Interallelic Recombination Research Articles

Interspecific introgression of MHC genes in Triturus newts: Evidence from multiple contact zones.

The major histocompatibility complex (MHC) genes are central to the adaptive immune response in vertebrates. Selection generally maintains high MHC variation because the spectrum of recognized pathogens depends on MHC polymorphism. Novel alleles favoured by selection originate by interallelic recombination or de novo mutations but may also be acquired by introgression from related species. However, the extent and prevalence of MHC introgression remain an open question. In this study, we tested for MHC introgression in six hybrid zones formed by six Triturus newt species. We sequenced and genotyped the polymorphic second exons of the MHC class I and II genes and compared their interspecific similarity at various distances from the centre of the hybrid zone. We found evidence for introgression of both MHC classes in the majority of examined hybrid zones, with support for a more substantial class I introgression. Furthermore, the overall MHC allele sharing outside of hybrid zones was elevated between pairs of Triturus species with abutting ranges, regardless of the phylogenetic distance between them. No effect of past hybrid zone movement on MHC allele sharing was found. Finally, using previously published genome-wide data, we demonstrated that MHC introgression was more extensive than genome-wide introgression, supporting its adaptive potential. Our study thus provides evidence for the prevalence of MHC introgression across multiple Triturus hybrid zones, indicating that MHC introgression between divergent hybridizing species may be widespread and adaptive.

Complete CSN1S2 Characterization, Novel Allele Identification and Association With Milk Fatty Acid Composition in River Buffalo.

The αs2-casein is one of the phosphoproteins secreted in all ruminants' milk, and it is the most hydrophilic of all caseins. However, this important gene (CSN1S2) has not been characterized in detail in buffaloes with only two alleles detected (reported as alleles A and B), and no association studies with milk traits have been carried out unlike what has been achieved for other species of ruminants. In this study, we sequenced the whole gene of two Mediterranean river buffalo homozygotes for the presence/absence of the nucleotide C (g.7539G>C) realized at the donor splice site of exon 7 and, therefore, responsible for the skipping of the same exon at mRNA level (allele B). A high genetic variability was found all over the two sequenced CSN1S2 alleles. In particular, 74 polymorphic sites were found in introns, six in the promoter, and three SNPs in the coding region (g.11072C>T, g.12803A>T, and g.14067A>G) with two of them responsible for amino acid replacements. Considering this genetic diversity, those found in the database and the SNP at the donor splice site of exon 7, it is possible to deduce at least eight different alleles (CSN1S2 A, B, B1, B2, C, D, E, and F) responsible for seven different possible translations of the buffalo αs2-casein. Haplotype data analysis suggests an evolutionary pathway of buffalo CSN1S2 gene consistent with our proposal that the published allele CSN1S2 A is the ancestral αs2-CN form, and the B2 probably arises from interallelic recombination (single crossing) between the alleles D and B (or B1). The allele CSN1S2 C is of new identification, while CSN1S2 B, B1, and B2 are deleted alleles because all are characterized by the mutation g.7539G>C. Two SNPs (g.7539G>C and g.14067A>G) were genotyped in 747 Italian buffaloes, and major alleles had a relative frequency of 0.83 and 0.51, respectively. An association study between these SNPs and milk traits including fatty acid composition was carried out. The SNP g.14067A>G showed a significant association (P < 0.05) on the content of palmitic acid in buffalo milk, thus suggesting its use in marker-assisted selection programs aiming for the improvement of buffalo milk fatty acid composition.

The DAU cluster: a comparative analysis of 18 RHD alleles, some forming partial D antigens.

