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Comparative genetics of a highly divergent DRB microsatellite in different macaque species.

de Groot N, Doxiadis GG, de Vos-Rouweler AJ, de Groot NG, Verschoor EJ, Bontrop RE - Immunogenetics (2008)

Bottom Line: Sequencing analysis resulted in the detection of 60 Mafa-DRB exon 2 sequences that were unambiguously linked to the corresponding microsatellite.Although both macaque species are known to share several identical DRB exon 2 sequences, the lengths of the corresponding microsatellites often differ.Thus, this method allows not only fast and accurate DRB haplotyping but may also permit discrimination between highly related macaque species.

View Article: PubMed Central - PubMed

Affiliation: Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands. nanine.de.groot@bprc.nl

ABSTRACT
The DRB region of the major histocompatibility complex (MHC) of cynomolgus and rhesus macaques is highly plastic, and extensive copy number variation together with allelic polymorphism makes it a challenging enterprise to design a typing protocol. All intact DRB genes in cynomolgus monkeys (Mafa) appear to possess a compound microsatellite, DRB-STR, in intron 2, which displays extensive length polymorphism. Therefore, this STR was studied in a large panel of animals, comprising pedigreed families as well. Sequencing analysis resulted in the detection of 60 Mafa-DRB exon 2 sequences that were unambiguously linked to the corresponding microsatellite. Its length is often allele specific and follows Mendelian segregation. In cynomolgus and rhesus macaques, the nucleotide composition of the DRB-STR is in concordance with the phylogeny of exon 2 sequences. As in humans and rhesus monkeys, this protocol detects specific combinations of different DRB-STR lengths that are unique for each haplotype. In the present panel, 22 Mafa-DRB region configurations could be defined, which exceeds the number detected in a comparable cohort of Indian rhesus macaques. The results suggest that, in cynomolgus monkeys, even more frequently than in rhesus macaques, new haplotypes are generated by recombination-like events. Although both macaque species are known to share several identical DRB exon 2 sequences, the lengths of the corresponding microsatellites often differ. Thus, this method allows not only fast and accurate DRB haplotyping but may also permit discrimination between highly related macaque species.

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a Phylogenetic tree of DRB exon 2 sequences of rhesus and cynomolgus macaques. DRB alleles of cynomolgus and rhesus macaques are depicted in yellow and blue boxes, respectively. b Composition of the DRB-STR microsatellite The order of the sequences follows the order of the exon 2 sequences as they cluster in the phylogenetic tree (a). Clustering of alleles shared between both macaque species is illustrated by color codes; the bordered sequence (yellow and green) highlights a crossing-over event. (a) (GT)n part of Mafa-DRB6*0107 belonging to haplotype 2, (b) (GT)n part of Mafa-DRB6*0107 belonging to haplotype 3
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Figure 3: a Phylogenetic tree of DRB exon 2 sequences of rhesus and cynomolgus macaques. DRB alleles of cynomolgus and rhesus macaques are depicted in yellow and blue boxes, respectively. b Composition of the DRB-STR microsatellite The order of the sequences follows the order of the exon 2 sequences as they cluster in the phylogenetic tree (a). Clustering of alleles shared between both macaque species is illustrated by color codes; the bordered sequence (yellow and green) highlights a crossing-over event. (a) (GT)n part of Mafa-DRB6*0107 belonging to haplotype 2, (b) (GT)n part of Mafa-DRB6*0107 belonging to haplotype 3

Mentions: The Mafa-DRB sequences described in this study were analyzed together with the Mamu-DRB alleles published previously (Doxiadis et al. 2007) (Fig. 3a), and the corresponding microsatellite sequences have been superimposed (Fig. 3b). The high number of branches as well as the complex microsatellite patterns correlates with the high number of DRB region configurations/haplotypes observed in rhesus as well as in cynomolgus macaques. As one would expect, the Mamu- and Mafa-DRB sequences intermingle in the phylogenetic tree, and alleles of identical loci/lineages of both species cluster together. Mamu/Mafa-DRB6 alleles form a distinct clade in the tree, which is in agreement with the fact that this locus is an old entity predating the divergence of Old World monkeys and humans and great apes (Fig. 3a). Furthermore, the composition of the microsatellite is alike in both macaque species, reflecting their common ancestry (Fig. 3b). Such sharing of similar sequence motifs has been highlighted by similar color codes (Fig. 3b). An example is given for the Mamu/Mafa-DRB alleles of the DRB*W3 lineage, which appear to be biphyletic, since they cluster on two branches in the tree (Fig. 3a and b). The composition of the adjacent DRB-STR matches the phylogeny (Fig. 3b, yellow). One of the DRB*W3 alleles of the second group, Mafa-DRB*W303, clusters slightly apart, next to DRB1*04 lineage members (Fig. 3b, green). As can be seen, its STR composition appears to be a mixture of the two lineages. The (GT)x part resembles the first part of the DRB*W3 members (Fig. 2b, yellow), the following parts of the STR are the same as in the DRB1*04 lineage (Fig. 3b, green). Thus, the genetic makeup of this DRB-STR suggests that it was generated by a crossing-over event between two different DRB lineages. This type of result underscores the above-described notion (Fig. 2, haplotypes 9, 10, and 11) that the generation—also called the birth and death process—of DRB genes and haplotypes is a steadily ongoing process, mostly propelled by recombination-like processes. These data are in concert with recent observations that illustrate that the DRB genes themselves, judged from an evolutionary perspective, are relatively young entities (von Salome et al. 2007), but that exon 2 gene segments that encode the peptide binding site represent much older gene segments that are frequently sprinkled over different duplicated DRB genes during primate evolution (Doxiadis et al. 2008b).


