TY - JOUR
T1 - A SINE-based dichotomous key for primate identification
AU - Herke, Scott W.
AU - Xing, Jinchuan
AU - Ray, David A.
AU - Zimmerman, Jacquelyn W.
AU - Cordaux, Richard
AU - Batzer, Mark A.
N1 - Funding Information:
We thank Drs. L. Chemnick, T. Disotell, O. Ryder, and C.-B. Stewart for providing DNA samples. This research was supported by the National Science Foundation grants BCS-0218338 and EPS-0346411 and by the State of Louisiana Board of Regents Support Fund (to M.A.B.). Jacquelyn Zimmerman was supported by a Howard Hughes Medical Institute grant to Louisiana State University through the Undergraduate Biological Sciences Education program.
PY - 2007/4/1
Y1 - 2007/4/1
N2 - For DNA samples or 'divorced' tissues, identifying the organism from which they were taken generally requires some type of analytical method. The ideal approach would be robust even in the hands of a novice, requiring minimal equipment, time, and effort. Genotyping SINEs (Short INterspersed Elements) is such an approach as it requires only PCR-related equipment, and the analysis consists solely of interpreting fragment sizes in agarose gels. Modern primate genomes are known to contain lineage-specific insertions of Alu elements (a primate-specific SINE); thus, to demonstrate the utility of this approach, we used members of the Alu family to identify DNA samples from evolutionarily divergent primate species. For each node of a combined phylogenetic tree (56 species; n = 8 [Hominids]; 11 [New World monkeys]; 21 [Old World monkeys]; 2 [Tarsiformes]; and, 14 [Strepsirrhines]), we tested loci (> 400 in total) from prior phylogenetic studies as well as newly identified elements for their ability to amplify in all 56 species. Ultimately, 195 loci were selected for inclusion in this Alu-based key for primate identification. This dichotomous SINE-based key is best used through hierarchical amplification, with the starting point determined by the level of initial uncertainty regarding sample origin. With newly emerging genome databases, finding informative retrotransposon insertions is becoming much more rapid; thus, the general principle of using SINEs to identify organisms is broadly applicable.
AB - For DNA samples or 'divorced' tissues, identifying the organism from which they were taken generally requires some type of analytical method. The ideal approach would be robust even in the hands of a novice, requiring minimal equipment, time, and effort. Genotyping SINEs (Short INterspersed Elements) is such an approach as it requires only PCR-related equipment, and the analysis consists solely of interpreting fragment sizes in agarose gels. Modern primate genomes are known to contain lineage-specific insertions of Alu elements (a primate-specific SINE); thus, to demonstrate the utility of this approach, we used members of the Alu family to identify DNA samples from evolutionarily divergent primate species. For each node of a combined phylogenetic tree (56 species; n = 8 [Hominids]; 11 [New World monkeys]; 21 [Old World monkeys]; 2 [Tarsiformes]; and, 14 [Strepsirrhines]), we tested loci (> 400 in total) from prior phylogenetic studies as well as newly identified elements for their ability to amplify in all 56 species. Ultimately, 195 loci were selected for inclusion in this Alu-based key for primate identification. This dichotomous SINE-based key is best used through hierarchical amplification, with the starting point determined by the level of initial uncertainty regarding sample origin. With newly emerging genome databases, finding informative retrotransposon insertions is becoming much more rapid; thus, the general principle of using SINEs to identify organisms is broadly applicable.
KW - Alu
KW - Mobile elements
KW - Retrotransposons
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U2 - 10.1016/j.gene.2006.08.015
DO - 10.1016/j.gene.2006.08.015
M3 - Article
C2 - 17056208
AN - SCOPUS:33846930573
SN - 0378-1119
VL - 390
SP - 39
EP - 51
JO - Gene
JF - Gene
IS - 1-2
ER -