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Identifying rhesus macaque gene orthologs using heterospecific human CNV probes.

Ng J, Fass JN, Durbin-Johnson B, Smith DG, Kanthaswamy S - Genom Data (2015)

Bottom Line: Observed genomic rearrangements and synteny were in agreement with the results of a previously published genomic comparison between humans and rhesus macaques.Comparisons between each of the two rhesus macaques and humans yielded 206 regions with copy numbers that differed by at least two fold in the Indian rhesus macaque and human, 32 in the Chinese rhesus macaque and human, and 147 in both rhesus macaques.The detailed genomic map and preliminary CNV data are useful for better understanding genetic variation in rhesus macaques, identifying derived changes in human CNVs that may have evolved by selection, and determining the suitability of rhesus macaques as human models for particular biomedical studies.

View Article: PubMed Central - PubMed

Affiliation: Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, CA, USA.

ABSTRACT
We used the Affymetrix(®) Genome-Wide Human SNP Array 6.0 to identify heterospecific markers and compare copy number and structural genomic variation between humans and rhesus macaques. Over 200,000 human copy number variation (CNV) probes were mapped to a Chinese and an Indian rhesus macaque sample. Observed genomic rearrangements and synteny were in agreement with the results of a previously published genomic comparison between humans and rhesus macaques. Comparisons between each of the two rhesus macaques and humans yielded 206 regions with copy numbers that differed by at least two fold in the Indian rhesus macaque and human, 32 in the Chinese rhesus macaque and human, and 147 in both rhesus macaques. The detailed genomic map and preliminary CNV data are useful for better understanding genetic variation in rhesus macaques, identifying derived changes in human CNVs that may have evolved by selection, and determining the suitability of rhesus macaques as human models for particular biomedical studies.

No MeSH data available.


Observed genetic rearrangement of rhesus macaque (R) chromosome 10 as compared to orthologous human (H) chromosomes 20 and 22 for (a) Indian rhesus macaque and human, (b) Chinese rhesus macaque and human, and (c) between the Indian and Chinese rhesus macaques. The colors indicate different gene blocks and arrows identify blocks with genomic inversions that were observed using the orthologous probes. Since each comparison set was done separately using markers found in both individuals compared, the number of genes identified differed and the color blocks do not represent the same segments between (a–c).
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f0030: Observed genetic rearrangement of rhesus macaque (R) chromosome 10 as compared to orthologous human (H) chromosomes 20 and 22 for (a) Indian rhesus macaque and human, (b) Chinese rhesus macaque and human, and (c) between the Indian and Chinese rhesus macaques. The colors indicate different gene blocks and arrows identify blocks with genomic inversions that were observed using the orthologous probes. Since each comparison set was done separately using markers found in both individuals compared, the number of genes identified differed and the color blocks do not represent the same segments between (a–c).

Mentions: Chromosomal rearrangements, such as the fusion of rhesus macaque chromosomes 12 and 13 that are orthologous to human chromosome 2, were in agreement with previous observations in great apes [26], baboons [27], and Japanese macaques [28]. Human chromosomes 5, 12, and X and their orthologous rhesus macaque chromosomes showed no microinversions or rearrangements in either the Indian or the Chinese rhesus macaque while human chromosome 19 also showed no rearrangement in the Chinese rhesus macaque. The chromosomal fission of human chromosome 2 corresponding to the orthologous rhesus macaque chromosomes 12 and 13 mentioned above and the chromosomal fusions of human chromosomes 7 and 21 to rhesus macaque chromosome 3, human 14 and 15 to rhesus macaque 7, and human 20 and 22 to rhesus macaque 10 were observed and consistent with previous studies [17], [23], [24], [26], [28], [29]. Despite being of the same species, rearrangements, albeit small compared to those observed between human and rhesus macaque, were observed in chromosomes 2, 4, 5, 7, 10, 14, 15, 16, 19, 20, and X in the Indian and Chinese rhesus macaque. Fig. 2 shows the large-scale chromosomal rearrangements and synteny observed in rhesus macaque chromosome 10 in both rhesus macaque reference genomes (Fig. 2a: Indian rheMac2; 2b: Chinese rheMac3) in relation to the human genome (hg19) and between the two rhesus macaques (Fig. 2c) for all mapped and annotated genes. Similar genomic rearrangements and regional inversions were observed in both Indian and Chinese rhesus macaques as compared to human with the exception of a single inversion block at the end of rhesus chromosome 10 and human chromosome 22 (Fig. 2b). Although the Chinese rhesus macaque-human inversion above was not observed when the two rhesus macaques were compared, a gene rearrangement was detected, indicating that structural genomic variation exists within the rhesus macaque species. Chromosomal rearrangement and microinversions for each comparison are shown in Supplementary File 1, Supplementary File 2, Supplementary File 3 for Indian rhesus-human, Chinese rhesus-human, and Indian-Chinese rhesus macaques, respectively.


