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Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility
- Warren, Wesley C;
- Harris, R Alan;
- Haukness, Marina;
- Fiddes, Ian T;
- Murali, Shwetha C;
- Fernandes, Jason;
- Dishuck, Philip C;
- Storer, Jessica M;
- Raveendran, Muthuswamy;
- Hillier, LaDeana W;
- Porubsky, David;
- Mao, Yafei;
- Gordon, David;
- Vollger, Mitchell R;
- Lewis, Alexandra P;
- Munson, Katherine M;
- DeVogelaere, Elizabeth;
- Armstrong, Joel;
- Diekhans, Mark;
- Walker, Jerilyn A;
- Tomlinson, Chad;
- Graves-Lindsay, Tina A;
- Kremitzki, Milinn;
- Salama, Sofie R;
- Audano, Peter A;
- Escalona, Merly;
- Maurer, Nicholas W;
- Antonacci, Francesca;
- Mercuri, Ludovica;
- Maggiolini, Flavia AM;
- Catacchio, Claudia Rita;
- Underwood, Jason G;
- O'Connor, David H;
- Sanders, Ashley D;
- Korbel, Jan O;
- Ferguson, Betsy;
- Kubisch, H Michael;
- Picker, Louis;
- Kalin, Ned H;
- Rosene, Douglas;
- Levine, Jon;
- Abbott, David H;
- Gray, Stanton B;
- Sanchez, Mar M;
- Kovacs-Balint, Zsofia A;
- Kemnitz, Joseph W;
- Thomasy, Sara M;
- Roberts, Jeffrey A;
- Kinnally, Erin L;
- Capitanio, John P;
- Skene, JH Pate;
- Platt, Michael;
- Cole, Shelley A;
- Green, Richard E;
- Ventura, Mario;
- Wiseman, Roger W;
- Paten, Benedict;
- Batzer, Mark A;
- Rogers, Jeffrey;
- Eichler, Evan E
- et al.
Published Web Location
https://doi.org/10.1126/science.abc6617Abstract
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. Whole-genome 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.
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