Variability in an MHCMosa class II beta chain-encoding gene in striped bass (Morone saxatilis)

Fate of MHCII in salmonids following 4WGD

Major histocompatibility complex (MHC) genes are key players in the adaptive immunity providing a defense against invading pathogens. Although the basic structures are similar when comparing mammalian and teleost MHC class II (MHCII) molecules, there are also clear-cut differences. Based on structural requirements, the teleosts non-classical MHCII molecules do not comply with a function similar to the human HLA-DM and HLA-DO, i.e., assisting in peptide loading and editing of classical MHCII molecules. We have previously studied the evolution of teleost class II genes identifying various lineages and tracing their phylogenetic occurrence back to ancient ray-finned fishes. We found no syntenic MHCII regions shared between cyprinids, salmonids, and neoteleosts, suggesting regional instabilities. Salmonids have experienced a unique whole genome duplication 94 million years ago, providing them with the opportunity to experiment with gene duplicates. Many salmonid genomes have recently become available, and here we set out to investigate how MHCII has evolved in salmonids using Northern pike as a diploid sister phyla, that split from the salmonid lineage prior to the fourth whole genome duplication (4WGD) event. We identified 120 MHCII genes in pike and salmonids, ranging from 11 to 20 genes per species analyzed where DB-group genes had the most expansions. Comparing the MHC of Northern pike with that of Atlantic salmon and other salmonids species provides a tale of gene loss, translocations, and genome rearrangements.

MHC II-β chain gene expression studies define the regional organization of the thymus in the developing bony fish Dicentrarchus labrax (L.)

MHC II-β chain gene transcripts were quantified by real-time PCR and localised by in situ hybridization in the developing thymus of the teleost Dicentrarchus labrax, regarding the specialization of the thymic compartments. MHC II-β expression significantly rose when the first lymphoid colonization of the thymus occurred, thereafter increased further when the organ progressively developed cortex and medulla regions. The evolving patterns of MHC II-β expression provided anatomical insights into some mechanisms of thymocyte selection. Among the stromal cells transcribing MHC II-β, scattered cortical epithelial cells appeared likely involved in the positive selection, while those abundant in the cortico-medullary border and medulla in the negative selection. These latter most represent dendritic cells, based on typical localization and phenotype. These findings provide further proofs that efficient mechanisms leading to maturation of naïve T cells are operative in teleosts, strongly reminiscent of the models conserved in more evolved gnathostomes.

Identification and expression analysis of major histocompatibility complex IIB gene in orange-spotted grouper Epinephelus coioides

In this study, complementary DNA (cDNA) and DNA sequences of major histocompatibility complex (MHC) class IIB genes (mhcIIB) were cloned from orange-spotted grouper Epinephelus coioides. The gene structure of E. coioides mhcIIB consists of five exons and four introns, and its deduced amino acid sequence length is 249 amino acids, including a signal peptide, a peptide-binding region, an IGC1 domain, a transmembrane region and a cytoplasmic tail. A phylogenetic study showed that E. coioides mhcIIB shared 32.0-79.1% identity with those of other teleosts and mammals. Real-time reverse transcriptase (RT)-PCR was performed to detect the class IIB gene expression in eight different tissues. To characterize the relationship between E. coioides mhcIIB gene and pathogens, in vivo and in vitro studies were performed. Challenge of Cryptocaryon irritans revealed that class IIB genes were down-regulated after 24 and 48 h of challenge, and their expression was later restored at 72 h. Stimulation of isolated E. coioides leukocytes with lipopolysaccharide (LPS) and polyinosinic:polycytidylic acid (PolyI:C) significantly increased peripheral blood and spleen mhcIIB expression, while head kidney mhcIIB expression remained constant.

MHC polymorphism and disease resistance to Vibrio anguillarum in 8 families of half-smooth tongue sole (Cynoglossus semilaevis)

Background

Genes in the major histocompatibility complex (MHC) have a critical role in both the innate and adaptive immune responses because of their involvement in presenting foreign peptides to T cells. However, the nature has remained largely unknown.

