Abstract Detail

Growing the Next Generation in Plant Genomics

Puzey, Joshua [1], Chen, Tao [2], Deyholos, Michael [3], Graham, Sean [4], Leebens-Mack, Jim [5], Stevenson, Dennis [6], Thomas, Philip [7], Wong, Gane Ka-Shu [8], Mathews, Sarah [9].

Nuclear phylogenomics of seed plants.

Relationships among major clades of living seed plants remain controversial despite substantial efforts to resolve them, and published trees inferred from multi-locus data sets are largely plastid-based. We are mining transcriptome assemblies from approximately 80 species of seed plants to infer a nuclear-genome based hypothesis of seed plant phylogeny. Using a bulk blast and gene prediction pipeline, we are extracting protein-coding sequences to assemble a matrix that samples approximately 130 genes from seed plants and outgroups. Nucleotide and amino acid matrices will be analyzed using a maximum likelihood approach and a posteriori data-partitioning schemes. Results will be discussed in the light of seed plant phylogenies inferred from plastid, multi-genome, and morphological data sets.

Broader Impacts:

1 - Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Cambridge, MA, 02138, USA
2 - Shenzen Fairy Lake Botanical Garden, 160 Xianhu Road, Liantang, Luohu District, Shenzen, Guangdong, 518004, CHINA
3 - University of Alberta, Biological Sciences, Edmonton, AB, T6G 2E9, CANADA
4 - University of British Columbia, UBC Botanical Garden, 6804 SW Marine Drive, Vancouver, BC, V6T 1Z4, CANADA
5 - University Of Georgia, 4503 Miller Plant Sciences, Athens, GA, 30602, USA
6 - THE NY BOTANICAL GARDEN, 2900 SOUTHERN BLVD, BRONX, NY, 10458-5126, USA, 718/817-8632
7 - Royal Botanic Garden Edinburgh, 20 Inverleith Row , Edinburgh, Scotland, EH3 5LR, UK
8 - University of Alberta, Biological Sciences, Edmonton, AB, T6G 2E1, CANADA
9 - Harvard University, Arnold Arboretum, 1300 Centre Street, Boston, MA, 02131, USA

Keywords:
seed plant phylogeny
nuclear genes
phylogenomics
data partitioning.

Presentation Type: Symposium or Colloquium Presentation
Session: SY04
Location: Franklin C and D/Hyatt
Date: Monday, July 9th, 2012
Time: 2:00 PM
Number: SY04002
Abstract ID:848