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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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Phylogenetic tree of mtDNA sequences coding for parts of the 12S rRNA of cynomolgus macaques. Brackets indicate the different geographic clusters. The tree was rooted with selected rhesus macaque sequences from India, China, and Burma. mtDNA sequences without accession numbers have been published recently (Doxiadis et al. 2006a) or have now been submitted to EMBL/GeneBank database. Juanita, Rastafa, Alfa, and Sayonara are representatives of the four Cynomolgus families, and Cyn81 and Cyn83 are the two unrelated animals analyzed in this study (shadowed)
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Figure 1: Phylogenetic tree of mtDNA sequences coding for parts of the 12S rRNA of cynomolgus macaques. Brackets indicate the different geographic clusters. The tree was rooted with selected rhesus macaque sequences from India, China, and Burma. mtDNA sequences without accession numbers have been published recently (Doxiadis et al. 2006a) or have now been submitted to EMBL/GeneBank database. Juanita, Rastafa, Alfa, and Sayonara are representatives of the four Cynomolgus families, and Cyn81 and Cyn83 are the two unrelated animals analyzed in this study (shadowed)

Mentions: Sequencing of the 3′ part of the 12S rRNA has been performed of cynomolgus monkeys of an outbred breeding colony, and all different mtDNA sequences detected were subjected to phylogenetic analysis in comparison to published mtDNA sequences of established geographic origin. The resulting tree reveals a differential clustering of mtDNA sequences reflecting the origin of the monkeys (Fig. 1). A main branching point can be observed separating mtDNA segments of cynomolgus macaques from Indochina, north of the isthmus of Kra including China and Vietnam on the one hand and Malaysia and the Indonesian/Malaysian islands on the other hand. These data confirm earlier observations that monkeys from Indochina and Malaysia/Indonesia are phylogenetically distinguishable by mtDNA analysis (Smith et al. 2007). Although the two samples from Thailand that are not supported by bootstrap values do not cluster together with the mtDNA sequences of animals from north of Kra, the data indicate that the families of Juanita and Rastafa originated from the Malaysian/Indonesian islands, whereas the families of Alfa and Sayonara, and the two unrelated monkeys, Cyn81 and Cyn83, have their roots in the Malaysian peninsula, south of the isthmus of Kra (Fig. 1).


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)

Phylogenetic tree of mtDNA sequences coding for parts of the 12S rRNA of cynomolgus macaques. Brackets indicate the different geographic clusters. The tree was rooted with selected rhesus macaque sequences from India, China, and Burma. mtDNA sequences without accession numbers have been published recently (Doxiadis et al. 2006a) or have now been submitted to EMBL/GeneBank database. Juanita, Rastafa, Alfa, and Sayonara are representatives of the four Cynomolgus families, and Cyn81 and Cyn83 are the two unrelated animals analyzed in this study (shadowed)
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Phylogenetic tree of mtDNA sequences coding for parts of the 12S rRNA of cynomolgus macaques. Brackets indicate the different geographic clusters. The tree was rooted with selected rhesus macaque sequences from India, China, and Burma. mtDNA sequences without accession numbers have been published recently (Doxiadis et al. 2006a) or have now been submitted to EMBL/GeneBank database. Juanita, Rastafa, Alfa, and Sayonara are representatives of the four Cynomolgus families, and Cyn81 and Cyn83 are the two unrelated animals analyzed in this study (shadowed)
Mentions: Sequencing of the 3′ part of the 12S rRNA has been performed of cynomolgus monkeys of an outbred breeding colony, and all different mtDNA sequences detected were subjected to phylogenetic analysis in comparison to published mtDNA sequences of established geographic origin. The resulting tree reveals a differential clustering of mtDNA sequences reflecting the origin of the monkeys (Fig. 1). A main branching point can be observed separating mtDNA segments of cynomolgus macaques from Indochina, north of the isthmus of Kra including China and Vietnam on the one hand and Malaysia and the Indonesian/Malaysian islands on the other hand. These data confirm earlier observations that monkeys from Indochina and Malaysia/Indonesia are phylogenetically distinguishable by mtDNA analysis (Smith et al. 2007). Although the two samples from Thailand that are not supported by bootstrap values do not cluster together with the mtDNA sequences of animals from north of Kra, the data indicate that the families of Juanita and Rastafa originated from the Malaysian/Indonesian islands, whereas the families of Alfa and Sayonara, and the two unrelated monkeys, Cyn81 and Cyn83, have their roots in the Malaysian peninsula, south of the isthmus of Kra (Fig. 1).

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