Results

We examined the genetic variation in MHC class IIB in half-smooth tongue sole (Cynoglossus semilaevis) after challenge with vibrio anguillarum. Two thousand and four hundred fry from 12 half-smooth tongue sole families were challenged with Vibrio anguillarum. To determine any association between alleles and resistance or susceptibility to V. anguillarum, 160 individuals from four high-resistance (HR, < 40.55% mortality) families and four low-resistance (LR, > 73.27% mortality) families were selected for MHC IIB exon2 gene sequence analysis. The MHC IIB exon2 genes of tongue sole displayed a high level of polymorphism and were discovered at least four loci. Meanwhile, the d_N/d_S [the ratio of non-synonymous (d_N) substitutions to synonymous (d_S) substitutions] in the peptide-binding region (PBR) was higher than that in the non-peptide-binding region (non-PBR). Eighty-eight alleles were discovered among 160 individuals, and 13 out of 88 alleles were used to analyze the distribution pattern between the resistant and susceptible families. Certain alleles presented in HR and LR with a different frequency, while other alleles were discovered in only the HR or LR families, not both. Five alleles, Cyse-DBB*6501, Cyse-DBB*4002, Cyse-DBB*6102, Cyse-DBB*5601 and Cyse-DBB*2801, were found to be associated with susceptibility to V. anguillarum with a frequency of 1.25%, 1.25%, 1.25%, 1.25% and 2.5% in the HR families, and 35%, 33.75%, 27.5%, 16.25%, 15% in the LR families (p < 0.01, 0.01, 0.01, 0.01, 0.01), respectively. Four alleles, Cyse-DBB*3301, Cyse-DBB*4701, Cyse-DBB*6801 and Cyse-DBB*5901, were found to be associated with resistance to V. anguillarum, with a frequency of 13.75%, 11.25%, 11.25%, 8.75% in the HR families and 1.25%, 1.25%, 1.25%, 1.25% and 1.25% in the LR families (p < 0.01, 0.05, 0.05 and p = 0.064), respectively.

Conclusions

Elucidation of the role of MHC II B genes in half-smooth tongue sole should prove to be helpful to the in-depth development of marker-assisted selective breeding in half-smooth tongue sole.

Molecular cloning, genomic structure, polymorphism and expression analysis of major histocompatibility complex class IIA and IIB genes of half-smooth tongue sole (Cynoglossus semilaevis)

Major histocompatibility complex (MHC) genes play an important role in the immune response of vertebrates. Its function is to present foreign peptide to the T-cell. In order to study the function and molecular polymorphism of class II genes in teleost, the full lengths of MHC class IIA and IIB cDNA were cloned from half-smooth tongue sole by homology cloning and rapid amplification of cDNA ends polymerase chain reaction (RACE-PCR). Genomic organizations, molecular polymorphism, and expression profiles of class IIA and IIB were examined to study the function in fish. As in other teleost, four exons and three introns were identified in half-smooth tongue sole class IIA gene, five exons and four introns were identified in class IIB gene. The deduced amino acid sequence of class IIA had 27.3-69.8% identity with those of mammal and teleost. Nine class IIA alleles were identified from four individuals. Four different alleles observed in a single individual may infer the existence of two loci at least. The deduced amino acid sequence of class IIB had 7.9-71.9% identity with those of other species. Fifteen class IIB alleles were identified. Six different alleles observed in a single individual may suggest that there are at least three loci in class IIB genes. Real-time quantitative RT-PCR demonstrated that the MHC class IIA and IIB were ubiquitously expressed in twelve normal tissues. Challenge of half-smooth tongue sole with the pathogenic bacteria, Vibrio anguillarum, resulted in significant changes in the expression of MHC IIA and IIB mRNA in three tissues.

Molecular characterization and expression analysis of MHC class II alpha and beta genes in large yellow croaker (Pseudosciaena crocea)

