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FecalSeq: methylation-based enrichment for noninvasive population genomics from feces

View ORCID ProfileKenneth L. Chiou, View ORCID ProfileChristina M. Bergey
doi: https://doi.org/10.1101/032870
Kenneth L. Chiou
1Department of Anthropology, Washington University, St. Louis, MO 63130, USA
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Christina M. Bergey
2Department of Anthropology, New York University, New York, NY 10003, USA
3New York Consortium in Evolutionary Primatology, New York, NY, USA
4Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
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Abstract

Obtaining high-quality samples from wild animals is a major obstacle for genomic studies of many taxa, particular at the population level, as collection methods for such samples are typically invasive. DNA from feces is easy to obtain noninvasively, but is dominated by a preponderance of bacterial and other non-host DNA. Because next-generation sequencing technology sequences DNA largely indiscriminately, the high proportion of exogenous DNA drastically reduces the efficiency of high-throughput sequencing for host animal genomics. In order to address this issue, we developed an inexpensive methylation-based capture method for enriching host DNA from noninvasively obtained fecal DNA samples. Our method exploits natural differences in CpG-methylation density between vertebrate and bacterial genomes to preferentially bind and isolate host DNA from majority-bacterial fecal DNA samples. We demonstrate that the enrichment is robust, efficient, and compatible with downstream library preparation methods useful for population studies (e.g., RADseq). Compared to other enrichment strategies, our method is quick and inexpensive, adding only a negligible cost to sample preparation for research that is often severely constrained by budgetary limitations. In combination with downstream methods such as RADseq, our approach allows for cost-effective and customizable genomic-scale genotyping that was previously feasible in practice only with invasive samples. Because feces are widely available and convenient to collect, our method empowers researchers to explore genomic-scale population-level questions in organisms for which invasive sampling is challenging or undesirable.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 02, 2017.
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FecalSeq: methylation-based enrichment for noninvasive population genomics from feces
Kenneth L. Chiou, Christina M. Bergey
bioRxiv 032870; doi: https://doi.org/10.1101/032870
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FecalSeq: methylation-based enrichment for noninvasive population genomics from feces
Kenneth L. Chiou, Christina M. Bergey
bioRxiv 032870; doi: https://doi.org/10.1101/032870

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