Abstract Detail

Colloquia: Emerging Results from Studies of Gymnosperms on the Tree of Life II

Parks, Matthew [1], Liston, Aaron [2], Cronn, RC [3].

Striving for the First Finish Line: A Whole-Plastome Phylogeny for the Entire Genus Pinus.

We describe our progress at reconstructing a genus-wide phylogeny based on plastome-scale sequence for all of the ca. 110 species of Pinus. Plastome enrichment was accomplished initially with a PCR strategy, and more recently with a solution-hybridization-based approach. Libraries were prepared with multiplexing adapters, and up to 16 samples were sequenced in a single lane of the Illumina GAII next-generation sequencer. Assembly of plastomes from resulting microreads was performed using a novel and efficient assembly pipeline based on the ‘reference-seeded’ assembler YASRA (Ratan 2009) and custom Python scripts. Our efforts allowed us to assemble plastome sequences for the majority of pine species, and result in unprecedented phylogenetic resolution both for pines and for any infrageneric phylogenetic analysis of this magnitude. Using conservative coverage cutoffs during assembly (5x and 20x depth for conserved positions and SNPs, respectively), all major clades (subgenera, sections and subsections) most recently documented by Gernandt et al. (2005) and Parks et al. (2009) were highly supported, and many, but not all, interspecific relationships were resolved with high support. These results demonstrate the feasibility of obtaining plastome-scale data sets for phylogenetic analysis at the genus level and below.

Broader Impacts:

1 - Oregon State University, Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA
2 - Oregon State University, Department of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, Oregon, 97331-2902, USA
3 - USDA Forest Service, Genetics, Pacific Northwest Research Station, Corvallis, OR, 97331, USA

Keywords:
Pinus
next-generation sequencing
Solution-Based Hybridization
Illumina
Plastome Phylogenetics.

Presentation Type: Symposium or Colloquium Presentation
Session: C2
Location: Ballroom C/Convention Center
Date: Monday, August 2nd, 2010
Time: 2:15 PM
Number: C2006
Abstract ID:689