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Abstract Detail


Lawrence, Travis Joseph [1], Ardell, David [1].

Using tRNA class informative features to determine the phylogenetic placement of Gnetophyta.

Gnetophyta is a small gymnosperm clade of about 90 species of tropical evergreen trees, shrubs, and lianas that have been one of the most enigmatic problems in seed plant phylogenetics. Before the use of cladistic methods early studies supported conflicting hypotheses placing Gnetophyta either with conifers, cone-bearing gymnosperms, or with angiosperms. The first set of cladistic studies using morphological data united Gnetophyta with angiosperms appearing to confirm earlier hypotheses. The close relationship of Gnetophyta and angiosperms was disputed by early studies analyzing molecular data which recovered Gnetophyta as either sister to all seed plants or sister to extant gymnosperms. Subsequent molecular phylogenetic and phylogenomic studies have converged on two hypotheses: 1) the Gnecup hypothesis that unites Gnetophyta with Cupressophyta conifers and 2) the Gnepine hypothesis that unites Gnetophyta with Pinaceae. Interestingly, the Gnecup hypothesis is supported by plastid phylogenomic data, whereas nuclear phylogenomic data and certain partitions of plastid data support the Gnepine hypothesis.
To address this conflict I used a new phylogenetic method currently being developed in my lab. This method is based on the putative tRNA-protein interaction determinants called tRNA class informative features (CIFs). Despite the very high structural similarity of all tRNAs each must interact productively with only one type of aminoacyl-tRNA synthetase (aaRS) to be charged with its cognate amino acid. CIFs are a set of structural features (e.g. Cytosine at position 7) on a tRNA that promote recognition by its cognate aaRS. These sets of structural features that determine a tRNAs class are not static and have been shown to vary widely across the tree of life providing a slowly evolving phylogenetic marker. Putative tRNA CIFs are determined bioinformatically from genomic sequence data using a conditional probability framework using the ideas of molecular information theory.
To test between the Gnecup and Gnepine hypotheses, I used all publicly available chloroplast genomes of Gymnosperms, Angiosperms, and ferns to determine tRNA CIFs. Chloroplast tRNA CIFs are unique because they are possibly influenced by both the evolutionary history of nuclear genome, where the aaRSs genes are located, and the evolutionary history of the chloroplast genome, where the tRNA genes are located. From the chloroplast tRNA CIFs I reconstructed phylogenetic trees using the neighbor-joining method with a distance metric calculated from tRNA CIFs.

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1 - University of California, Merced, Quantitative and Systems Biology Program, 5200 North Lake Rd., Merced, CA, 95343, USA


Presentation Type: Poster
Session: P, Phylogenomics Posters
Location: Exhibit Hall/Savannah International Trade and Convention Center
Date: Monday, August 1st, 2016
Time: 5:30 PM This poster will be presented at 6:15 pm. The Poster Session runs from 5:30 pm to 7:00 pm. Posters with odd poster numbers are presented at 5:30 pm, and posters with even poster numbers are presented at 6:15 pm.
Number: PPY002
Abstract ID:109
Candidate for Awards:None

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