Abstract Detail

Botany 2015 Colloquium: Phylogenomics and the 1000 plants (1KP) initiative 

Leebens-Mack, James H. [1], Mirarab, Siavash [2], Nguyen, Nam-phuong [3], Wafula, Eric [4], Ayyampalayam, Raj [5], Der, Joshua [6], dePamphilis, Claude D. [7], Warnow, Tandy [8], Wong, Gane Ka-Shu [9].

The power and perils of phylotranscriptomics deep in the green tree of life.

Phylogenetic frameworks for species relationships and gene families are becoming increasingly essential for organization and analysis of the avalanche of sequence data that has come with development of massively parallel sequencing technologies. Phylogenetic analyses of approximated gene families are yielding improved understanding of species relationships and new insights into gene and genome evolution. The OneKP consortium has generated transcriptome data for over 1200 species distributed across the Viridiplantae and related taxa within the Archaeplastida. Use of these data to estimate species is dependent of accurate gene family circumscription and identification of gene families that tend to have remained single copy over a billion years of evolution. Further, phylogenetic inferences can vary depending on filtering strategies and methods of analysis.
We have performed Orthofinder analysis on gene models from 31 genomes available for species across Viridiplantae. OneKP transcript assemblies were sorted into the resulting gene family circumscriptions and over 400 single copy gene families were included in supermatrix and coalescence-based phylogenetic analyses. A variety of filtering strategies were employed to remove putative contaminants, sequence assembly artifacts and poorly sampled gene. Robust branching patterns were found among major lineages across the Viridiplantae, but resolution of some relationships varied among trees derived from alternative data filtering and inference methods. Thoughtful interpretation of these conflicts will be discussed.

Related Links:
The 1000 plants (oneKP or 1KP) initiative

1 - University of Georgia, 2505 Miller Plant Sciences, Plant Biology, Athens, GA, 30602, United States
2 - University of Texas, Computer Science, Austin, TX
3 - University of Illinois , Institute for Genomic Biology, Urbana, IL
4 - The Pennsylvania State University , Biology, University Park, PA
5 - University of Georgia, Plant Biology, Athens, GA
6 - California State University, Fullerton , Biology, Fullerton, CA
7 - Pennsylvania State University, Department Of Biology, 101 Life Sciences Building, University Park, PA, 16802, USA
8 - University of Illinois , Departments of Computer Science and Bioengineering , Urbana, IL
9 - University of Alberta, Biological Sciences; Medicine (Gastroenterology), CW405 Biological Sciences, Edmonton, AB, T6G 2E9, Canada

Keywords:
phylogenomics
Phylogenetics
transcriptomics
Viridiplantae.

Presentation Type: Colloquium Presentations
Session: C1
Location: Salon 4/The Shaw Conference Centre
Date: Monday, July 27th, 2015
Time: 8:15 AM
Number: C1002
Abstract ID:1117
Candidate for Awards:None