The Rh system is the most complex and polymorphic blood group system in humans with more than 460 alleles known for the RHD gene. The DAU cluster of RHD alleles is characterized by the single-nucleotide change producing the p.Thr379Met amino acid substitution. It is called the DAU-0 allele and has been postulated to be the primordial allele, from which all other alleles of the DAU cluster have eventually evolved. For two novel DAU alleles, the nucleotide sequences of all 10 exons as well as adjacent intronic regions, including the 5' and 3' untranslated regions (UTR), were determined for the RHD and RHCE genes. A phylogenetic tree for all DAU alleles was established using the neighbor-joining method with Pan troglodytes as root. Standard hemagglutination and flow cytometry tests were performed. We characterized two DAU alleles, DAU-11 and DAU-5.1, closely related to DAU-3 and DAU-5, respectively. A phylogenetic analysis of the 18 known DAU alleles indicated point mutations and interallelic recombination contributing to diversification of the DAU cluster. The DAU alleles encode a group of RhD protein variants, some forming partial D antigens known to permit anti-D in carriers; all are expected to cause anti-D alloimmunization in recipients of red blood cell transfusions. The DAU alleles evolved through genomic point mutations and recombination. These results suggest that the cluster of DAU alleles represent a clade, which is concordant with our previous postulate that they derived from the primordial DAU-0 allele.

Recombination and selection in the major histocompatibility complex of the endangered forest musk deer (Moschus berezovskii).

The forest musk deer (Moschus berezovskii) is a high elevation species distributed across western China and northern Vietnam. Once abundant, habitat loss and poaching has led to a dramatic decrease in population numbers prompting the IUCN to list the species as endangered. Here, we characterized the genetic diversity of a Major Histocompatibility Complex (MHC) locus and teased apart driving factors shaping its variation. Seven DRB exon 2 alleles were identified among a group of randomly sampled forest musk deer from a captive population in the Sichuan province of China. Compared to other endangered or captive ungulates, forest musk deer have relatively low levels of MHC genetic diversity. Non-synonymous substitutions primarily occurred in the putative peptide-binding region (PBR), with analyses suggesting that recombination and selection has shaped the genetic diversity across the locus. Specifically, inter-allelic recombination generated novel allelic combinations, with evidence for both positive selection acting on the PBR and negative selection on the non-PBR. An improved understanding of functional genetic variability of the MHC will facilitate better design and management of captive breeding programs for this endangered species.

The Plasmodium gaboni genome illuminates allelic dimorphism of immunologically important surface antigens in P. falciparum

In the deadly human malaria parasite Plasmodium falciparum, several major merozoite surface proteins (MSPs) show a striking pattern of allelic diversity called allelic dimorphism (AD). In AD, the vast majority of observed alleles fall into two highly divergent allelic classes, with recombinant alleles being rare or not observed, presumably due to repression by natural selection (recombination suppression, or RS). The three AD loci, merozoite surface proteins (MSPs) 1, 2, and 6, along with MSP3, which also exhibits RS among four allelic classes, can be collectively called AD/RS. The causes of AD/RS and the evolutionary history of allelic diversity at these loci remain mysterious. The few available sequences from a single closely related chimpanzee parasite, P. reichenowi, have suggested that for 3/4 loci, AD/RS is an ancient state that has been retained in P. falciparum since well before the P. falciparum–P. reichenowi ancestor. On the other hand, based on comparative sequence analysis, we recently suggested that (i) AD/RS P. falciparum loci have undergone interallelic recombination over longer evolutionary times (on the timescale of recent speciation events), and thus (ii) AD/RS may be a recent phenomenon. The recent publication of genomic sequencing efforts for P. gaboni, an outgroup to P. falciparum and P. reichenowi, allows for improved reconstruction of the evolutionary history of these loci. In this work, I report genic sequence for P. gaboni for all four AD/RS P. falciparum loci (MSP1, 2, 3, and 6). Comparison of these sequences with available P. falciparum and P. reichenowi data strengthens the evidence for interallelic recombination over the evolutionary history of these species and also strengthens the case that AD/RS at these loci is ancient. Combined with previous results, these data provide evidence that AD/RS at different loci has evolved at several different times in the evolutionary history of P. falciparum: (i) before the P. gaboni–P. falciparum divergence, for much of MSP1 and MSP3; (ii) between the P. gaboni–P. falciparum and P. reichenowi–P. falciparum divergences, for the 5′ end of the AD region of MSP6 and block 3 of MSP1; (iii) near the P. reichenowi–P. falciparum divergence, for the 3′ end of the AD region of MSP6; and (iv) after the P. reichenowi–P. falciparum divergence, for MSP2. Based on these results, I suggest a new hypothesis for long-term evolutionary maintenance of AD/RS by recombination within allelic groups.

