Detecting alternatively spliced transcript isoforms from single-molecule long-read sequences without a reference genome

December 31st, 2017
By Gitzendanner, Matt

Liu, X., W. Mei, P. S. Soltis, D. E. Soltis, and W. B. Barbazuk. 2017. Detecting alternatively spliced transcript isoforms from single-molecule long-read sequences without a reference genome. Mol Ecol Resour 17:1243–1256. [View on publisher’s site]

Abstract

Alternative splicing (AS) is a major source of transcript and proteome diversity, but examining AS in species without well-annotated reference genomes remains difficult. Research on both human and mouse has demonstrated the advantages of using Iso-Seq™ data for isoform-level transcriptome analysis, including the study of AS and gene fusion. We applied Iso-Seq™ to investigate AS in Amborella trichopoda, a phylogenetically pivotal species that is sister to all other living angiosperms. Our data show that, compared with RNA-Seq data, the Iso-Seq™ platform provides better recovery on large transcripts, new gene locus identification and gene model correction. Reference-based AS detection with Iso-Seq™ data identifies AS within a higher fraction of multi-exonic genes than observed for published RNA-Seq analysis (45.8% vs. 37.5%). These data demonstrate that the Iso-Seq™ approach is useful for detecting AS events. Using the Iso-Seq-defined transcript collection in Amborella as a reference, we further describe a pipeline for detection of AS isoforms from PacBio Iso-Seq™ without using a reference sequence (de novo). Results using this pipeline show a 66%–76% overall success rate in identifying AS events. This de novoAS detection pipeline provides a method to accurately characterize and identify bona fide alternatively spliced transcripts in any nonmodel system that lacks a reference genome sequence. Hence, our pipeline has huge potential applications and benefits to the broader biology community.

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