| Abstract Detail
Genomics / Proteomics Liu, Xiaoxian [1], Barbazuk, William B. [1], Soltis, Pamela S. [2], Soltis, Douglas E. [1]. A de novo detection pipeline for alternative splicing based on single-molecule long-read isoforms using Amborella trichopoda. RNA alternative splicing (AS), which occurs after a pre-mRNA transcript is formed from a template DNA, is a major means of generating diverse transcripts and protein products. Research on human and mouse shows the unique advantages of Iso-SeqTM data in isoform-level transcriptome analysis, such as in the study of alternative splicing (AS) and gene fusion. In this study, we applied the Iso-SeqTM approach to investigate AS detection in Amborella trichopoda, a phylogenetically pivotal species that is sister to all other living flowering plants. A comparison between Iso-SeqTM data and existing data suggests that the Iso-SeqTM platform provides better recovery than what is obtained for short reads on large transcripts, new gene locus identification, and gene model prediction. Reference-based AS detection with Iso-SeqTM data shows that 45.8% of the multi-exonic genes in Amborella trichopoda showed evidence of AS. This percentage is higher than that obtained from previously published RNA-Seq analysis (37.5%) and suggests that the Iso-SeqTM long-read approach might be useful for detecting more AS events than in previous analyses. Reference-based AS detection using different error correction methods yielded different results, and we therefore recommend an approach that combines elements of multiple methods. We also developed a de novo AS detection pipeline for Iso-SeqTM data. The pipeline was validated by both the existing AS database and RT-PCR experiments. Validation results show a 63.5% overall success rate in identifying AS events and suggest that this method could be successfully applied to a non-model system with limited genetic resources.
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1 - University of Florida, Dept. of Biology, 1659 Museum Road, Gainesville, Florida, 32611, United States
2 - University Of Florida, Florida Museum Of Natural History, PO BOX 117800, Gainesville, FL, 32611-7800, USA, 352/273-1964
Keywords:
RNA alternative splicing
de novo pipeline
Amborella trichopoda
Transcriptome.
Presentation Type: Oral Paper
Session: 19, Genomics & Proteomics I
Location: 105/Savannah International Trade and Convention Center
Date: Tuesday, August 2nd, 2016
Time: 11:00 AM
Number: 19012
Abstract ID:562
Candidate for Awards:None |
