Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing.
For 150 years or more, specimens were routinely collected and deposited in natural history collections without preserving fresh tissue samples for genetic analysis. In the case of most herpetological specimens (i.e. amphibians and reptiles), attempts to extract and sequence DNA from formalin-fixed, ethanol-preserved specimens-particularly for use in phylogenetic analyses-has been laborious and largely ineffective due to the highly fragmented nature of the DNA. As a result, tens of thousands of specimens in herpetological collections have not been available for sequence-based phylogenetic studies. Massively parallel High-Throughput Sequencing methods and the associated bioinformatics, however, are particularly suited to recovering meaningful genetic markers from severely degraded/fragmented DNA sequences such as DNA damaged by formalin-fixation. In this study, we compared previously published DNA extraction methods on three tissue types subsampled from formalin-fixed specimens of Anolis carolinensis, followed by sequencing. Sufficient quality DNA was recovered from liver tissue, making this technique minimally destructive to museum specimens. Sequencing was only successful for the more recently collected specimen (collected ~30 ybp). We suspect this could be due either to the conditions of preservation and/or the amount of tissue used for extraction purposes. For the successfully sequenced sample, we found a high rate of base misincorporation. After rigorous trimming, we successfully mapped 27.93% of the cleaned reads to the reference genome, were able to reconstruct the complete mitochondrial genome, and recovered an accurate phylogenetic placement for our specimen. We conclude that the amount of DNA available, which can vary depending on specimen age and preservation conditions, will determine if sequencing will be successful. The technique described here will greatly improve the value of museum collections by making many formalin-fixed specimens available for genetic analysis.
Department of Integrative Biology, 3101 Valley Life Sciences Building, University of California, Berkeley, California, United States of America; Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California, Berkeley, California, United States of America.
Sarah M
SM
Hykin
Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, United States of America; Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California, Berkeley, California, United States of America.
Ke
K
Bi
Department of Integrative Biology, 3101 Valley Life Sciences Building, University of California, Berkeley, California, United States of America; Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California, Berkeley, California, United States of America.
Jimmy A
JA
McGuire
D004247:DNA / Q000737:chemistry / Q000235:genetics*; D053938:DNA Fragmentation / Q000187:drug effects; D005557:Formaldehyde / Q000737:chemistry; D054629:Genome, Mitochondrial / Q000235:genetics*; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009144:Museums; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013048:Specimen Handling; D016707:Tissue Fixation
D005557:Formaldehyde; D004247:DNA