Abstract Detail

Phylogenomics

Literman, Robert [1], Fairbanks, Regina [2], Liu, Jing [3], Liu, Bin-Bin [4], Nie, Zelong [5], Ren, Chen [6], Johnson, Gabriel [7], Wen, Jun [8], Zimmer, Elizabeth [9], Hunter, Elizabeth [10], Handy, Sara [11].

Reference-free and bait-guided phylogenetic inference and species identification in the ginseng genus Panax (Araliaceae) using genome skim data.

Species of Panax L. (Araliaceae) or ginseng have historical roots in Chinese medicine and are commonly used as dietary supplements. The genus contains approximately 18 species, which are asymmetrically distributed, with two species native to North America and the rest in Asia. Several molecular phylogenetic studies have attempted to resolve their evolutionary relationships. However, the relationships within the genus, and especially within the P. bipinnatifidus complex, have been difficult to resolve. This project assesses the utility of different datasets to improve the phylogenetic resolution for this genus, including (1) whole genome skimming, (2) 900 targeted nuclear DNA sequences designed from the Panax ginseng and P. notoginseng genomes, and (3) plastid genomes. To aid in this process, we employed the bioinformatic pipeline SISRS, which can generate genome‐wide single‐nucleotide polymorphism (SNP) data while circumventing the need for any reference genome or annotation data. Here we present an updated phylogeny for the genus and provide a comparison between the phylogenies generated by analyzing the random whole genome, target-seq, and plastid sequence data. Results from this study can also inform species identification assays, even on products that have fragmented DNA. This talk will cover the updated phylogeny of the ginseng genus, the comparison between genome skimming, target-seq, and organellar results, and a teaser on species identification in the era of genomics.

1 - US Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-717, 5001 Campus Dr., College Park, MD, 20740, USA
2 - University of California, Davis, Department of Evolution & Ecology, 2320 Storer Hall, 1 Shields Ave., Davis, CA, 95616, USA
3 - Sichuan Agricultural University, College of Life Science, 625014, China
4 - Institute of Botany, Chinese Academy of Sciences, State Key Laboratory of Systematic and Evolutionary Botany, Beijing 100093, China
5 - Jishou University, College of Biology and Environmental Sciences, Jishou, Hunan, 416000, China
6 - South China Botanical Garden, Herbarium, Guangzhou, Guangdong, 510650, China
7 - 3300 16th Street NW, #404, Washington, DC, 20010, United States
8 - Botany, MRC-166 National Museum Of Natural History, 10th St. & Constitution Ave., NW, Mrc 166, Washington/DC, 20013, United States
9 - Smithsonian NMNH, Botany MRC 166, P.O. Box 37102, Smithsonian National Museum Of Natural History, Washington, DC, 20013, United States
10 - US Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-717, 5001 Campus Dr., College Park, MD, 20740, USA
11 - HFS-717, 5001 Campus Dr., College Park, MD, 20740, United States

Keywords:
Panax
ginseng
baits
genome skimming
phylogeny
species identification.

Presentation Type: Oral Paper
Number: PHYLO III012
Abstract ID:77
Candidate for Awards:None