Abstract Detail

Phylogenomics

Johnson , Matthew G [1], Wickett, Norman [2], Devos, Nicolas [3], Liu, Yang [4], Medina, Rafael [4], Goffinet, Bernard [5], Shaw, Jonathan [6].

Constructing phylogenetic datasets from bait-capture data without a genome: strategies and challenges.

Liquid-phase DNA capture technology has the potential to generate very large phylogenetic datasets (hundreds of loci) for non-model organisms for a very low cost, compared to traditional sequencing. In this technique, oligonucleotides representing genes of interest are hybridized with genomic DNA and then sequenced using an Illlumina system.  Here, we explore the specificity of baits for use with a wide range of species, for instance baits designed for organellar coding sequences may be successfully used on any land plant, or baits designed for hundreds of low copy nuclear loci that my be used for a targeted clade (here, pleurocarpous mosses). In order to use the data for phylogeny reconstruction, the reads must be assembled and sorted into loci. However, without a sequenced genome for reference, data generated for nuclear coding regions must allow for the presence of introns, and variability in intron structure across species. This presents a particular challenge when exons are short or species-specific coverage is low. We describe a bioinformatics pipeline that uses sequence similarity, exon detection, and reciprocal best hits to generate multiple sequence alignments from sequence capture assemblies.

1 - Chicago Botanic Garden, Plant Sciences, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
2 - Chicago Botanic Garden, 1000 Lake Cook Rd., Apt 2, Glencoe, IL, 60022, USA
3 - Duke University, 130 Science Dr, Box 90338, Durham, North Carolina, 27708, USA
4 - University of Connecticut, 75 North Eaglevlle Rd, Storrs, CT, 06269, USA
5 - University Of Connecticut, Department Of Ecology & Evolutionary Biology, 75 N. Eagleville Road, U-3043, STORRS, CT, 06269-3043, USA
6 - 130 Science Drive, Box 90338, Durham, NC, 27708, USA, 919/660-7344

Keywords:
targeted sequence capture
bioinformatics pipeline
bryophtyes
plastid data.

Presentation Type: Oral Paper:Papers for Topics
Session: 43
Location: Evergreen/Grove
Date: Wednesday, July 30th, 2014
Time: 2:15 PM
Number: 43004
Abstract ID:606
Candidate for Awards:None