The genetic study on arare inter-allelic recombination of HLA-C locus in a Chinese Han family

：Objective To study theinter-allelic recombination event occurring in the HLA-C locus in a family of Chinese Hannationality, and to evaluate the molecular genetic background of the new HLAallele.Methods Peripheral blood samples were collected from a Chinese leukemia womanpatient, as well as her healthy parents and two brothers.HLA-A, C, B, DRB1 and DQB1alleles were typed by high-resolution PCR-sequence-based typing (SBT) method using AtriaGenetic AlleleSEQR HLA SBT kits.The Protrans S4 HLA-C single allele-specific sequencingstrategy was used to separate the two HLA-C alleles and to determine novelty of theallele.The full length sequences of HLA-C alleles of the patient and her parents werefurther analyzed using cloning and haplotype sequencing method. The HLA five loci linkedhaplotypes and the recombination site were analyzed by family study, meanwhile the fulllength sequences of the five HLA-C alleles were compared with the IMGT/HLA database by theprogram BLAST.Results The two haplotypes of the father and mother werea:A*0207-C*010201-B*550201-DRB1*090102-DRQ1*030302 andb:A*240201-C*120202-B*5201-DRB1*1502-DRQ1*0601,c:A*300101-C*060201-B*130201-DRB1*0405-DRQ1*0401 andd:A*110101-C*070201-B*4001-DRB1*080302-DRQ1*0601,respectively.The two brothers inheritedtheir parent′s haplotypes a, d and b, c respectively.The two haplotypes of thepatient were the maternal c and paternal recombinant a/b haplotype.The recombinant a/bhaplotype A*240201-C*new-B*550201-DRB1*090102-DRQ1*030302, A*240201 came from the paternalhaplotype b,while B*550201-DRB1*090102-DRQ1*030302 came from the other paternal haplotypea.When comparing the full length sequences of the HLA-C new allele with the father′s allele C*010201 and C*120202,it could deduce that the recombinant a/b haplotype derived from a recombination eventoccurring between the paternal chromosome 6 during meiosis.The crossover site was betweengenomic nt273 and nt330 of HLA-C alleles, which created a HLA-C new allele and the fifthhaplotype of the family, and inherited it to the patient.The full length sequences of thenew allele had been submitted to Genbank, and officially named C*0121 by WHO nomenclaturecommittee.Conclusion This study demonstrates a rare inter-allelic recombination eventoccurring in the HLA-C locus within a Chinese Han family and illustrates the process ofnovel allele and haplotype, and provides direct theory for further studying the mechanismsof gene recombination and HLA polymorphism. Key words: HLA-C antigens; Alleles; Pedigree; Recombination,genetic

