Sequence diversity analyses of an improved rhesus macaque genome enhances its biomedical utility

The rhesus macaque ( Macaca mulatta ) is the most widely studied nonhuman primate (NHP) in biomedical research. We present an updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp), increasing the sequence contiguity 120-fold and annotate it using 6.5 million full-length transcripts, thus improving our understanding of gene content, isoform diversity, and repeat organization. With the improved assembly of segmental duplications, we discover novel lineage-specific genes and expand gene families that are potentially informative in studies of evolution and disease susceptibility. Whole-genome sequence data from 853 captive rhesus macaques identifies polymorphism in 85.7 million single-nucleotide and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay, providing a framework for developing non-invasive NHP models of human disease. A compendium of rhesus macaque genome variation