The 81st Annual Meeting of the American Association of Physical Anthropologists (2012)


Concurrent isolation and amplification of primate genomes, trancriptomes and microbiomes from small tissue (hair) samples

JASON M. KAMILAR1,2, ANNICK MCINTOSH1 and BRENDA J. BRADLEY1.

1Department of Anthropology, Yale University, 2Department of Anatomy, Midwestern University

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Recent advances in high-throughput DNA sequencing and bioinformatics are opening new avenues of research in primatology. This includes population-level genome sequencing (population genomics) and gene expression profiling (comparative transcriptomics). In addition to DNA sequences representing the genome and RNA sequences representing the transcriptome, biological samples also contain sequences representing the bacterial community of the sample; this microbiome can also be characterized and studied using a meta-genomic sequencing approach. Although methods for sequencing are advancing rapidly, obtaining adequate sample material remains a limiting factor for many studies, especially those focused on wild primate populations. A possible means to overcome the limits of small samples would be to amplify the starting material (DNA and RNA) prior to sequencing. We evaluated the potential for this approach by testing several commercial reagents and protocols for whole genome amplification (WGA) and whole transcriptome amplification (WTA) using DNA and RNA from plucked primate hair follicles. Hair samples were collected from three primate species: Homo sapiens, Symphalangus syndactylus, Eulemur mongoz. Using matched samples, we independently tested two WGA protocols (Qiagen, Illustra) and two WTA protocols (Qiagen, Sigma-Aldrich). PCR and qPCR results for primate nuclear DNA and RNA (ACTB, MITF) and microbrial DNA (16S rRNA) were compared between original DNA and RNA products and those of the WGA and WTA kits, respectively. Results indicate that both WGA protocols generally worked well for primate and microbial DNA. Gene expression comparisons using qPCR, however, indicate that one protocol (Sigma-Aldrich) yielded more consistent results when comparing original RNA and WTA amplicons.

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