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

In this review, Faulk describes his graduate course in which students used Oxford Nanopore sequencing to provide a high-quality, highly contiguous genome assembly, including the mitochondrial genome, and DNA methylation analysis for the endangered Przewalski’s horse, which previously lacked a complete reference genome. The review highlights the accessibility and affordability of Oxford Nanopore technology, with only $4,000 of materials required for this project.

Key points:

• With Oxford Nanopore technology, genome sequencing is now feasible in educational settings, allowing students to get hands-on experience whilst contributing to scientific knowledge

• The previous genome assembly for Przewalski’s horse was highly fragmented and incomplete, limiting its use in conservation and research

• The new EquPr2 assembly has 25-fold fewer scaffolds and a 166-fold increase in read length N50

• The students found that the mitochondrial genome was 99.63% identical to that of the domestic horse, aiding evolutionary research

• Oxford Nanopore sequencing enabled allele-specific epigenetic analysis, identifying 226 differentially methylated regions, including key imprinting genes

• Pseudohaplotype phasing allowed for precise analysis of heterozygosity and inbreeding, which could inform breeding strategies for endangered populations

Sample type: Przewalski’s horse blood

Kit: Ligation Sequencing Kit