| Abstract Detail
Phylogenomics Johnson, Matthew [1], Audi, Lauren [2], Zerega, Nyree [3], Gardner, Elliot M. [4]. Damage in Antique DNA from Herbarium Specimens: Harmful Rust or Healthy Patina? DNA sequences from ancient sources have an established pattern of damage, most commonly from cytosine deanimation in degraded single-stranded overhangs. When sequenced, these spontaneous mutations can be scored as genetic variation if not addressed during quality control of sequencing reads. However, the extent to which these same spontaneous mutations occur in “antique DNA” – for example, herbarium specimens that are decades to centuries old – is not established. We adapt standard methods to assess DNA damage using a large dataset of target capture sequences in Artocarpus (Moraceae) using modern specimens as genomic reference sequences. We establish patterns in DNA damage within species by comparing sequences from fresh tissue with herbarium specimens up to 230 years old, and also assess damage in more recent specimens preserved using ethanol. We provide recommendations for researchers incorporating modern and antique specimens in phylogenomic and population genomic studies to minimize artifacts from DNA damage.
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1 - Texas Tech University, Biological Sciences, 2901 Main Street, Ms3131, Lubbock, TX, 79409, United States
2 - 65-35 108th St, Apt C1, Apt C1, Forest Hills, NY, 11375, United States
3 - Northwestern University And The Chicago Botanic Garden, Plant Biology And Conservation, 2205 Tech Drive, Hogan 2-144, Evanston, IL, 60202, United States
4 - Florida International University, Institute Of Environment, 11200 SW 8th Street, OE 148, Miami, FL, 33199, United States
Keywords:
target capture
Herbariomics
Artocarpus
bioinformatics.
Presentation Type: Oral Paper
Session: PHYLOIII, Phylogenomics III
Location: Virtual/Virtual
Date: Thursday, July 22nd, 2021
Time: 11:30 AM(EDT)
Number: PHYLOIII007
Abstract ID:625
Candidate for Awards:None |