MHC class II molecules play an important role in the activation of CD4(+) T cells, which are the central orchestrating cells of an immune response. Here, we report the cloning of MHC class II alpha and beta cDNAs from large yellow croaker (Pscr-DAAs and Pscr-DAB) by expressed sequence tags analysis and RACE-PCR techniques. Three different class II alpha and two class II beta sequences were obtained from spleens of two individual fish. Each of the three class II alpha sequences encodes a polypeptide of 239 amino acids while the two class II beta cDNA sequences encode for a protein of 249 aa. All the characteristic features of MHC class II chain structure could be identified in the deduced proteins of three class II alpha and two class II beta sequences, including the leader peptide, alpha1/beta1 and alpha2/beta2 domains, connecting peptide and transmembrane and cytoplasmic regions, as well as conserved cysteines and N-glycosylation site. RT-PCR analysis showed that MHC class II alpha and beta mRNAs were broadly expressed in various tissues examined, although at different levels. Upon stimulation with inactivated trivalent bacterial vaccine or polyinosinic polycytidylic acid (poly(I:C)), the expression levels of both alpha and beta genes were obviously up-regulated in intestine, kidney and spleen. Real-time PCR analysis demonstrated that the expression levels of class II alpha and beta were quickly up-regulated in spleen, kidney, and intestine at 12 h after induction with poly(I:C), while their expression levels significantly increased at 48 h upon immunization with bacterial vaccine, indicating that the up-regulation of both class II alpha and beta expression was induced by bacterial vaccine or poly(I:C) at the early phase of induction, and that class II alpha and beta transcripts were quicker up-regulated by poly I:C than by bacterial vaccine.

Cell markers and determinants in fish immunology

Despite the impressive increase in the cloning and expression of genes encoding fish immunoregulatory molecules, the knowledge on "in vivo" and "in vitro" functional immunology of the corresponding peptide products is still at an initial stage. This is partly due to the lacking of specific markers for immunoregulatory peptides, that represent an indispensible tool to dissect immune reactions and to trace the fate of cellular events downstream of the activation. In this review we summarise the available information on functional immune activities of some teleost species and discuss the obtained data in an evolutionary and applied context.

Molecular cloning, differential expression and 3D structural analysis of the MHC class-II beta chain from sea bass (Dicentrarchus labrax L.)

The major histocompatibility complex class I and II molecules (MHC-I and MHC-II) play a pivotal role in vertebrate immune response to antigenic peptides. In this paper we report the cloning and sequencing of the MHC class II beta chain from sea bass (Dicentrarchus labrax L.). The six obtained cDNA sequences (designated as Dila-DAB) code for 250 amino acids, with a predicted 21 amino acid signal peptide and contain a 28bp 5'-UTR and a 478bp 3'-UTR. A multiple alignment of the predicted translation of the Dila-DAB sequences was assembled together with other fish and mammalian sequences and it showed the conservation of most amino acid residues characteristic of the MHC class II beta chain structure. The highest basal Dila-DAB expression was found in gills, followed by gut and thymus, lower mRNA levels were found in spleen, peripheral blood leucocytes (PBL) and liver. Stimulation of head kidney leukocytes with LPS for 4h showed very little difference in the Dila-DAB expression, but after 24h the Dila-DAB level decreased to a large extent and the difference was statistically significant. Stimulation of head kidney leukocytes with different concentrations of rIL-1beta (ranging from 0 to 100ng/ml) resulted in a dose-dependent reduction of the Dila-DAB expression. Moreover, two 3D Dila-DAB*0101 homology models were obtained based on crystallographic mouse MHC-II structures complexed with D10 T-cell antigen receptor or human CD4; features and differences between the models were evaluated and discussed. Taken together these results are of interest as MHC-II structure and function, molecular polymorphism and differential gene expression are in correlation with disease resistance to virus and bacteria in teleost fish.

Major histocompatibility complex class IIB allele polymorphism and its association with resistance/susceptibility to Vibrio anguillarum in Japanese flounder (Paralichthys olivaceus)

The full length of major histocompatibility complex (MHC) class IIB cDNA was cloned from a Chinese population of Paralichthys olivaceus by homology cloning and rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR). The MHC IIB genomic sequence is 1,864 bp long and consists of 34-bp 5'UTR, 741-bp open reading frame, 407-bp 3'UTR, 96-bp intron1, 392-bp intron2, 85-bp intron3, and 109-bp intron4. Phylogenetic analysis showed that the putative MHC class IIB amino acid of the Chinese P. olivaceus shared 28.3% to 85.4% identity with that of the reported MHC class IIB in other species. A significant association between MHC IIB polymorphism and disease resistance/susceptibility was found in Chinese P. olivaceus. Thirteen different MHC IIB alleles were identified among 411 clones from 84 individuals. Among the 280 (268) nucleotides, 32 (11.4%) nucleotide positions were variable. Most alleles such as alleles a, b, c, d, e, f, j, k, i, m were commonly found in both resistant and susceptible stock. Via chi2 test, allele d was significantly more prevalent in individuals from susceptible stock than from resistant stock, and their percentages were 23.80% and 7.14%, respectively. In addition, allele g occurred in 9 and allele h in 4 of 42 resistant individuals that were not present in the susceptible stock; their percentages were 21.4% and 9.52%, respectively. Although allele l was found only in 8 individuals from the susceptible stock, its percentage is 19.05%.

