Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility.
Wesley C WarrenRonald Alan HarrisMarina HauknessIan T FiddesShwetha C MuraliJason D FernandesPhilip C DishuckJessica M StorerMuthuswamy RaveendranLaDeana W HillierDavid PorubskyYafei MaoDavid GordonMitchell R VollgerAlexandra P LewisKatherine M MunsonElizabeth DeVogelaereJoel ArmstrongMark E DiekhansJerilyn A WalkerChad TomlinsonTina A Graves-LindsayMilinn KremitzkiSofie R SalamaPeter A AudanoMerly EscalonaNicholas W MaurerFrancesca AntonacciLudovica MercuriFlavia Angela Maria MaggioliniClaudia Rita CatacchioJason G UnderwoodDavid H O'ConnorAshley D SandersJan O KorbelBetsy M FergusonH Michael KubischLouis J PickerNed H KalinDouglas RoseneJon E LevineDavid H AbbottStanton B GrayMar M SanchezZsofia A Kovacs-BalintJoseph W KemnitzSara M ThomasyJeffrey A RobertsErin L KinnallyJohn P CapitanioJesse A G SkeneMichael Louis PlattShelley A ColeRichard E GreenMario VenturaRoger W WisemanBenedict PatenMark A BatzerJeffrey RogersEvan E EichlerPublished in: Science (New York, N.Y.) (2021)
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.