A novel HLA-B*40 sequence - B*40:92

A new allele, HLA-B*40:92, was identified in a north-western European subject during polymerase chain reaction using sequence-specific priming (PCR-SSP)-based typing of haematopoietic stem cell (HSC) donors. B*40:92 differs from B*40:01:01 by six nucleotides at positions 559, 560, 603, 605, 610 and 618 in exon 3 which represents a substitution motif of at least 60 nucleotides. This motif, which occurs in numerous HLA alleles including the relatively high frequency B*15 and B*35 allele families, encode four amino acid changes at positions 163 (glutamic acid > leucine), 177 (aspartic acid > glutamic acid), 178 (lysine > threonine), 180 (glutamic acid > glutamine) and a silent substitution, conserved alanine, at codon 182. Thus, it is likely that HLA-B*40:92 occurred following a gene conversion-like or interallelic recombination event involving B*40:01:01 and probably a B*15 or more likely a B*35 family allele. HLA-B*40:92 was found on a haplotype with HLA-A*02:01, B*40:92, C*03:04, DRB1*13:02, DRB3*03:01, DQA1*01:02, DQB1*06:04, DPA1*02:02, DPB1*05:01. Tests on 69 selected B40 and B35 antisera and Lambda Monoclonal Trays™ show that B*40:92 encodes a 'short' B40/B60 serological specificity which displays some HLA-B35 reactivity. The HLA-B40 and HLA-B35 motifs (possible epitopes) responsible for this serological reactivity were identified. This single example of HLA- B*40:92 was found in 56,823 consecutive HLA PCR-SSP typed HSC donors indicating a carriage frequency of 0.00176% (allele frequency 0.00001) in blood donors resident in Wales. An Epstein-Barr virus transformed B-cell line from the HLA-B*40:92 donor is available.

Genetic diversity of the allodeterminant alr2 in Hydractinia symbiolongicarpus.

Hydractinia symbiolongicarpus, a colonial cnidarian (class Hydrozoa) epibiont on hermit crab shells, is well established as a model for genetic studies of allorecognition. Recently, two linked loci, allorecognition (alr) 1 and alr2, were identified by positional cloning and shown to be major determinants of histocompatibility. Both genes encode putative transmembrane proteins with hypervariable extracellular domains similar to immunoglobulin (Ig)-like domains. We sought to characterize the naturally occurring variation at the alr2 locus and to understand the origins of this molecular diversity. We examined full-length cDNA coding sequences derived from a sample of 21 field-collected colonies, including 18 chosen haphazardly and two laboratory reference strains. Of the 35 alleles recovered from the 18 unbiased samples, 34 encoded unique gene products. We identified two distinct structural classes of alleles that varied over a large central region of the gene but both possessed highly polymorphic extracellular domains I, similar to an Ig-like V-set domain. The discovery of structurally chimeric alleles provided evidence that interallelic recombination may contribute to alr2 variation. Comparisons of the genomic region encompassing alr2 from two field-derived haplotypes and one laboratory reference sequence revealed a history of structural variation at the haplotype level as well. Maintenance of large numbers of equally rare alleles in a natural population is a hallmark of negative frequency-dependent selection and is expected to produce high levels of heterozygosity. The observed alr2 allelic diversity is comparable with that found in immune recognition molecules such as human leukocyte antigens, B cell Igs, or natural killer cell Ig-like receptors.

Genetic diversity and recombination at the C-terminal fragment of the merozoite surface protein-1 of Plasmodium vivax (PvMSP-1) in Sri Lanka

Extensive polymorphism in the genes encoding for surface antigens of Plasmodium falciparum and Plasmodium vivax has been a serious impediment for malaria vaccine development. One such antigen is the merozoite surface protein-1 (MSP-1). The MSP-1 precursor after proteolytic cleavage generates a C-terminal fragment of 42 kDa (MSP-1 42), which subsequently produces 33 kDa (MSP-1 33) and 19 kDa (MSP-1 19) fragments. Since MSP-1 42 is currently being considered as a candidate for vaccine development against blood stage malaria it is important to catalogue the existing diversity in this antigen in natural P. vivax infections. Here we investigated the level of genetic diversity in the PvMSP-1 42 gene fragment in 95 single clone P. vivax infections in Sri Lanka. We observed that the PvMSP-1 19 fragment was highly conserved among these samples, whereas the PvMSP-1 33 fragment exhibited extensive diversity with 39 polymorphic amino acid positions (corresponding to 27 haplotypes, 19 of which were unique to Sri Lanka). Of these 27 PvMSP-1 42 haplotypes, 24 belonged to hypervariable region (HVR) T1-T7 types, while 3 haplotypes were generated by interallelic recombination between T1/T3 (HVRT8-T9) and T2/T3 (HVRT10). In addition, we analysed 107 PvMSP-1 42 sequences (corresponding to 62 haplotypes, H28 to H89) deposited in the NCBI GenBank database from other regions of the world. Seventy-four of these correspond to 9 of the 10 HVR types (HVR-T7 was unique to Sri Lanka). Two novel HVR types, T11 and T12, with a double recombination between HVR-T1/T3 and HVRT6/T2, were derived from South America and Thailand, respectively. T cell epitope polymorphism arising due to non-synonymous substitutions in PvMSP-1 33 may result in differential binding of the polymorphic peptides to class II MHC alleles, inducing different host immune responses. In conclusion, under low transmission and unstable malaria conditions prevalent in Sri Lanka, extensive allelic polymorphism was evident at PvMSP-1 33 due to recombination, mutation, and balancing selection. In contrast, PvMSP-1 19 is highly conserved , greatly enhancing its suitability as a malaria vaccine candidate.