Molecular identification, polymorphism, and expression analysis of major histocompatibility complex class IIA and B genes of turbot (Scophthalmus maximus)

Major histocompatibility complex (MHC) class II has a central role in the adaptive immune system by presenting foreign peptides to the T-cell receptor. The full lengths of MHC class II A and B cDNA were cloned from turbot by homology cloning and rapid amplification of cDNA ends polymerase chain reaction (RACE PCR), and genomic organization, molecular polymorphism, and expression of turbot class IIB gene were examined to study the function of class IIB gene in fish. The deduced amino acid sequence of turbot class II A (GenBank accession no.DQ001730) and turbot class IIB (GenBank accession no. DQ094170) had 69.8%, 67.6%, 65.5%, 59.2%, 54.5%, 52.8%, 46.2%, 46.6%, 28.3%, 28.5%, 22.2% identity and 71.5%, 70.7%, 67.1%, 68.4%, 46.7%, 53.5%, 46.7%, 50.0%, 25.2%, 29.2%, 27.6% identity with those of Japanese flounder, striped sea bass, red sea bream, cichlid, rainbow trout, Atlantic salmon, carp, zebrafish, nurse shark, mouse and human, respectively. Eleven class IIB alleles were identified from three turbot individuals. The amino acid sequence of turbot class IIB designated as Scma-DAB*0101 had 86.9%, 88.6%, 88.6%, 89.4%, 87.8%, 86.9%, 84.1%, 86.5%, 87.3%, 77.1%, and 86.9% identity with those of turbot class IIB 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 (Scma-DAB*0201- Scma-DAB*1201), respectively. Six different class IIB alleles observed in a single individual may infer the existence of three loci at least. Semiquantitative reverse transcriptase PCR (RT-PCR) demonstrated that turbot class IIA and B were ubiquitously expressed in normal tissues. Challenge of turbot with pathogenic bacteria, Vibrio anguillarum, resulted in a significant decrease in the expression of MHC class IIB mRNA from 24 h to 48 h after infection in liver and head kidney, and a significant decrease from 24 h to 72 h after infection in spleen, followed by an increase after 96 h, respectively.

Coding sequences of the MHC II beta chain of homozygous rainbow trout (Oncorhynchus mykiss)

Six lines of homozygous rainbow trout (Oncorhynchus mikiss) from different genetic and geographical backgrounds have been produced as aquatic models for biomedical research by the chromosome set manipulation techniques of androgenesis and gynogenesis. Messenger RNA from spleens was extracted. and the MHC II B cDNA sequences, amplified by RT PCR, were cloned into plasmids. Sequences of the MHC II beta2 domains were highly conserved between the different plasmids from the same and different lines of trout. Most of the variability among sequences was found in the amino terminal half of the beta1 domain, which corresponds with the peptide binding region of the MHC II molecule. This diversity suggests that the different lines of trout may exhibit differences in immune response. Rainbow trout MHC II B sequences were similar to the MHC II B sequences of the Pacific salmon (O. gorbuscha, O. tshawytscha, O. nerka, O. miasou, O. kisutch). Southern blot analysis performed on the restricted DNA of the OSU and Hot Creek trout, and the doubled haploid progeny produced by androgenesis from OSU x Hot Creek hybrids indicates that two distinct genes encode the MHC II B sequences and that these genes are unlinked.

Expressed major histocompatibility complex class II loci in fishes

Peptides derived from parasites are presented to T helper cells by major histocompatibility complex (MHC) class II alpha beta heterodimeric cell-surface molecules. In mice and humans, the genes encoding these antigen-presenting molecules are known to be polymorphic and polygenic. Multiple loci for MHC class II A and B genes are proposed to allow for an increased peptide-binding repertoire. The multigenic nature of expressed MHC class II loci and the differences between these loci in fishes are the focus of this review. Particular emphasis is placed on an evolutionary comparison of class II B loci, especially two class II B loci that have undergone dramatic changes from one another suggesting an ancestral gene duplication event that took place at an early stage in the evolution of teleosts. The number of functional class II alpha beta heterodimers may have a profound impact on the organisms ability to battle constantly evolving parasitic infections.

