I gene, comprises a nonpolymorphic transcribed gene related to dog DLA-79 and giant panda Aime-1906. The third is the diversity lineage, which includes 62 of the 71 seal MHC class I variants. All are transcribed, and they minimally represent six harbor and 12 gray seal MHC class I genes. Besides species-specific differences in gene number, seal MHC class I haplotypes exhibit gene content variation and allelic polymorphism. Patterns of sequence variation, and of positions for positively selected sites, indicate the diversity lineage genes are the seals' classical MHC class I genes. Evidence that expansion of diversity lineage genes began before gray and harbor seals diverged is the presence in both species of two distinctive sublineages of diversity lineage genes. Pointing to further expansion following the divergence are the presence of species-specific genes and greater MHC class I diversity in gray seals than harbor seals. The elaboration of a complex variable family of classical MHC class I genes in pinnipeds contrasts with the single, highly polymorphic classical MHC class I gene of dog and giant panda, terrestrial carnivores.

Evolution of MHC class I genes in the European badger (Meles meles)

The major histocompatibility complex (MHC) plays a central role in the adaptive immune system and provides a good model with which to understand the evolutionary processes underlying functional genes. Trans-species polymorphism and orthology are both commonly found in MHC genes; however, mammalian MHC class I genes tend to cluster by species. Concerted evolution has the potential to homogenize different loci, whereas birth-and-death evolution can lead to the loss of orthologs; both processes result in monophyletic groups within species. Studies investigating the evolution of MHC class I genes have been biased toward a few particular taxa and model species. We present the first study of MHC class I genes in a species from the superfamily Musteloidea. The European badger (Meles meles) exhibits moderate variation in MHC class I sequences when compared to other carnivores. We identified seven putatively functional sequences and nine pseudogenes from genomic (gDNA) and complementary (cDNA) DNA, signifying at least two functional class I loci. We found evidence for separate evolutionary histories of the α1 and α2/α3 domains. In the α1 domain, several sequences from different species were more closely related to each other than to sequences from the same species, resembling orthology or trans-species polymorphism. Balancing selection and probable recombination maintain genetic diversity in the α1 domain, evidenced by the detection of positive selection and a recombination event. By comparison, two recombination breakpoints indicate that the α2/α3 domains have most likely undergone concerted evolution, where recombination has homogenized the α2/α3 domains between genes, leading to species-specific clusters of sequences. Our findings highlight the importance of analyzing MHC domains separately.

Identification of the expressed MHC class II DQB gene of the Asiatic black bear, Ursus thibetanus, in Japan

Genetic diversity estimation of the major histocompatibility complex (MHC) gene may be an important tool in the assessment of immune response ability against infectious disease. We were able to identify a near full-length expressed DQB sequence by RACE-PCR method from the Asiatic black bear, Ursus thibetanus in Japan. This is the first such full length expression in the Ursidae. The bear had at least one functional DQB locus. In phylogenetic tree analysis its DQB amino acid sequence formed a monophyletic group with DQB sequences from members of the order Carnivora and had a 90% nucleotide sequence similarity with the DQB allele of the California sea lion, Zalophus californianus. We compared the DQB amino acid composition of U. thibetanus with those of several other mammalian species including Homo sapiens. Amino acid residues known to be functionally important for human MHC genes, tended to be also conserved among other mammalian species while PBRs in the beta1 domain were heterogeneous among mammalian species. The DQB sequence obtained from the bear had not only no putative frameshifts or deletions but also no abnormal amino acid mutations such as had been observed in human DQB molecules. This suggests that the bear DQB sequence was an apparently functional DQB allele. As a preliminary study, we sequenced the exon 2 region of DQB alleles from genomic DNA, and succeeded to amplify the exon 2 of DQB loci. Our study will provide useful information for conservation genetics of the U. thibetanus as well as more generally regarding the mammalian MHC region.

Allelic diversity of the MHC class II DRB genes in brown bears (Ursus arctos) and a comparison of DRB sequences within the family Ursidae

The allelic diversity of the DRB locus in major histocompatibility complex (MHC) genes was analyzed in the brown bear (Ursus arctos) from the Hokkaido Island of Japan, Siberia, and Kodiak of Alaska. Nineteen alleles of the DRB exon 2 were identified from a total of 38 individuals of U. arctos and were highly polymorphic. Comparisons of non-synonymous and synonymous substitutions in the antigen-binding sites of deduced amino acid sequences indicated evidence for balancing selection on the bear DRB locus. The phylogenetic analysis of the DRB alleles among three genera (Ursus, Tremarctos, and Ailuropoda) in the family Ursidae revealed that DRB allelic lineages were not separated according to species. This strongly shows trans-species persistence of DRB alleles within the Ursidae.