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Abstract Detail

Population Genetics/Genomics

Motley, M'Kayla [1], Hofford, Nate [2], Barrett, Craig [3], Beck, James [4], Khanal, Deva Raj [5], Kooyers, Nicholas [6], Latvis, Maribeth [7], Ramachandran, Dhanushya [8], Sutherland, Brittany [9], McKain, Michael [10], Sigel, Erin [11].

Assessment of sequencing bias in genomic-level projects using herbarium specimens.

Comparative genomics studies, such as phylogenomics and those using genotyping via SNP analysis, are hampered by poor DNA quality and purity. Though they represent amazing genetic diversity resources categorized by both timing and location of collection, herbarium specimens are challenging to use in genomics studies due to the inherent damage of specimen DNA caused by the preservation process and contamination sources like mold. The vast amount of genomic diversity stored in natural history collections provides us with access to the global diversity of various lineages, extinct taxa, and chronological samplings of population genetic diversity of various species. These resources aid in our reconstruction of phylogenetic relationships and allow us to better understand changes in population distributions and genetic diversity throughout the last 200 years. Given the immense promise of herbarium specimens in these types of studies, it is necessary to understand the limitations and expected biases potentially introduced through their use. To identify biases associated with base calling from herbarium specimens, we compared whole-genome shotgun sequencing data from contemporary and herbarium specimens representing five invasive species: Sorghum halepense (L.) Pers., Trifolium repens L., Salvinia molesta D. Mitch, Microstegium vimineum (Trin.) A. Camus, and Salsola spp. L. For each species, we constructed libraries for 20 fresh, 20 herbarium, and 20 of the same herbarium samples but using a protocol designed to repair damaged DNA. For each library, we assembled whole chloroplast genomes. We then mapped reads back to the chloroplast genomes and looked at variation in base pair frequency across all reads at each site. We compared variation between fresh and all herbarium specimens, and untreated and treated herbarium specimens. From these comparisons, we are able to better understand the expected bias introduced through herbarium specimens. The use of fresh and historic specimens contributes to our understanding of invasive species population distributions and provides insight into their genetic adaptations as they invade novel habitats. To profit from this resource, it is critical to understand the process of DNA degradation in herbarium specimens and its impact on sequencing technology. This research aims to refine modern techniques to produce best practices for the use of historical specimens in population-level genomics.

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1 - University Of Alabama, Box 870118, Box 870118, Tuscaloosa, AL, 35487, United States
2 - University Of Alabama, Biology, 530 18th Street, Unit 206, Tuscaloosa, AL, 35401, United States
3 - West Virginia University, Department of Biology, Life Sciences Building, PO Box 6057, Morgantown, WV, 26506, USA
4 - Wichita State University , Department of Biological Sciences, 537 Hubbard Hall , Wichita, KS, 67260
5 - South Dakota State University, Natural Resource Management , McFadden Biostress Laboratory 144 Natural Resource Management-Box 2140B University Station, Brookings, SD, 57007, United States
6 - Univerity Of Louisiana, Lafayette, Biology, 410 E. St. Mary Blvd. , Billeaud Hall, Rm 108, Lafayette, LA, 70503, United States
7 - South Dakota State University, Department Of Natural Resource Management, 1390 College Avenue, Box 2140B, South Dakota State University , Brookings , SD, 57006, United States
8 - West Virginia University, Biology, 53, Campus Drive, Morgantown, WV, 26501, USA
9 - University of Louisiana at Lafayette
10 - University Of Alabama, 411 Mary Harmon Bryant Hall, Tuscaloosa, AL, 35487, United States
11 - University of New Hampshire, College of Life Sciences and Agriculture, Spaulding Hall, Durham, NH, 03824, USA

invasive species
Comparative genomics

Presentation Type: Poster
Session: P3, Population Genetics/Genomics Posters
Location: Virtual/Virtual
Date: Wednesday, July 21st, 2021
Time: 5:00 PM(EDT)
Number: P3PG005
Abstract ID:980
Candidate for Awards:None


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