Comparative genetics of a highly divergent DRB microsatellite in different macaque species.

de Groot N, Doxiadis GG, de Vos-Rouweler AJ, de Groot NG, Verschoor EJ, Bontrop RE - Immunogenetics (2008)

a Phylogenetic tree of DRB exon 2 sequences of rhesus and cynomolgus macaques. DRB alleles of cynomolgus and rhesus macaques are depicted in yellow and blue boxes, respectively. b Composition of the DRB-STR microsatellite The order of the sequences follows the order of the exon 2 sequences as they cluster in the phylogenetic tree (a). Clustering of alleles shared between both macaque species is illustrated by color codes; the bordered sequence (yellow and green) highlights a crossing-over event. (a) (GT)n part of Mafa-DRB6*0107 belonging to haplotype 2, (b) (GT)n part of Mafa-DRB6*0107 belonging to haplotype 3
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
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getmorefigures.php?uid=PMC4629986&req=5

Figure 3: a Phylogenetic tree of DRB exon 2 sequences of rhesus and cynomolgus macaques. DRB alleles of cynomolgus and rhesus macaques are depicted in yellow and blue boxes, respectively. b Composition of the DRB-STR microsatellite The order of the sequences follows the order of the exon 2 sequences as they cluster in the phylogenetic tree (a). Clustering of alleles shared between both macaque species is illustrated by color codes; the bordered sequence (yellow and green) highlights a crossing-over event. (a) (GT)n part of Mafa-DRB6*0107 belonging to haplotype 2, (b) (GT)n part of Mafa-DRB6*0107 belonging to haplotype 3
Mentions: The Mafa-DRB sequences described in this study were analyzed together with the Mamu-DRB alleles published previously (Doxiadis et al. 2007) (Fig. 3a), and the corresponding microsatellite sequences have been superimposed (Fig. 3b). The high number of branches as well as the complex microsatellite patterns correlates with the high number of DRB region configurations/haplotypes observed in rhesus as well as in cynomolgus macaques. As one would expect, the Mamu- and Mafa-DRB sequences intermingle in the phylogenetic tree, and alleles of identical loci/lineages of both species cluster together. Mamu/Mafa-DRB6 alleles form a distinct clade in the tree, which is in agreement with the fact that this locus is an old entity predating the divergence of Old World monkeys and humans and great apes (Fig. 3a). Furthermore, the composition of the microsatellite is alike in both macaque species, reflecting their common ancestry (Fig. 3b). Such sharing of similar sequence motifs has been highlighted by similar color codes (Fig. 3b). An example is given for the Mamu/Mafa-DRB alleles of the DRB*W3 lineage, which appear to be biphyletic, since they cluster on two branches in the tree (Fig. 3a and b). The composition of the adjacent DRB-STR matches the phylogeny (Fig. 3b, yellow). One of the DRB*W3 alleles of the second group, Mafa-DRB*W303, clusters slightly apart, next to DRB1*04 lineage members (Fig. 3b, green). As can be seen, its STR composition appears to be a mixture of the two lineages. The (GT)x part resembles the first part of the DRB*W3 members (Fig. 2b, yellow), the following parts of the STR are the same as in the DRB1*04 lineage (Fig. 3b, green). Thus, the genetic makeup of this DRB-STR suggests that it was generated by a crossing-over event between two different DRB lineages. This type of result underscores the above-described notion (Fig. 2, haplotypes 9, 10, and 11) that the generation—also called the birth and death process—of DRB genes and haplotypes is a steadily ongoing process, mostly propelled by recombination-like processes. These data are in concert with recent observations that illustrate that the DRB genes themselves, judged from an evolutionary perspective, are relatively young entities (von Salome et al. 2007), but that exon 2 gene segments that encode the peptide binding site represent much older gene segments that are frequently sprinkled over different duplicated DRB genes during primate evolution (Doxiadis et al. 2008b).

Bottom Line: Sequencing analysis resulted in the detection of 60 Mafa-DRB exon 2 sequences that were unambiguously linked to the corresponding microsatellite.Although both macaque species are known to share several identical DRB exon 2 sequences, the lengths of the corresponding microsatellites often differ.Thus, this method allows not only fast and accurate DRB haplotyping but may also permit discrimination between highly related macaque species.

View Article: PubMed Central - PubMed

Affiliation: Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands. nanine.de.groot@bprc.nl

ABSTRACT
The DRB region of the major histocompatibility complex (MHC) of cynomolgus and rhesus macaques is highly plastic, and extensive copy number variation together with allelic polymorphism makes it a challenging enterprise to design a typing protocol. All intact DRB genes in cynomolgus monkeys (Mafa) appear to possess a compound microsatellite, DRB-STR, in intron 2, which displays extensive length polymorphism. Therefore, this STR was studied in a large panel of animals, comprising pedigreed families as well. Sequencing analysis resulted in the detection of 60 Mafa-DRB exon 2 sequences that were unambiguously linked to the corresponding microsatellite. Its length is often allele specific and follows Mendelian segregation. In cynomolgus and rhesus macaques, the nucleotide composition of the DRB-STR is in concordance with the phylogeny of exon 2 sequences. As in humans and rhesus monkeys, this protocol detects specific combinations of different DRB-STR lengths that are unique for each haplotype. In the present panel, 22 Mafa-DRB region configurations could be defined, which exceeds the number detected in a comparable cohort of Indian rhesus macaques. The results suggest that, in cynomolgus monkeys, even more frequently than in rhesus macaques, new haplotypes are generated by recombination-like events. Although both macaque species are known to share several identical DRB exon 2 sequences, the lengths of the corresponding microsatellites often differ. Thus, this method allows not only fast and accurate DRB haplotyping but may also permit discrimination between highly related macaque species.

Show MeSH
Related in: MedlinePlus