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