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Abstract Detail



Conference Wide

Mandel, Jennifer [1], Funk, Vicki [2], Dikow, Rebecca [3], Noyes, Richard [4].

A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae, a.k.a. Asteraceae.

The Compositae (Asteraceae) are a large (25,000-33,000 species) and important family of plants that include critical members of threatened ecosystems and species of economic importance, as well as invasives. The most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several important unresolved areas. We have developed the tools and workflow necessary to enable the rapid sequencing of large numbers of orthologous nuclear loci in order to facilitate efficient phylogenomic analyses and the testing of hypotheses of phenotypic evolution across the family. Specifically, we have designed a set of sequence capture probes that represent conserved orthologous sequences from existing sunflower, lettuce, and safflower genomic resources. We then performed sequence capture using this probe set on 15 species from diverse clades of the Compositae followed by bioinformatic and phylogenetic analyses on the resulting dataset.
In this workshop, we will present an overview of the probe design process and the web lab protocol for performing sequence capture including helpful information for designing similar experiments for one’s own research system. Participants are also asked to bring their laptops and will be given a sample dataset from the project. The organizers will demonstrate the bioinformatic and phylogenetic workflow, walk participants through the process on their own computers, and be available to answer questions about the process. Examples will be given for implementing this method in the Compositae but will generalizable to other species groups. 


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Related Links:
GitHub Code Repository for Compositae-COS-workflow
Mandel research website


1 - University of Memphis, Department of Plant Biology, 3774 Walker Avenue, Memphis, TN, 38152, USA
2 - Smithsonian Institution, DEPT OF BOTANY-NHB 166, P.O. Box 37012, Washington, DC, 20013-7012, USA, 202/357-2560
3 - Smithsonian Institution, National Zoo Center for Conservation and Evolutionary Genetics, Division of Mammals, NMNH, PO Box 37012, MRC 108, Washington, DC, 20013-7012, USA
4 - University Of Central Arkansas, Department Of Biology, Lewis Science Center 180, Conway, AR, 72035, USA, 501-450-5926

Keywords:
base-tree
conserved
exon capture
high-throughput
next-generation sequencing
orthologs
phylogenomics.

Presentation Type: Workshop
Session: WS14
Location: Pines South/Boise Centre
Date: Sunday, July 27th, 2014
Time: 1:00 PM
Number: WS14001
Abstract ID:32
Candidate for Awards:None


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