What sharks can tell us about the evolution of MHC genes

Similarity in structural features would argue that sharks possess class I, class IIA and class IIB genes, coding for classical peptide-presenting molecules, as well as non-classical class I genes. Some aspects of shark major histocompatibility complex genes are similar to teleost genes and others are similar to tetrapod genes. Shark class I genes form a monophyletic group, as also seen for tetrapods, but the classical and nonclassical genes form two orthologous clades, as seen for teleosts. Teleost class I genes arose independently at least four different times with the nonclassical genes of ray-finned fishes and all the shark and lobe-finned fish class I genes forming 1 clade. The ray-finned fish classical class I genes arose separately. In phylogenetic trees of class II alpha 2 and beta 2 domains, the shark and tetrapod genes cluster more closely than the teleost genes and, unlike the teleost sequences, the class II alpha 1 domains of sharks and tetrapods lack cysteines. On the other hand, both shark and teleost genes display sequence motifs in the antigen-binding cleft that have persisted over very long time periods. The similarities may reflect common selective pressures on species in aqueous environments while differences may be due to different evolutionary rates.

Identification and mapping of two divergent, unlinked major histocompatibility complex class II B genes in Xiphophorus fishes

We have isolated two major histocompatibility complex (MHC) class II B genes from the inbred fish strain Xiphophorus maculatus Jp 163 A. We mapped one of these genes, designated here as DXB, to linkage group III, linked to a malic enzyme locus, also syntenic with human and mouse MHC. Comparison of genomic and cDNA clones shows the gene consists of six exons and five introns. The encoded beta1 domain has three amino acids deleted and a cytoplasmic tail nine amino acids longer than in other teleost class II beta chains, more similar to HLA-DRB, clawed frog Xela-F3, and nurse shark Gici-B. Key residues for disulfide bonds, glycosylation, and interaction with alpha chains are conserved. These same features are also present in a swordtail (Xiphophorus helleri) genomic DXB PCR clone. A second type of class II B clone was amplified by PCR from X. maculatus and found to be orthologous to class II genes identified in other fishes. This DAB-like gene is 63% identical to the X. maculatus DXB sequence in the conserved beta2-encoding exon and was mapped to new unassigned linkage group LG U24. The DXB gene, then, represents an unlinked duplicated locus not previously identified in teleosts.

MHC class II B genes in the channel catfish (Ictalurus punctatus)

Two different cDNA sequences for major histocompatibility complex (MHC) class II beta chains from the channel catfish (Ictalurus punctatus) have been identified. Homology between these sequences and those previously identified as MHC class II B genes in other teleosts suggests they represent alleles of the DAB locus. The inferred amino acid sequences show strong evidence for a functional polypeptide chain with a peptide binding region. Southern blot analysis reveals polymorphism in the MHC class II B gene(s) of the channel catfish and suggests the presence of two to four genes.

Characterization of class II A and B genes in a gynogenetic carp clone

A prerequisite for carrying out functional studies on major histocompatibility complex (Mhc) molecules of fish is the availability of genetically well-defined homozygous strains. Previously we have applied gynogenetic reproduction to generate isogenic carp, denoted clone A410. This clone has recently been demonstrated to express a single class I gene, Cyca-UA1(*)01, and in the present study two class II B and two class II A transcripts were obtained. The two class II B transcripts, Cyca-D(CB3)B and Cyca-D(CB4)B, as well as the class II A transcripts, Cyca-D(10A)A and Cyca-D(15A)A, appear to be bona fide class II transcripts, based on the presence of conserved protein characteristics of the inferred class II molecules. With the isolation of class II A sequences, representatives of all major classes of Mhc genes have been identified in the carp. To assess the relationship between the different class II genes, segregation studies, comparison of cDNA and intron 1 sequence data, and phylogenetic analyses were undertaken. These showed that the class II B transcripts, Cyca-D(CB3)B and Cyca-D(CB4)B, are derived from related, closely linked loci. In addition, these studies indicated that the previously described Cyca-DAB*01 and Cyca-DAB*02 are also closely linked, but that this linked pair segregates independently from the Cyca-D(CB3)B and Cyca-D(CB4)B loci. The class II A transcripts are most likely derived from separate loci and do not represent alleles, as they were found not to segregate in the individuals of the clone which was generated by meiogenetic gynogenesis.

