Abstract:

The formation of universitary undergraduates in the Genetics field of the latest sequencing techniques is of great relevance for addressing the challenges associated with important biological questions and current societal demands. To achieve this goal, it is important to understand genome structure and acquire bioinformatics skills in order to analyse raw sequences from sequencing projects. Unfortunately, sequencing experiments require specialized instruments that often are too expensive to be widely widespread into compulsory courses of undergraduate students. For this reason, practical lessons are usually focused on sequence analysis platforms. Since the discovery of the deoxyribonucleic acid (DNA) structure by Watson, Crick and Franklin in 1953, continuous efforts have been made by the scientific community to sequence DNA. The first Sanger technology was incredibly accurate but required lots of processing, increasing thus the cost of sequencing and sequencers. However, DNA sequencing has come a long way from traditional Sanger, and next-generation sequencing (NGS) technologies dramatically reduced the sequencing cost and increased throughput per sample but not the sequencers cost. In this respect, Nanopore third-generation genomic sequencing is a unique opportunity for undergraduates to explore developing sequencing technologies due to its low-cost, high repeatability, and ease of sample preparation. MinION is a portable, simple mechanism and real-time device for DNA sequencing developed by Oxford Nanopore Technologies. The introduction of this sequencing technology in the “Genomics” course (e.g., for biotechnology students) may provide a complete live sequencing experience. Here, we propose a model that bridges experimental and bioinformatic concepts using the MinION sequencer to analyse the microbial profile of different soil samples thanks to the conserved and variable regions of the 16S rRNA gene. This practical lesson requires nine hours divided into three blocks involving: i) the DNA extraction and polymerase chain reaction (PCR) amplification of the 16S rRNA gene, ii) the library preparation and MinION sample loading, and iii) the bioinformatic analysis of the final MinION raw data sequences. All this together will enhance students’ skills for hands-on basic research experiments, and they will also be introduced to the fundamentals of bioinformatics.

Keywords:

Genome, bioinformatics, Nanopore sequencing, microbial profile, 16S rRNA.