Abstract Detail

Phylogenomics

Timilsena, Prakash Raj [1], Wafula, Eric K. [2], Leebens-Mack, Jim [3], dePamphilis, Claude W. [4].

Phylogenetic study of the monocots using many single copy nuclear genes.

Monocots are a monophyletic group within angiosperms, that comprises of 11 orders, 77 families (APG III) and about 60,000 species. In addition, it contains an unplaced family Dasypogonaceae. The phylogenetic positions of some orders, especially within the commelinid clade remains yet fully unresolved. The objective of this study is to resolve these relationships using a large set of nuclear genes, that were mostly retained as single copies across a set of 12 monocot genomes. An ortho-MCL based classification of proteomes was performed using 9 monocot genomes along with additional 2 eudicot genomes and the basal angiosperm Amborella trichopoda genome to create a plants tribe database. From the global classifications of the target set of transcriptomes, using this database, a set of 602 orthogroups, were identified as putatively single copy and used for phylogenomic studies. Several post processing analyses were performed to for the removal of contaminants, duplicated sequences and fragmented sequences. Phylogenetic trees were obtained using coalescent as well as concatenated methods. Our coalescent and concatenated trees were highly consistent and strongly congruent, with strong bootstrap supports. We will be presenting the results of the analysis.

1 - The Pennsylvania State Univers, Biology, University Park, Pennsylvania, 16802, USA
2 - The Pennsylvania State Univers, University Park, Pennsylvania, 16802, USA
3 - University Of Georgia, 4503 Miller Plant Sciences, Athens, GA, 30602, USA
4 - The Pennsylvania State University, Department of Biology, University Park, State College

Keywords:
phylogenomics
monocots
Phylotranscriptomics
low-copy nuclear markers
phylogeny
Plants Tribe.

Presentation Type: Oral Paper
Session: 38, Phylogenomics III
Location: 204/Savannah International Trade and Convention Center
Date: Wednesday, August 3rd, 2016
Time: 11:15 AM
Number: 38013
Abstract ID:866
Candidate for Awards:Margaret Menzel Award