Trans-species polymorphism of class II Mhc loci in danio fishes

A characteristic feature of the major histocompatibility complex (Mhc) polymorphism in mammals is the existence of allelic lineages shared by related species. This trans-species polymorphism has thus far been documented only in primates, rodents, and artiodactyls. In this communication we provide evidence that it also exists in cyprinid (bony) fishes at the class II A and B loci coding for the alpha and beta polypeptide chains of the class II alpha:beta heterodimers. The study has focused on three species of the family Cyprinidae, subfamily Rasborinae: the zebrafish (Danio rerio), the giant danio (D. malabaricus), and the pearl danio (D. albolineatus). The polymerase chain reaction was used to amplify and then sequence intron 1 and exon 2 of the class II B loci and exon 2 of the class II A loci in these species. Phylogenetic analysis of the sequences revealed the existence of allelic lineages whose divergence predates the divergence of the three species at both the A and B loci. The lineages at the B locus in particular are separated by large genetic distances. The polymorphism is concentrated in the peptide-binding region sites and is apparently maintained by balancing selection. Sharing of this unique Mhc feature by both bony fishes and mammals suggests that the main function of the Mhc (presentation of peptides to T lymphocytes) has not changed during the last 400 million years of its evolution.

cDNA analysis of the mite allergen Lep d 1 identifies two different isoallergens and variants

For the first time the complete cDNA encoding two isoallergens of the non-pyroglyphid dust mite Lepidoglyphus destructor, Lep d 1, allergen has been sequenced. In addition, one of the isoallergens was found to have two variants. Oligonucleotides were designed from known amino acid sequences. The cDNA sequences were obtained by hybridizing these primers to mRNA and enhancement by the RT-PCR technique. To obtain the different complete encoding cDNA sequences and eliminate heteroduplex artifacts, we performed PCR + 1 reactions. Comparison of the amino acid sequence of the allergen shows leader sequences of 16 amino acids for both isoforms.

Fish major histocompatibility complex genes: an expansion

The advent of polymerase chain reaction technology has provoked a large amount of progress in the field of fish major histocompatibility complex (MHC) research. Many new teleost sequences have been reported in the last four years, including representatives of all classes of MHC genes. While the intron-exon structure of teleost MHC genes is now becoming clear, the organisation of the genes within the teleost MHC is still unclear. The sequences reported to date have been used for phylogenetic analysis and, due to their evolutionary position, are discussed in relation to hypotheses regarding the origin of the MHC. Teleost MHC gene sequences are also examined to see if conserved features of the both the nucleotide and amino acid sequences of higher vertebrate MHC genes are present. Differences in these features will reflect functional differences between teleost and mammalian MHC genes and may also have evolutionary implications.

Identification of major histocompatibility complex genes in the guppy, Poecilia reticulata

The guppy, Poecilia reticulata, a teleostean fish of the order Cyprinodontiformes, has been used extensively in studies of host-parasite interactions, courtship behavior, and mating preference, as well as in ecological and evolutionary genetics. A related species was among the first poikilotherm vertebrates to be used in the study of histocompatibility genes. All these studies could benefit from the identification and characterization of the guppy major histocompatibility complex (Mhc) genes. Here, both class I and class II genes of the guppy are described. The number of expressed loci, as determined by representation of clones in a cDNA library, sequencing, and Southern blot analysis, may be low in both Mhc classes: combined evidence suggests that there may be one expressed class II locus only and one or two expressed class I loci. The variability of aquaristic guppy stocks is very low: only three and two genes have been detected at the class I and class II loci, respectively, in the stocks examined. This genetic paucity is most likely the consequence of breeding practices employed by aquarists and commercial establishments. Limited sampling of wild guppy populations revealed extensive Mhc polymorphism at loci of both classes in nature. Comparison of guppy Mhc sequences with those of other vertebrates has revealed the existence of a set of insertions/deletions which can be used as characters in cladistic analysis to infer phylogenetic relationships among vertebrate taxa and the Mhc genes themselves. These indels are particularly frequent in the regions coding for the loops of alpha 1 and alpha 2 domains of class I proteins.