Evolutionary analysis of two classical MHC class I loci of the medaka fish, Oryzias latipes: haplotype-specific genomic diversity, locus-specific polymorphisms, and interlocus homogenization

The major histocompatibility complex (MHC) region of the teleost medaka (Oryzias latipes) contains two classical class I loci, UAA and UBA, whereas most lower vertebrates possess or express a single locus. To elucidate the allelic diversification and evolutionary relationships of these loci, we compared the BAC-based complete genomic sequences of the MHC class I region of three medaka strains and the PCR-based cDNA sequences of two more strains and two wild individuals, representing nine haplotypes. These were derived from two geographically distinct medaka populations isolated for four to five million years. Comparison of the genomic sequences showed a marked diversity in the region encompassing UAA and UBA even between the strains derived from the same population, and also showed an ancient divergence of these loci. cDNA analysis indicated that the peptide-binding domains of both UAA and UBA are highly polymorphic and that most of the polymorphisms were established in a locus-specific manner before the divergence of the two populations. Interallelic recombination between exons 2 and 3 encoding these domains was observed. The second intron of the UAA genes contains a highly conserved region with a palindromic sequence, suggesting that this region contributed to the recombination events. In contrast, the alpha3 domain is extremely homogenized not only within each locus but also between UAA and UBA regardless of populations. Two lineages of the transmembrane and cytoplasmic regions are also shared by UAA and UBA, suggesting that these two loci evolved with intimate genetic interaction through gene conversion or unequal crossing over.

Intragenic Recombination Events and Evidence for Hybrid Speciation in Nicotiana (Solanaceae)

Reticulate evolution may function both at the species level, through homoploid and polyploid hybridization, and below the species level, through inter and intragenic recombination. These processes represent challenges for the reconstruction of evolutionary relationships between species, because they cannot be represented adequately with bifurcating trees. We use data from low-copy nuclear genes to evaluate long-standing hypotheses of homoploid (interspecific) hybrid speciation in Nicotiana (Solanaceae) and reconstruct a complex series of reticulation events that have been important in the evolutionary history of this genus. Hybrid origins for three diploid species (Nicotiana glauca, N. linearis, and N. spegazzinii) are inferred on the basis of gene tree incongruence, evidence for interallelic recombination between likely parental alleles, and support for incompatible splits in Lento plots. Phylogenetic analysis of recombinant gene sequences illustrates that recombinants may be resolved with one of their progenitor lineages with a high posterior probability under Bayesian inference, and thus there is no indication of the conflict between phylogenetic signals that results from reticulation. Our results illustrate the importance of hybridization in shaping evolution in Nicotiana and also show that intragenic recombination may be relatively common. This finding demonstrates that it is important to investigate the possibility of recombination when aiming to detect hybrids from DNA-sequence data and reconstruct patterns of reticulate evolution between species.

