Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing

PeerJ. 2015 Nov 24;3:e1441. doi: 10.7717/peerj.1441. eCollection 2015.

Abstract

Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we show that single-molecule cDNA sequencing using the MinION accurately characterises venom toxin-encoding genes in the painted saw-scaled viper, Echis coloratus. We find the raw sequencing error rate to be around 12%, improved to 0-2% with hybrid error correction and 3% with de novo error correction. Our corrected data provides full coding sequences and 5' and 3' UTRs for 29 of 33 candidate venom toxins detected, far superior to Illumina data (13/40 complete) and Sanger-based ESTs (15/29). We suggest that, should the current pace of improvement continue, the MinION will become the default approach for cDNA sequencing in a variety of species.

Keywords: Echis; MinION; Nanopore; Sequencing; Transcriptomics; Venom; Venom gland; Viper; cDNA.

Grant support

This research was partially supported by a Royal Society Research Grant awarded to JFM (grant number RG100514) and JFM has also been generously supported by the Biosciences, Environment and Agriculture Alliance (BEAA) between Bangor University and Aberystwyth University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.