Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, <i>Otocolobus manul</i>

Abstract

Pallas's cat, or the manul cat (<i>Otocolobus manul</i>), is a small felid native to the grasslands and steppes of central Asia. Population strongholds in Mongolia and China face growing challenges from climate change, habitat fragmentation, poaching, and other sources. These threats, combined with <i>O. manul</i>'s zoo collection popularity and value in evolutionary biology, necessitate improvement of species genomic resources. We used standalone nanopore sequencing to assemble a 2.5 Gb, 61-contig nuclear assembly and 17097 bp mitogenome for <i>O. manul</i>. The primary nuclear assembly had 56× sequencing coverage, a contig N50 of 118 Mb, and a 94.7% BUSCO completeness score for <i>Carnivora</i>-specific genes. High genome collinearity within <i>Felidae</i> permitted alignment-based scaffolding onto the fishing cat (<i>Prionailurus viverrinus</i>) reference genome. Manul contigs spanned all 19 felid chromosomes with an inferred total gap length of less than 400 kilobases. Modified basecalling and variant phasing produced an alternate pseudohaplotype assembly and allele-specific DNA methylation calls; 61 differentially methylated regions were identified between haplotypes. Nearest features included classical imprinted genes, non-coding RNAs, and putative novel imprinted loci. The assembled mitogenome successfully resolved existing discordance between <i>Felinae</i> nuclear and mtDNA phylogenies. All assembly drafts were generated from 158 Gb of sequence using seven minION flow cells.