Clonal diversity in Giardia duodenalis isolates from Thailand: Evidences for intragenic recombination and purifying selection at the beta giardin locus

The beta giardin locus of Giardia duodenalis encodes a structural component of ventral disc and exhibits sequence variation among isolates rendering it a useful marker for genotypic analysis. To determine the distribution of genotypes of G. duodenalis in Thailand and to explore the extent of sequence variation in this locus, we deployed the PCR-RFLP method and sequence analysis of recombinant subclones from 30 clinical isolates. In total, assemblage B was more prevalent than assemblage A. Sequence analysis revealed that 13 isolates had clonal mixtures, comprising three to five distinct sequences per isolate. Nucleotide diversity of assemblage B was greater than that of assemblage A. A striking transitional bias was noted at the first and the third positions of codons in both assemblages; however, they differed in the patterns of nucleotide diversity at 0-fold and 4-fold-degenerate sites. Most amino acid exchanges were conservative in terms of polarity, charge and volume. Both assemblages have evolved under purifying selection as evidenced by a significantly greater number of mean synonymous substitutions per synonymous site ( d S) than that of nonsynonymous substitutions per nonsynonymous site ( d N) as well as significant negative Tajima's D values and its related statistics. The significant negative Tajima's D test at nonsynonymous sites further suggests that elimination of slightly deleterious mutations at these sites by purifying selection is ongoing as predicted in the nearly neutral theory. Furthermore, a minimum number of seven recombination sites was detected by the four gamete test in assemblage B, consistent with previous reports on meiotic recombination in G. duodenalis. Therefore, accurate subassemblage assignment of clinical isolates that has practical consequence for disease control could be complicated by the presence of intra-isolate clonal diversity and interallelic recombination.

Differentiation in Phytophthora infestans II. Somatic recombination in vegetative mycelium

Mutation from single to double pathogenicity in races 1, 3 and 4 of Phytophthora infestans was studied. Transfer from suboptimal to optimal cultural conditions facilitated the development of pathogenicity 4 in the races 1 and 3 and pathogenicity 3 in race 4. The new pathogenicities functioned for some time independently of the original. The mere presence of two pathogenicities in the same mycelium did not result in pathogenicity on the corresponding double-R-genotype. The reasons for this and for the finally developing ability for the P-genes to interact and attack double resisters of the potato is discussed. It is concluded that the R-genes of the potato interact to produce a specific substance impossible for the single P-genes to overcome when separate. The results support the hypothesis that the P-genes are allelic and that interallelic recombination results in the creation of a new allele causing pathogenicity on corresponding combined R-genotypes. This hypothesis is tentative in the absence of fundamental facts regarding the nuclear cycle of Phytophthora. Recombination of pathogenicities was studied after mixed infection with pairwise combinations of the races 1, 3 and 4. Out of those 1+3 and 1+4 yielded race 1234 while 3+4 only resulted in race 34. Race 1 on one hand and races 3 and 4 on the other are supposed to carry different parts of a P2 structure. The results indicate noncomplementation within the nucleus. Interallelic recombination is therefore supposed to yield a complete P2 in combination with P1 and P3 or P4 plus the mutated P4 and P3 respectively. The possible occurrence and action of an extranuclear structure, temporarily selfreplicating and distributing in vast sectors of the mycelium, can not for the present be neglected.

Genomic investigation of α‐synuclein multiplication and parkinsonism

Copy number variation is a common polymorphic phenomenon within the human genome. Although the majority of these events are non-deleterious they can also be highly pathogenic. Herein we characterize five families with parkinsonism that have been identified to harbor multiplication of the chromosomal 4q21 locus containing the alpha-synuclein gene (SNCA). A methodological approach using fluorescent in situ hybridization and Affymetrix (Santa Clara, CA) 250K SNP microarrays was used to characterize the multiplication in each family and to identify the genes encoded within the region. The telomeric and centromeric breakpoints of each family were further narrowed using semiquantitative polymerase chain reaction with microsatellite markers and then screened for transposable repeat elements. The severity of clinical presentation is correlated with SNCA dosage and does not appear to be overtly affected by the presence of other genes in the multiplicated region. With the exception of the Lister kindred, in each family the multiplication event appears de novo. The type and position of Alu/LINE repeats are also different at each breakpoint. Microsatellite analysis demonstrates two genomic mechanisms are responsible for chromosome 4q21 multiplications, including both SNCA duplication and recombination. SNCA dosage is responsible for parkinsonism, autonomic dysfunction, and dementia observed within each family. We hypothesize dysregulated expression of wild-type alpha-synuclein results in parkinsonism and may explain the recent association of common SNCA variants in sporadic Parkinson's disease. SNCA genomic duplication results from intraallelic (segmental duplication) or interallelic recombination with unequal crossing over, whereas both mechanisms appear to be required for genomic SNCA triplication.

