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

Item Type:	Article
Title:	Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility.
Creators Name:	Warren, W.C. and Harris, R.A. and Haukness, M. and Fiddes, I.T. and Murali, S.C. and Fernandes, J. and Dishuck, P.C. and Storer, J.M and Raveendran, M. and Hillier, L.W. and Porubsky, D. and Mao, Y. and Gordon, D. and Vollger, M.R. and Lewis, A.P. and Munson, K.M. and DeVogelaere, E. and Armstrong, J. and Diekhans, M. and Walker, J.A. and Tomlinson, C. and Graves-Lindsay, T.A. and Kremitzki, M. and Salama, S.R. and Audano, P.A. and Escalona, M. and Maurer, N.W. and Antonacci, F. and Mercuri, L. and Maggiolini, F.A.M. and Catacchio, C.R. and Underwood, J.G. and O'Connor, D.H. and Sanders, A.D. and Korbel, J.O. and Ferguson, B. and Kubisch, H.M. and Picker, L. and Kalin, N.H. and Rosene, D. and Levine, J. and Abbott, D.H. and Gray, S.B. and Sanchez, M.M. and Kovacs-Balint, Z.A. and Kemnitz, J.W. and Thomasy, S.M. and Roberts, J.A. and Kinnally, E.L. and Capitanio, J.P. and Skene, J.H.Pate and Platt, M. and Cole, S.A. and Green, R.E. and Ventura, M. and Wiseman, R.W. and Paten, B. and Batzer, M.A. and Rogers, J. and Eichler, E.E.
Abstract:	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.
Keywords:	Genetic Predisposition to Disease, Genetic Variation, Genome, Molecular Sequence Annotation, Single Nucleotide Polymorphism, Whole Genome Sequencing, Animals, Macaca mulatta
Source:	Science
ISSN:	0036-8075
Publisher:	American Association for the Advancement of Science
Volume:	370
Number:	6523
Page Range:	eabc6617
Date:	18 December 2020
Official Publication:	https://doi.org/10.1126/science.abc6617
External Fulltext:	View full text on PubMed Central
PubMed:	View item in PubMed

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