Advancing pre-clinical species genetic utility through a high-quality assembly of the cynomolgus monkey (Macaca fascicularis) genome

The cynomolgus macaque is a non-human primate (NHP) model, heavily used in biomedical research, but with outdated genomic resources. Here we have used the latest long-read sequencing technologies in order to assemble a fully phased, chromosome-level assembly for the cynomolgus macaque. We have built a hybrid assembly with PacBio, 10x Genomics, HiC and HiSeq technologies, resulting in a diploid assembly that spans a length of 5.1 Gb with a total of 16,741 contigs (N50 of 0.86Mb) contained in 370 scaffolds (N50 of 138 Mb) positioned on 42 chromosomes (21 homologous pairs). This assembly is highly homologous to former assemblies but identifies novel inversions and provides higher confidence in the genetic architecture of the cynomolgus macaque genome. A demographic estimation is also able to capture the recent genetic bottleneck in the Mauritius population, from which the sequenced individual originates. We offer this resource as an enablement for genetic tools to be built around this important model for biomedical research.