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Abstract Detail

Revolutionizing systematics: Herbaria in the Genomics Age

McKain, Michael [1], Pienaar, Jason [2], Saeidi, Saman [3], AuBuchon, Taylor [3], Lewis, Michelle [2], McAllister, Chrissy [4], Kellogg, Elizabeth [5].

More than a phylogeny: Evolutionary genomics in the herbarium.

High-throughput sequencing has allowed for unprecedented use of herbaria in molecular phylogenetic studies. The often denatured and fragmented DNA of herbarium specimens, which has historically been problematic for PCR-based studies, is no longer a hurdle to the incorporation of these historic specimens in molecular systematics. The opening of the “treasure trove” of biodiversity in herbaria to molecular studies allows for the inclusion of species that would otherwise require expensive expeditions to acquire. Our understanding of species relationships will greatly improve through the use of extinct and endangered species, unique populations, and even type specimens all sampled from herbaria. A phylogeny, however, is only the beginning of the genomic information we can obtain from herbarium specimens. Here, we demonstrate how genome skimming, as one possible method for obtaining genomic information from herbaria, can not only provide whole chloroplast sequences for phylogenetics but can help us understand the dynamics of transposable element diversity and abundance across species and landscapes as well as through time. The unique opportunity of herbaria to provide a temporal history of populations and species, and their genomic composition, allows us to see how aspects of the genome can change over short periods of time and in relationship to shifts in climate and human interference. We focus on the grass tribe Andropogoneae (Poaceae), which includes agricultural species such as maize, sorghum, and sugarcane; a number of ecologically important species like Andropogon gerardi, Schizachyrium scoparium, and Sorghastrum nutans; and multiple invasive species such as Sorghum halepense, Imperata cylindrica, and Rottboellia cochinchinensis. Using genome skimming data from over 100 herbarium specimens and dozens of freshly collected specimens, we are able to identify trends in the relative abundance of transposon superfamilies in the genomes of different Andropogoneae species. We caution that there are limitations to what these data can tell us and identify potential problems with using herbarium-derived genomic data.

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1 - The University of Alabama, Biological Sciences, 300 Hackberry Lane, Tuscaloosa, Alabama, 35487, United States
2 - The University of Alabama, Biological Sciences, 300 Hackberry Lane, Box 870344, Tuscaloosa, Alabama, 35487, United States
3 - Donald Danforth Plant Science Center, 975 N Warson, St Louis, MO, 63132, United States
4 - 1 Maybeck Place, Principia College, Elsah, IL, 62028, United States
5 - Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, United States

evolutionary genomics
genome skimming

Presentation Type: Colloquium Presentations
Session: C10, Revolutionizing Systematics: Herbaria in the Genomics Age
Location: 103/Mayo Civic Center
Date: Wednesday, July 25th, 2018
Time: 11:45 AM
Number: C10015
Abstract ID:968
Candidate for Awards:None

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