The study of the extended haplotypes of rare HLA‐B*2730 allele using microsatellite loci

The aim of the present study was to compare haplotypes of the most frequent B*27 alleles among Croatians (B*2702 and *2705) and the rare B*2730 allele. For this purpose, 37 families with members carrying human leukocyte antigen (HLA)-B27 were selected. All individuals were analysed for eight microsatellites (Msats): D6S2927, short tandem repeat - MHC class I-related gene (STR_MICA), D6S2793, D6S2811, tumor necrosis factor a (TNFa), tumor necrosis factor d (TNFd), D6S273 and D6S1014, while individuals carrying the HLA-B27 specificity were subtyped. Of 39 analysed haplotypes, 20 individuals had B*2702, 15 subjects were positive for the B*2705 allele, the B*2730 allele was found in three haplotypes from different families, while one individual carried the B*2703 allele. HLA-A3 and -DRB1*16 were shared by all three B*2730 haplotypes. The DRB1*16 allele was also observed in the majority of B*2702 haplotypes (76.5%), while HLA-A3 was, after HLA-A2, the second most frequent HLA-A specificity in B*2702 haplotypes. No such correlation was found for the B*2705 haplotypes. Msat analysis showed that B*2730 haplotypes also share the same allele at all tested Msats. The D6S2927, D6S2793, MICA and TNFd Msats were not useful in distinguishing B*2702 and B*2705 alleles because D6S2927-213bp, STR_MICA-179bp, D6S2793-206bp, D6S2811-83bp and TNFd-130bp were detected in almost all cases. Conversely, for the TNFa, D6S273 and D6S1014 loci, haplotypes carrying B*2702 and B*2730 shared a single Msat allele in the majority of cases (TNFa-113bp, D6S1014-134bp and D6S273-134bp), which was not observed for B*2705 haplotypes. In conclusion, the similarity between B*2702 and B*2730 DNA sequences as well as their sharing of the same haplotypic combinations corroborates the proposed mechanism of B*2730 evolution from B*2702 by interallelic recombination.

Identification of the very uncommon allele HLA‐Cw*0716 in a Caucasian renal transplant recipient: extension of the exon 4 sequence

This report describes the unknown exon 4 sequence of the rare human leukocyte antigen-Cw*0716 allele, identified in a Caucasian renal transplant recipient from Italy. This sequence is identical to the Cw*070101 allele, and this result allowed us to confirm the hypothesis of the generation of Cw*0716 allele by an interallelic recombination event between Cw*0701/0706/0718 and Cw*020202 allele.

Allelic dimorphism-associated restriction of recombination in Plasmodium falciparum msp1