Identifying rhesus macaque gene orthologs using heterospecific human CNV probes.

Ng J, Fass JN, Durbin-Johnson B, Smith DG, Kanthaswamy S - Genom Data (2015)

Observed genetic rearrangement of rhesus macaque (R) chromosome 10 as compared to orthologous human (H) chromosomes 20 and 22 for (a) Indian rhesus macaque and human, (b) Chinese rhesus macaque and human, and (c) between the Indian and Chinese rhesus macaques. The colors indicate different gene blocks and arrows identify blocks with genomic inversions that were observed using the orthologous probes. Since each comparison set was done separately using markers found in both individuals compared, the number of genes identified differed and the color blocks do not represent the same segments between (a–c).
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664757&req=5

f0030: Observed genetic rearrangement of rhesus macaque (R) chromosome 10 as compared to orthologous human (H) chromosomes 20 and 22 for (a) Indian rhesus macaque and human, (b) Chinese rhesus macaque and human, and (c) between the Indian and Chinese rhesus macaques. The colors indicate different gene blocks and arrows identify blocks with genomic inversions that were observed using the orthologous probes. Since each comparison set was done separately using markers found in both individuals compared, the number of genes identified differed and the color blocks do not represent the same segments between (a–c).
Mentions: Chromosomal rearrangements, such as the fusion of rhesus macaque chromosomes 12 and 13 that are orthologous to human chromosome 2, were in agreement with previous observations in great apes [26], baboons [27], and Japanese macaques [28]. Human chromosomes 5, 12, and X and their orthologous rhesus macaque chromosomes showed no microinversions or rearrangements in either the Indian or the Chinese rhesus macaque while human chromosome 19 also showed no rearrangement in the Chinese rhesus macaque. The chromosomal fission of human chromosome 2 corresponding to the orthologous rhesus macaque chromosomes 12 and 13 mentioned above and the chromosomal fusions of human chromosomes 7 and 21 to rhesus macaque chromosome 3, human 14 and 15 to rhesus macaque 7, and human 20 and 22 to rhesus macaque 10 were observed and consistent with previous studies [17], [23], [24], [26], [28], [29]. Despite being of the same species, rearrangements, albeit small compared to those observed between human and rhesus macaque, were observed in chromosomes 2, 4, 5, 7, 10, 14, 15, 16, 19, 20, and X in the Indian and Chinese rhesus macaque. Fig. 2 shows the large-scale chromosomal rearrangements and synteny observed in rhesus macaque chromosome 10 in both rhesus macaque reference genomes (Fig. 2a: Indian rheMac2; 2b: Chinese rheMac3) in relation to the human genome (hg19) and between the two rhesus macaques (Fig. 2c) for all mapped and annotated genes. Similar genomic rearrangements and regional inversions were observed in both Indian and Chinese rhesus macaques as compared to human with the exception of a single inversion block at the end of rhesus chromosome 10 and human chromosome 22 (Fig. 2b). Although the Chinese rhesus macaque-human inversion above was not observed when the two rhesus macaques were compared, a gene rearrangement was detected, indicating that structural genomic variation exists within the rhesus macaque species. Chromosomal rearrangement and microinversions for each comparison are shown in Supplementary File 1, Supplementary File 2, Supplementary File 3 for Indian rhesus-human, Chinese rhesus-human, and Indian-Chinese rhesus macaques, respectively.

Bottom Line: Observed genomic rearrangements and synteny were in agreement with the results of a previously published genomic comparison between humans and rhesus macaques.Comparisons between each of the two rhesus macaques and humans yielded 206 regions with copy numbers that differed by at least two fold in the Indian rhesus macaque and human, 32 in the Chinese rhesus macaque and human, and 147 in both rhesus macaques.The detailed genomic map and preliminary CNV data are useful for better understanding genetic variation in rhesus macaques, identifying derived changes in human CNVs that may have evolved by selection, and determining the suitability of rhesus macaques as human models for particular biomedical studies.

View Article: PubMed Central - PubMed

Affiliation: Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, CA, USA.

ABSTRACT
We used the Affymetrix(®) Genome-Wide Human SNP Array 6.0 to identify heterospecific markers and compare copy number and structural genomic variation between humans and rhesus macaques. Over 200,000 human copy number variation (CNV) probes were mapped to a Chinese and an Indian rhesus macaque sample. Observed genomic rearrangements and synteny were in agreement with the results of a previously published genomic comparison between humans and rhesus macaques. Comparisons between each of the two rhesus macaques and humans yielded 206 regions with copy numbers that differed by at least two fold in the Indian rhesus macaque and human, 32 in the Chinese rhesus macaque and human, and 147 in both rhesus macaques. The detailed genomic map and preliminary CNV data are useful for better understanding genetic variation in rhesus macaques, identifying derived changes in human CNVs that may have evolved by selection, and determining the suitability of rhesus macaques as human models for particular biomedical studies.

No MeSH data available.