A high-resolution radiation hybrid map of rhesus macaque chromosome 5 identifies rearrangements in the genome assembly

Abstract

A 10,000-rad radiation hybrid (RH) cell panel of the rhesus macaque was generated to construct a comprehensive RH map of chromosome 5. The map represents 218 markers typed in 185 RH clones. The 4846-cR map has an average marker spacing of 798 kb. Alignments of the RH map to macaque and human genome sequences confirm a large inversion and reveal a previously unreported telomeric inversion. The macaque genome sequence indicates small translocations from the ancestral homolog of macaque chromosome 5 to macaque chromosomes 1 and 6. The RH map suggests that these are probably assembly artifacts. Unlike the genome sequence, the RH mapping data indicate the conservation of synteny between macaque chromosome 5 and human chromosome 4. This study shows that the 10,000-rad panel is appropriate for the generation of a high-resolution whole-genome RH map suitable for the verification of the rhesus genome assembly.

Fig. 1. Comparison of marker order on the 10,000-rad RH map of the rhesus macaque chromosome 5 (Mmul5) with the macaque genomic map and the human homolog, Hsap 4

Left: Hsap 4 genomic map, Middle: RH map developed in this report, Right: Macaque genome sequence assembly of Mmul5 (Ensembl v.47, UCSC v.173). The positions of the BACs used to orient the linkage groups are indicated by asterisks added to the corresponding markers. The extent of the initial large linkage groups is indicated by the grey shaded vertical bars to the left of the macaque RH-map data. Comparisons of the RH and human genomic maps reveal two larger rearrangements, one involving the centromere and a second subtelomeric inversion on the p-arm. Comparisons of the RH and macaque genomic maps detect likely genome sequence assembly artifacts for regions assigned to Mmul 1 and 6. These regions are identified by four genes (WHSC2, MAEA, SLC26A1, CPLX1) and a single gene (PTTG2). The RH map displays complete synteny conservation between Mmul 5 and Hsap 4.

Fig. 1. Comparison of marker order on the 10,000-rad RH map of the rhesus macaque chromosome 5 (Mmul5) with the macaque genomic map and the human homolog, Hsap 4

Left: Hsap 4 genomic map, Middle: RH map developed in this report, Right: Macaque genome sequence assembly of Mmul5 (Ensembl v.47, UCSC v.173). The positions of the BACs used to orient the linkage groups are indicated by asterisks added to the corresponding markers. The extent of the initial large linkage groups is indicated by the grey shaded vertical bars to the left of the macaque RH-map data. Comparisons of the RH and human genomic maps reveal two larger rearrangements, one involving the centromere and a second subtelomeric inversion on the p-arm. Comparisons of the RH and macaque genomic maps detect likely genome sequence assembly artifacts for regions assigned to Mmul 1 and 6. These regions are identified by four genes (WHSC2, MAEA, SLC26A1, CPLX1) and a single gene (PTTG2). The RH map displays complete synteny conservation between Mmul 5 and Hsap 4.

Fig. 1. Comparison of marker order on the 10,000-rad RH map of the rhesus macaque chromosome 5 (Mmul5) with the macaque genomic map and the human homolog, Hsap 4

Left: Hsap 4 genomic map, Middle: RH map developed in this report, Right: Macaque genome sequence assembly of Mmul5 (Ensembl v.47, UCSC v.173). The positions of the BACs used to orient the linkage groups are indicated by asterisks added to the corresponding markers. The extent of the initial large linkage groups is indicated by the grey shaded vertical bars to the left of the macaque RH-map data. Comparisons of the RH and human genomic maps reveal two larger rearrangements, one involving the centromere and a second subtelomeric inversion on the p-arm. Comparisons of the RH and macaque genomic maps detect likely genome sequence assembly artifacts for regions assigned to Mmul 1 and 6. These regions are identified by four genes (WHSC2, MAEA, SLC26A1, CPLX1) and a single gene (PTTG2). The RH map displays complete synteny conservation between Mmul 5 and Hsap 4.

Fig. 1. Comparison of marker order on the 10,000-rad RH map of the rhesus macaque chromosome 5 (Mmul5) with the macaque genomic map and the human homolog, Hsap 4

Left: Hsap 4 genomic map, Middle: RH map developed in this report, Right: Macaque genome sequence assembly of Mmul5 (Ensembl v.47, UCSC v.173). The positions of the BACs used to orient the linkage groups are indicated by asterisks added to the corresponding markers. The extent of the initial large linkage groups is indicated by the grey shaded vertical bars to the left of the macaque RH-map data. Comparisons of the RH and human genomic maps reveal two larger rearrangements, one involving the centromere and a second subtelomeric inversion on the p-arm. Comparisons of the RH and macaque genomic maps detect likely genome sequence assembly artifacts for regions assigned to Mmul 1 and 6. These regions are identified by four genes (WHSC2, MAEA, SLC26A1, CPLX1) and a single gene (PTTG2). The RH map displays complete synteny conservation between Mmul 5 and Hsap 4.

Fig. 2. A scattergram of the retention frequencies of 218 markers along rhesus macaque chromosome 5

High retention frequencies were observed for the markers mapped around the centromere. On average, the markers on the short-arm exhibited a higher retention frequency than markers of the long-arm of the chromosome.

Fig. 3. Three color fluorescent in situ hybridization with BAC clones identifying the orientation of RH linkage groups on macaque chromosome 5

The red and green signals (BAC clone CH-250 14B16 and CH-250 11I13, respectively) delineate the adjoining borders of two RH linkage groups. The yellow signal delineates the hybridization of BAC clone CH-250 1K22. The picture shows hybridization signals of three out of seven BAC clones used to orient the linkage groups.

Fig. 4. Schematic comparison of the macaque RH map with human and macaque genome sequence maps

The figure depicts only markers revealing rearrangements between the different maps as recognized by the crossing lines. Markers in regions for which the maps are collinear are not connected for simplification.