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Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

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Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse Deanna M. Church1.*, Leo Goodstadt2.*, LaDeana W. Hillier3, Michael C. Zody4,5, Steve Goldstein6, Xinwe She7, Carol J. Bult8, Richa Agarwala1, Joshua L. Cherry1, Michael DiCuccio1, Wratko Hlavina1,Yuri Kapustin1, Peter Meric1, Donna Maglott1, Zoe¨ Birtle2, Ana C. Marques2, Tina Graves3, Shiguo Zhou6, Brian Teague6, Konstantinos Potamousis6, Christopher Churas6, Michael Place9, Jill Herschleb6, Ron Runnheim6, Daniel Forrest6, James Amos-Landgraf10, David C. Schwartz6, Ze Cheng7, Kerstin Lindblad- Toh4,5*, Evan E. Eichler7*, Chris P. Ponting2*, The Mouse Genome Sequencing Consortium" 1 National Center for Biotechnology Information, Bethesda, Maryland, United States of America, 2 MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom, 3 The Genome Center at Washington University, St. Louis, Missouri, United States of America, 4 The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, 5 Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden, 6 Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America, 7 Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America, 8 The Jackson Laboratory, Bar Harbor, Maine, United States of America, 9 Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America, 10 McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America Abstract The mouse (Mus musculus) is the premier animal model for understanding human disease and development. Here we show that a comprehensive understanding of mouse biology is only possible with the availability of a finished, high-quality genome assembly. The finished clone-based assembly of the mouse strain C57BL/6J reported here has over 175,000 fewer gaps and over 139 Mb more of novel sequence, compared with the earlier MGSCv3 draft genome assembly. In a comprehensive analysis of this revised genome sequence, we are now able to define 20,210 protein-coding genes, over a thousand more than predicted in the human genome (19,042 genes). In addition, we identified 439 long, non–protein- coding RNAs with evidence for transcribed orthologs in human. We analyzed the complex and repetitive landscape of 267 Mb of sequence that was missing or misassembled in the previously published assembly, and we provide insights into the reasons for its resistance to sequencing and assembly by whole-genome shotgun approaches. Duplicated regions within newly assembled sequence tend to be of more recent ancestry than duplicates in the published draft, correcting our initial understanding of recent evolution on the mouse lineage. These duplicates appear to be largely composed of sequence regions containing transposable elements and duplicated protein-coding genes; of these, some may be fixed in the mouse population, but at least 40% of segmentally duplicated sequences are copy number variable even among laboratory mouse strains. Mouse lineage-specific regions contain 3,767 genes drawn mainly from rapidly-changing gene families associated with reproductive functions. The finished mouse genome assembly, therefore, greatly improves our understanding of rodent-specific biology and allows the delineation of ancestral biological functions that are shared with human from derived functions that are not. Citation: Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, et al. (2009) Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse. PLoS Biol 7(5): e1000112. doi:10.1371/journal.pbio.1000112 Academic Editor: Richard J. Roberts, New England Biolabs, United States of America Received December 19, 2008; Accepted April 3, 2009; Published May 26, 2009 This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. Funding: DMC, RA, JC, MD, DM, WH, YK, and the National Institutes of Health Intramural Sequencing Center were supported by the Intramural Research Program of the NIH. CPP, ZB, and LG were supported by the UK Medical Research Council. ACM was supported by the Swiss National Science Foundation. EEE, XS, and ZC were supported in part by National Institutes of Health grant HG002385. EEE is an investigator of the Howard Hughes Medical Institute. The Genome Center at Washington University, The Human Genome Sequencing Center at the Baylor College of Medicine, and The Broad Institute of Harvard and MIT are supported by genome sequencing grants from National Human Genome Research Institute. Chromosomes 2, 4, 11 and X were completed with funding from the Wellcome Trust. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Abbreviations: EST, expressed sequence tag; ncRNA, noncoding RNA; SSR, simple sequence repeat; TPF, tiling path file; VR, vomeronasal receptors; WGSA, Whole Genome Sequence and Assembly. * E-mail: [email protected] (DMC); [email protected] (LG); [email protected] (KL-T); [email protected] (EEE); [email protected] (CPP) . These authors contributed equally to this work. " Membership of The Mouse Genome Sequencing Consortium is provided in the Acknowledgments. Introduction human disease and development and the mammalian genome against which human DNA, genes, and genomes are most The mouse (Mus musculus) occupies a singular position in frequently compared. Despite approximately 90 million years of genetics and genomics. It is both the premier animal model for independent evolution [1], the laboratory mouse remains an PLoS Biology | www.plosbiology.org 1 May 2009 | Volume 7 | Issue 5 | e1000112 Lineage-Specific Biology of the Mouse Author Summary of the draft assembly might harbour large numbers of rapidly evolving genes whose identification might illuminate mouse- The availability of an accurate genome sequence provides specific biology. Only by accounting for these missing genes could the bedrock upon which modern biomedical research is we obtain a comprehensive understanding of the biology that based. Here we describe a high-quality assembly, Build 36, distinguishes these two species. Given this, it has been a goal of the of the mouse genome. This assembly was put together by international consortium to produce a mouse genome assembly of aligning overlapping individual clones representing parts coverage and quality comparable to that of the human genome of the genome, and it provides a more complete picture described in 2004 [19]. Although it was anticipated that the effort than previous assemblies, because it adds much rodent- and expense required for producing such an assembly via a clone- specific sequence that was previously unavailable. The based approach would be substantial, this would be justified by the addition of these sequences provides insight into both the increased fidelity, and thus utility, of the higher quality genome genomic architecture and the gene complement of the assembly to the biomedical research community. mouse. In particular, it highlights recent gene duplications and the expansion of certain gene families during rodent Here we report the completion of this effort and present a high- evolution. An improved understanding of the mouse quality, largely finished clone-based genome assembly of the genome and thus mouse biology will enhance the utility C57BL/6J strain of mouse, here referred to as Build 36. This new of the mouse as a model for human disease. assembly includes 267 Mb of sequence (Protocol S1) that was either missing or misassembled, much of which consists of repetitive and segmentally duplicated sequence (4.94% of the excellent model for many human phenotypes and thus is critical to genome). Over 175,000 gaps in MGSCv3 have been closed, and the study of human disease and mammalian development. Its genome-wide continuity has improved accordingly, with scaffold small size and rapid breeding cycle are of immense practical N50 lengths (the scaffold length in which at least half of the bases utility, and the mature mouse genetics system, with hundreds of of the assembly reside) increasing from 17 Mb to 40 Mb. inbred lines, allows phenotypic consequences of sequence variation The availability of finished sequence for human, and now to be inferred [2]. mouse, enables more-complete surveys of protein-coding genes in Given the critical role of the mouse as a model organism, it is both species. We now estimate that mouse and human reference particularly important to separate shared ancestral characteristics genomes contain 20,210 and 19,042 protein-coding genes, that have been conserved in the mouse and human since their respectively. The number of mouse genes had been missing or divergence from derived characteristics that are unique to either substantially disrupted in the previous MGSCv3 assembly is 2,185. lineage. Mouse and human genes whose coding sequences have The majority of these arise from rodent lineage-specific duplica- scarcely changed
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