The Challenges Posed by Large Data Sets in Assembling the Plant and Fungal Trees of Life
Ickert-Bond, Steffi , Peery, Rhiannon , Raubeson, Linda A. , Metzgar, Jordan S. , Parks, Matthew , Cronn, RC , Liston, Aaron .
Will everything be enough? Plastid phylogenomics and the resolution of closely related species in Ephedra and Pinus.
The conservative nature of chloroplast sequence evolution often limits phylogenetic resolution at the species level. In Ephedra resolution of species-level phylogenies has been particularly challenging due to the low sequence divergence observed in several plastid markers used to date, e.g., rps4, matK, and rbcL. Here we present results from multiplex sequencing-by-synthesis (MSBS) of multiple plastomes on the Illumina Genome Analyzer to resolve phylogenetic relationships in Ephedra and compare the Ephedra results with those obtained using a similar approach in Pinus. First, we PCR-amplified the plastomes using 25 primer pairs. Tagged microreads from each species were then assembled with a combination of de novo (Velvet and Edena) and reference-guided (RGA) assembly using previously published plastomes as references. We have amplified and obtained draft sequences using this method for 23 of the 45 species of Ephedra. Such a “whole” genome approach has worked well in Pinus, where nearly all ingroup clades (30/33) were resolved with ≥95% maximum likelihood bootstrap support. Initial analyses suggest that variation among the Ephedra species is minimal; however, most comparisons remain to be conducted. These results might reflect that extant Ephedra species are the result of relatively recent diversification following massive extinctions in the Oligocene and Miocene as compared to the older divergences in Pinus primarily during the Miocene.
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Ickert-Bond Lab, University of Alaska
UA Museum Herbarium
1 - University of Alaska Fairbanks, Department of Biology and Wildlife and Institute of Arctic Biology, 907 Yukon Dr., Fairbanks, Alaska, 99775-6960, U.S.A.
2 - Central Washington University, Department of Biological Sciences, 400 E University Way, Ellensburg, WA, 98926-7537, USA
3 - University of Alaska Fairbanks, Department of Biology and Wildlife, 211 Irving 1, Fairbanks, AK, 99775, USA
4 - Oregon State University, Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA
5 - USDA Forest Service, Forest Genetics, Pacific Nothwest Research Station, 3200 SW Jefferson Way, Corvallis, Oregon, 97331, USA
6 - Oregon State University, Department of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, Oregon, 97331-2902, USA
Presentation Type: Symposium or Colloquium Presentation
Location: Ballroom 2/Cliff Lodge - Level B
Date: Tuesday, July 28th, 2009
Time: 10:45 AM