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. 2013 Jan;101(1):30-7.
doi: 10.1016/j.ygeno.2012.09.001. Epub 2012 Sep 12.

Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes

Sree Kanthaswamy  1 , Jillian Ng, Cody T Ross, Jessica Satkoski Trask, David Glenn Smith, Vince S Buffalo, Joseph N Fass, Dawei Lin
Affiliations

Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes

Sree Kanthaswamy et al. Genomics. 2013 Jan.

Abstract

We genotyped a Chinese and an Indian-origin rhesus macaque using the Affymetrix Genome-Wide Human SNP Array 6.0 and cataloged 85,473 uniquely mapping heterospecific SNPs. These SNPs were assigned to rhesus chromosomes according to their probe sequence alignments as displayed in the human and rhesus reference sequences. The conserved gene order (synteny) revealed by heterospecific SNP maps is in concordance with that of the published human and rhesus macaque genomes. Using these SNPs' original human rs numbers, we identified 12,328 genes annotated in humans that are associated with these SNPs, 3674 of which were found in at least one of the two rhesus macaques studied. Due to their density, the heterospecific SNPs allow fine-grained comparisons, including approximate boundaries of intra- and extra-chromosomal rearrangements involving gene orthologs, which can be used to distinguish rhesus macaque chromosomes from human chromosomes.

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Figures

Figure 1
Figure 1
Density of single-hit heterospecific SNPs in rhesus macaque autosomes and the X chromosome (the same trend was observed when the Chinese and Indian individuals were analyzed separately). Black bars represent median values. Y chromosomes were not analyzed due to the absence of a Y-chromosome in the rhesus draft sequence.
Figure 2
Figure 2
Figure 2a. Associations among rhesus chromosomes and human chromosomes. Colors and horizontal arrows represent syntynic order and opposite directionality of heterospecific SNPs and vertical arrows denote chromosome fusion. Figure 2b. A generalized image of conserved synteny of the rhesus macaque reference genome (RheMac2) chromosomal segments (colored) relative to the 23 human (HG19) chromosomes. Note that the absence of SNP probes in either species marks the approximate locations of centromeric regions. Colored vertical bars represent heterospecific SNPs within the conserved probes. Figure 2c. Gene orthologs on rhesus macaque chromosome 9 and human chromosome 10 revealed by single-hit heterospecific SNPs. The bars are the conserved gene orthologs. The colored blocks define the conserved gene orders in both species; black font indicates human and rhesus macaque gene orders that are in the same direction, and white font highlights inverted gene orders (Top). An overlapping section of the human and rhesus chromosomes is magnified (Below).
Figure 2
Figure 2
Figure 2a. Associations among rhesus chromosomes and human chromosomes. Colors and horizontal arrows represent syntynic order and opposite directionality of heterospecific SNPs and vertical arrows denote chromosome fusion. Figure 2b. A generalized image of conserved synteny of the rhesus macaque reference genome (RheMac2) chromosomal segments (colored) relative to the 23 human (HG19) chromosomes. Note that the absence of SNP probes in either species marks the approximate locations of centromeric regions. Colored vertical bars represent heterospecific SNPs within the conserved probes. Figure 2c. Gene orthologs on rhesus macaque chromosome 9 and human chromosome 10 revealed by single-hit heterospecific SNPs. The bars are the conserved gene orthologs. The colored blocks define the conserved gene orders in both species; black font indicates human and rhesus macaque gene orders that are in the same direction, and white font highlights inverted gene orders (Top). An overlapping section of the human and rhesus chromosomes is magnified (Below).
Figure 2
Figure 2
Figure 2a. Associations among rhesus chromosomes and human chromosomes. Colors and horizontal arrows represent syntynic order and opposite directionality of heterospecific SNPs and vertical arrows denote chromosome fusion. Figure 2b. A generalized image of conserved synteny of the rhesus macaque reference genome (RheMac2) chromosomal segments (colored) relative to the 23 human (HG19) chromosomes. Note that the absence of SNP probes in either species marks the approximate locations of centromeric regions. Colored vertical bars represent heterospecific SNPs within the conserved probes. Figure 2c. Gene orthologs on rhesus macaque chromosome 9 and human chromosome 10 revealed by single-hit heterospecific SNPs. The bars are the conserved gene orthologs. The colored blocks define the conserved gene orders in both species; black font indicates human and rhesus macaque gene orders that are in the same direction, and white font highlights inverted gene orders (Top). An overlapping section of the human and rhesus chromosomes is magnified (Below).
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References

    1. Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu Y-s, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers Y-H, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang S-P, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX-Z, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AFA, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han S-G, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu L-L, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O’Brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu X-M, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS Rhesus Macaque Genome Sequencing Analysis Consortium. Evolutionary and Biomedical Insights from the Rhesus Macaque Genome. Science. 2007;316:222–234. - PubMed
    1. Kumar S, Hedges SB. A molecular timescale for vertebrate evolution. Nature. 1998;392:917–920. - PubMed
    1. Yan G, Zhang G, Fang X, Zhang Y, Li C, Ling F, Cooper DN, Li Q, Li Y, van Gool AJ, Du H, Chen J, Chen R, Zhang P, Huang Z, Thompson JR, Meng Y, Bai Y, Wang J, Zhuo M, Wang T, Huang Y, Wei L, Li J, Wang Z, Hu H, Yang P, Le L, Stenson PD, Li B, Liu X, Ball EV, An N, Huang Q, Zhang Y, Fan W, Zhang X, Li Y, Wang W, Katze MG, Su B, Nielsen R, Yang H, Wang J, Wang X, Wang J. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotech. 2011;29:1019–1023. - PubMed
    1. Ferguson B, Street S, Wright H, Pearson C, Jia Y, Thompson S, Allibone P, Dubay C, Spindel E, Norgren R. Single nucleotide polymorphisms (SNPs) distinguish Indian-origin and Chinese-origin rhesus macaques (Macaca mulatta) BMC Genomics. 2007;8:43. - PMC - PubMed
    1. Malhi RS, Sickler B, Lin D, Satkoski J, Tito RY, George D, Kanthaswamy S, Smith DG. MamuSNP: A Resource for Rhesus Macaque (Macaca mulatta) Genomics. PLoS ONE. 2007;2:e438. - PMC - PubMed

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