Abstract Detail

Biodiversity Informatics & Herbarium Digitization

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], Sigel, Erin [9], Sutherland, Brittany [9], McKain, Michael [10].

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

Modern genotyping techniques, such as SNP analysis, are hampered by poor DNA quality and purity, particularly in challenging plant species that are rich in secondary metabolites or herbarium specimens containing fungal contamination. Though the age of the specimen can play a role in the amount of DNA degradation or contamination, the literature suggests that improper collection methods and storage conditions have a higher contribution than the age of the voucher (Graper, et al., 2020). Herbaria house millions of specimens that contain DNA suitable for genome sequencing, but challenges such as DNA degradation, fungal or glue contamination, and deamination hinders genomic analyses. Unlocking the vast genomic diversity stored in natural history collections will aid in our understanding of modern phylogenetic, domestication, and population distribution studies. Using invasive species’ herbarium specimens and their associated data can be useful to compare to contemporary specimens to gain insight into shifts in population distribution, population genetics, and invasive species' impact on native species populations. Our analysis of five invasive plant species—Microstegium vimineum (Trin.) A. Camus, Salsola spp. (L.), Salvinia spp. S g., Trifolium repens L., and Sorghum halepense. (L.) Pers.--using total genomic DNA from contemporary tissue and herbarium tissue will provide insight into the presence (or absence) of sequence bias caused by DNA degradation and contamination. We further the utility of this study by testing a DNA-repair protocol on our herbarium DNA to see if herbarium-based damage can be mitigated. It is fundamental to understand the process of DNA degradation in herbarium specimens and its impact on our ability to identify patterns of allelic variation to make full use of herbarium specimens in modern genomics studies.

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, Biology, 53 Campus Drive, Morgantown, WV, 26506, United States
4 - Wichita State University, Biology, 1845 Fairmount, Box 26, Wichita, KS, 67260, United States
5 - South Dakota State University, Department of Natural Resource Management, McFadden Biostress Laboratory 144 Natural Resource Management-Box 2140B University Station Brookings, 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, 57007, United States
8 - 2179 SAINT JOHNS ALCOVE, WOODBURY, MN, 55129, United States
9 - 3146 E 4th ST, Tucson, AZ, 85716, United States
10 - University Of Alabama, 411 Mary Harmon Bryant Hall, Tuscaloosa, AL, 35487, United States

herbarium genomics
sequencing bias

Presentation Type: Oral Paper
Number: BI&HD I003
Abstract ID:878
Candidate for Awards:None

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