Abstract Detail

Recent Topics Posters

McFadden , Angela M [1], Raubeson, Linda [2], Guo, Wenhu [3], Mower, Jeffrey [4], Mathews, Sarah [5].

Resolving Gnetum Evolutionary History with Organellar Genome Sequences.

Gnetums are non-flowering seed plants of the tropics; they are indigenous to South America, Africa, and Asia. This group of about 30 species has long been fascinating to botanists because it shares distinctive morphological characteristics with flowering plants. The relationships of the Gnetum species to one another are only beginning to be understood. With that in mind, we focused our work on using molecular techniques to generate a phylogenetic tree for the genus Gnetum. We generated Illumina TruSeq libraries of total genomic DNA, and used the libraries to produce millions of 101 base-pair single-end sequencing reads using Illumina technology. We then used various trimming and filtering functions of Trimmomatic-0.30 to remove adapter artifacts, and reads and regions of reads where the average quality was below a certain threshold (Phred score of 26, within a sliding window of 5 base pairs). Next, we used reference-guided assembly in Geneious 8.0.5 (using the Gnetum parvifolium sequence in Genbank, NC_011942) to identify chloroplast reads and assemble chloroplast genomes for each species. Thus far, we have used this approach to determine the chloroplast genome sequences for 10 species of Gnetum. The alignment of these genome sequences was the basis of phylogenetic analyzes using Maximum Parsimony and Maximum Likelihood. Under both models, the trees were compatible, the confidence levels for most nodes were very high, and the trees show clades consistent with biogeography – New World taxa separate from Old World taxa, and two clades within the Asian species (compatible with the work of Won and Renner). We are currently attempting to use a Gnetum mitochondrial genome sequence as a reference to assemble mitochondrial genome sequences from the pool of total genomic Illumina reads. If successful, these mitochondrial genome sequences will be analyzed using comparable phylogenetic approaches and compared to the chloroplast phylogeny. We are also currently in the process of sequencing additional species to add to our analysis to further elucidate the relationships and evolutionary history of this genus. 

1 - Central Washington University, Biology, 400 E University Way, Ellensburg, WA, 98926, USA
2 - Central Washington University, 400 E University Way, Ellensburg, WA, 98926, United States
3 - University of Nebraska-Lincoln, Agronomy & Horticulture, 202 Keim, Lincoln, NE, 68583, USA
4 - University of Nebraska-Lincoln, Agronomy & Horticulture, 202 Keim, Lincoln, NE, 68583, United States
5 - CSIRO National Research Collections Australia, The Australian National Herbarium, Canberra, ACT, 2601, Australia

Keywords:
Gnetum
Gnetales
chloroplast
Phylogeny.

Presentation Type: Recent Topics Poster
Session: P
Location: Hall D/The Shaw Conference Centre
Date: Monday, July 27th, 2015
Time: 5:30 PM
Number: PRT053
Abstract ID:1839
Candidate for Awards:None