Abstract Detail

Genomics / Proteomics

Liu, Xiaoxian [1], Soltis, Pamela [2], Soltis, Douglas [3], Barbazuk, W. Brad [4].

Searching for alternative splicing candidate genes using next-generation sequencing in Tragopogon (Asteraceae).

Polyploidization is a major driving force in angiosperm evolution and diversification; all angiosperms have experienced at least one round of genome duplication. These features have prompted a dramatic increase in the study of polyploidy. Two Tragopogon polyploids represent an important model for the study of recent and recurrent polyploidy. The system has five species: three diploids (T. dubius, T. pratensis and T. porrifolius) and two allotetraploids (T. mirus, T. miscellus). The polyploids formed during the last 80 years in the western U.S. via hybridization and genome doubling after introduction of the diploids from Europe. RNA alternative splicing (AS) produces multiple transcript forms (isoforms) from a single pre-mRNA through selective use of splice sites. The multiple isoforms from a single gene could contribute to proteome diversity and hence influence plant evolution and diversification. A common method to detect AS events involves alignment of transcriptome sequences to a reference genome. However, Tragopogon is not a genetic model, and the genome has not yet been sequenced. In this project, we are working on a new bioinformatics pipeline associated with next-generation sequencing (NGS), to detect AS events in Tragopogon. Transcriptome sequence of T. dubius is being produced using the PacBio long-read NGS platform, which can generate reads in excess of 1000bp. Available Illumina transcriptome data from the same population of T. dubius is being used to error-correct the PacBio sequence data. A substantial portion of these corrected long-sequence reads will represent close to full-length transcripts. AS events should be directly detected within the corrected PacBio reads; alternatively, the reads can be used to help better assemble collections of Illumina and 454 Tragopogon transcripts, within which AS events can be detected. We will present our data processing and analysis pipeline and our current Tragopogon AS isoform mining results. Genes with evidence of AS are the candidate genes for future Tragopogon study.

Broader Impacts:

1 - University of Florida, Department of Biology, Gainesville, FL, 32611, USA
2 - University of Florida, Florida Museum of Natural History, PO BOX 117800, Gainesville, FL, 32611-7800, USA
3 - University of Florida, Biology and Florida Museum of Natural History, PO BOX 117800,, Gainesville, FL, 32611-7800, USA
4 - University of Florida, Department of Biology, Gaineville, FL, 32611, USA

Keywords:
Polyploidization
Tragopogon
RNA alternative splicing
Next-generation sequencing
PicBio error correction..

Presentation Type: Poster:Posters for Topics
Session: P
Location: Grand Salon A - D/Riverside Hilton
Date: Monday, July 29th, 2013
Time: 5:30 PM
Number: PGP004
Abstract ID:434
Candidate for Awards:Genetics Section Poster Award