Abstract Detail

Pteridological Section/AFS

Li, Fay-Wei [1], Rothfels, Carl [2], Larsson, Anders [3], Sigel, Erin [1], Huiet, Layne [1], Korall, Petra [3], Ruhsam, Markus [4], Stevenson, Dennis [5], Graham, Sean [6], Wong, Gane Ka-Shu [7], Pryer, Kathleen [1].

Mining fern transcriptome data for low-copy nuclear markers.

Over the past twenty years, our understanding of the fern tree of life has been greatly advanced due, in large part, to the rapid pace of molecular phylogenetic studies. However, the majority of these studies relied exclusively on plastid DNA sequence data, reflecting a near-complete absence of nuclear genomic resources available for fern phylogenetics. Unfortunately, this has been particularly disadvantageous for species-level work in many fern groups where polyploidy and hybridization are prevalent, because plastids are maternally inherited in ferns and therefore only tell “half the story”. The recent sequencing of more than 70 fern transcriptomes (1KP; onekp.com) provides an extraordinary opportunity for the fern biologist to develop an array of biparentally-inherited, low-copy nuclear markers for use in evolutionary studies. Here, we summarize the bioinformatic methods we used to mine these transcriptome data, resulting in the development of 10 nuclear markers that can be successfully amplified across the majority of polypod ferns (about two thirds of extant leptosporangiate fern species). We not only examine the species-level sequence variation, but also test the potential efficacy of these markers to infer deeper phylogenetic relationships in ferns.

Broader Impacts:

1 - Duke University, Department of Biology, Box 90338, Durham, NC, 27708, USA
2 - University of British Columbia, Department of Zoology, 6270 University Blvd., Vancouver, Canada
3 - Uppsala University, PHANEROGAMIC BOTANY, Norbyvägen 18D, Uppsala, SE-752 36, Sweden
4 - Royal Botanic Garden Edinburgh, Edinburgh, UK
5 - The New York Botanical Garden, 2900 Southern Blvd., Bronx, NY, 10458, USA
6 - University of British Columbia , Department of Botany, 6804 SW Marine Drive, Vancouver, British Columbia, Canada
7 - University of Alberta, Department of Biological Sciences, 4-126 Katz Group Centre for Health and Pharmacy, Edmonton, Alberta, Canada

Keywords:
bioinformatics
Low-copy nuclear loci
nuclear marker
Phylogenetics
Polypodiales
transcriptome
ferns.

Presentation Type: Oral Paper:Papers for Sections
Session: 34
Location: Melrose/Riverside Hilton
Date: Tuesday, July 30th, 2013
Time: 3:00 PM
Number: 34007
Abstract ID:626
Candidate for Awards:Edgar T. Wherry award