Allelic dimorphism is a characteristic feature of the Plasmodium falciparum msp1 gene encoding the merozoite surface protein 1, a strong malaria vaccine candidate. Meiotic recombination is a major mechanism for the generation of msp1 allelic diversity. Potential recombination sites have previously been mapped to specific regions within msp1 (a 5′ 1-kb region and a 3′ 0.4-kb region) with no evidence for recombination events in a central 3.5-kb region. However, evidence for the lack of recombination events is circumstantial and inconclusive because the number of msp1 sequences analysed is limited, and the frequency of recombination events has not been addressed previously in a high transmission area, where the frequency of meiotic recombination is expected to be high. In the present study, we have mapped potential allelic recombination sites in 34 full-length msp1 sequences, including 24 new sequences, from various geographic origins. We also investigated recombination events in blocks 6 to 16 by population genetic analysis of P. falciparum populations in Tanzania, where malaria transmission is intense. The results clearly provide no evidence of recombination events occurring between the two major msp1 allelic types, K1-type and Mad20-type, in the central region, but do show recombination events occurring throughout the entire gene within sequences of the Mad20-type. Thus, the present study indicates that allelic dimorphism of msp1 greatly affects inter-allelic recombination events, highlighting a unique feature of allelic diversity of P. falciparum msp1.

Reconstructing Historical Events that Occurred in the Petunia Hf1 Gene, which Governs Anthocyanin Biosynthesis, and Effects of Artificial Selection by Breeding

The nucleotide sequence of a gene, Hf1, encoding the flavonoid 3′,5′-hydroxylase in commercial petunias was compared to those in natural species to reconstruct historical events that occurred at the Hf1 locus in commercial petunias in the course of breeding since the 1830s. Intact Hf1 genes of any natural species so far studied were not detectable in 84 commercial petunias examined and were considered to have been removed by breeders. The dominant Hf1 alleles isolated from 14 Hf1 Hf1 cultivars showed an identical open reading frame (ORF) sequence and were considered to result from inter-allelic recombination between Hf1 of Petunia axillaris subsp. axillaris or subsp. parodii and Hf1 of P. integrifolia subsp. integrifolia or P. inflata, which were recorded as or assumed to be the historical parents of commercial petunias. Recessive hf1-3 was considered to be a mutant allele of the recombined Hf1 associated with the insertion of a retrotransposable element (rTph1) into exon III. The recessive hf1-2 allele showed a sequence identical to that of Hf1 of P. integrifolia subsp. integrifolia and P. inflata, except for a transposable element (dTph9) inserted into exon III and a target site duplication. We analyzed the potential causes of the recombination that occurred at the Hf1 locus and of the removal of dominant Hf1 genes of natural species from commercial petunias.

Interallelic class switch recombination can reverse allelic exclusion and allow trans‐complementation of an IgH locus switching defect

The predominant path of immunoglobulin class switch recombination follows the paradigm of intra-chromosomal deletion enabling expression of another heavy chain instead of micro and delta. This was, however, challenged by observations of inter-allelic class switch recombination in rabbit or mouse IgG3- or IgA-producing B cells. Assuming that the conditions of inter-chromosomal exchange are likely present at any target S regions in stimulated B cells, we explored trans-association of VH and C genes in a model allowing all C genes to be checked simultaneously. Heterozygous mutant mice are thus studied, which carry one non-functional IgH allele inactivated by a non-translatable mutation of VDJ-CH transcripts, while the functional allele is deficient for class switching due to a truncated 3'regulatory region. A fair level of switching to all Ig classes is restored in heterozygous mice despite the fact that cis-recombination is either non productive on one allele or deficient on the other. Molecular evidence at the DNA level of trans-CSR to IgG3 was demonstrated by cloning and sequencing Smu-Sgamma3 hybrid junctions. These data demonstrate that inter-allelic recombination may broadly rescue the production of various class-switched isotypes and allow complementation between mutations located at both ends of the IgH constant gene cluster.

Four new HLA class I alleles in Cauacasoids*

Four new HLA classical class I alleles in the three loci are described in Caucasian individuals. A*3012 was first suspected by an abnormal serologic pattern that would be explained by the single amino acid substitution at the A30-specific Ser17. B*270505 differs from B*270502 in a silent substitution at an up to now constant position in the B locus. B*3541 encodes for a new Cys at position 118 that has not been encountered in neither human nor primate alleles. Cw*0716 seems to be originated by a large-scale interallelic recombination event between Cw*0701/*0706/*0718 and Cw*020202, giving rise to a new antigen-binding cleft conformation.