Abstract Detail

Phylogenomics

Jordon-Thaden, Ingrid [1], Gilman, Ian [2], Uribe-Convers, Simon [3], Chamala, Srikar [4], Tank, David [5], Martine, Chris [1].

Selection and validation of transcriptome-mined intronic primers for Fluidigm PCR and Illumina sequencing.

This presentation outlines the steps necessary to test primers specifically designed for Fluidigm digital PCR and Illumina MiSeq next generation sequencing for phylogenetic investigations. The primers validated for this study were designed from 12 transcriptomes from the One Thousand Plants Project (1KP) using MarkerMiner 1.0 (6 Solanum sp. (Solanceae) and 6 Draba sp. (Brassicaceae)). The primers chosen were used for phylogenetic inferences in the Australian monsoon tropical spiny solanum group (Solanaceae) and the North American Cordilleran species of Draba (Brassicaceae). Previous investigations of these taxa have recovered poor phylogenetic resolution with only a few commonly employed loci (e.g., ITS, trnL-trnF, matK-trnK), and additional loci are needed to confidently reconstruct their evolutionary histories. MarkerMiner 1.0 identified a large set of orthologous SCN genes and, from these, we selected 192 loci with intronic regions to validate. Three taxa from each phylogenetic study were used for validation. After primer pair validation, phylogenetically diverse taxa were amplified with these primers using Fluidigm and sequenced with MiSeq Illumina. Details of the primer design and validation steps will be presented here.

1 - Bucknell University, Biological Sciences, 203 Biology Building, Lewisburg, PA, 17837, USA, 570/577-1135
2 - Bucknell University, Dept Biology, Biology Bldg 203, Lewisburg, PA, 17837, USA
3 - University of Idaho, Moscow, ID
4 - University of Florida, Gainesville, FL, USA
5 - University of Idaho, Department of Biological Sciences, 875 Perimeter Dr. MS 3051, Moscow, ID, 83844-3051, USA

Keywords:
transcriptomics
Fluidigm
introns
phylogenomics
marker development
solanaceae
Solanum
Draba
Brassicaceae.

Presentation Type: Poster:Posters for Topics
Session: P
Location: Hall D/The Shaw Conference Centre
Date: Monday, July 27th, 2015
Time: 5:30 PM
Number: PPY007
Abstract ID:1296
Candidate for Awards:Genetics Section Poster Award