Sequencing and assembling the genome of Przewalski's horse in the classroom

Abstract

Sequencing a genome by students has now become practical as we demonstrated with our recent publication of the Przewalski's horse (Equus ferus przewalskii) genome. In this review, I describe my experience teaching genome assembly in the classroom. In my course, students sequenced, assembled, and published a high-quality genome for Przewalski's horse using Oxford Nanopore long-read sequencing with only $4000 of materials. Along with the genome, we assembled the mitochondrial genome, sequence variants, predicted gene annotations, and DNA methylation levels. Our genome statistics far exceeded the previous Przewalski's horse assembly and is on par the domestic horse genome, EquCab3.0. Methods were streamlined, simplified, and conveyed in markdown for complete recording and use in the classroom. All students were authors on the resulting manuscript. By bringing genome assembly into the classroom, we provide both new reference genomes and new genomics expertise to the scientific community at the same time.