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Abstract Detail



Phylogenomics

FISHER, Amanda [1], Bell , Hester [1], Ingram, Amanda L. [2], Hasenstab, Kristen [3], Columbus, J. Travis [4].

Phylogenetic Estimation in Chloridoid Grasses (Poaceae) using Hyb-Seq NGS Data.

Over the past few decades we have largely relied on chloroplast sequence data to estimate the evolutionary history of plant lineages, while admitting that our studies would be improved with data from the nuclear genome. The development of next-generation sequencing technologies now allows us to recover large amounts of nuclear data in a relatively short time. We sought to test our chloroplast-based hypotheses of relationships in the grass subfamily Chloridoideae with a large number of nuclear loci. We used hyb-seq targeted-enrichment next-generation sequencing to recover numerous nuclear loci. Our gene sample included housekeeping genes, as well as genes that have been implicated in traits that are characteristic of or particularly labile in chloridoids: e.g., floral unisexuality, inflorescence branching, photosynthetic pathway, and salt tolerance. We used tools available in Geneious software to develop a workflow that extracts single copies of exons from pools of sequence fragments, even for samples from polyploid species. We used these data to assess the phylogeny from the perspective of the nuclear genome and improve our understanding of evolutionary history in this grass lineage.


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1 - Rancho Santa Ana Botanic Garden, 1500 N. College Ave., Claremont, CA, 91711, USA
2 - Wabash College, Department Of Biology, P.O. BOX 352, CRAWFORDSVILLE, IN, 47933, USA
3 - Rancho Santa Ana Botanic Garden, Research, 1500 N College Ave, Claremont, CA, 91711, USA
4 - Rancho Santa Ana Botanic Garden, 1500 North College Avenue, Claremont, CA, 91711-3157, USA

Keywords:
grass phylogeny
next-generation sequencing
polyploidy.

Presentation Type: Oral Paper:Papers for Topics
Session: 43
Location: Evergreen/Grove
Date: Wednesday, July 30th, 2014
Time: 4:45 PM
Number: 43012
Abstract ID:752
Candidate for Awards:None


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