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

Wesley C. Warren, R. Alan Harris, Marina Haukness, Ian T. Fiddes, Shwetha C. Murali, Jason Fernandes, Philip C. Dishuck, Jessica M. Storer, Muthuswamy Raveendran, La Deana W. Hillier, David Porubsky, Yafei Mao, David Gordon, Mitchell R. Vollger, Alexandra P. Lewis, Katherine M. Munson, Elizabeth Devogelaere, Joel Armstrong, Mark Diekhans, Jerilyn A. WalkerChad Tomlinson, Tina A. Graves-Lindsay, Milinn Kremitzki, Sofie R. Salama, Peter A. Audano, Merly Escalona9, Nicholas W. Maurer, Francesca Antonacci, Ludovica Mercuri, Flavia A.M. Maggiolini, Claudia Rita Catacchio, Jason G. Underwood, David H. O'Connor, Ashley D. Sanders, Jan O. Korbel, Betsy Ferguson, H. Michael Kubisch, Louis Picker, Ned H. Kalin, Douglas Rosene, Jon Levine, David H. Abbott, Stanton B. Gray25, Mar M. Sanchez, Zsofia A. Kovacs-Balint, Joseph W. Kemnitz, Sara M. Thomasy, Jeffrey A. Roberts, Erin L. Kinnally, John P. Capitanio, J. H.Pate Skene, Michael Platt, Shelley A. Cole, Richard E. Green, Mario Ventura, Roger W. Wiseman, Benedict Paten, Mark A. Batzer, Jeffrey Rogers, Evan E. Eichler

Research output: Contribution to journalArticlepeer-review

57 Scopus citations


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) that increases 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 discovered new lineage-specific genes and expanded gene families that are potentially informative in studies of evolution and disease susceptibility. Wholegenome sequencing (WGS) data from 853 rhesus macaques identified 85.7 million single-nucleotide variants (SNVs) and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay, providing a framework for developing noninvasive NHP models of human disease.

Original languageEnglish
Article numbereabc6617
Issue number6523
StatePublished - Dec 18 2020


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