Open Peer Review RESEARCH ARTICLE Long read assemblies of geographically dispersed Plasmodium isolates reveal highly structured subtelomeres falciparum [version 1; referees: 3 approved] Thomas D. Otto , Ulrike Böhme , Mandy Sanders , Adam Reid , Ellen I. Bruske , Craig W. Duffy , Pete C. Bull , Richard D. Pearson , Abdirahman Abdi , Sandra Dimonte , Lindsay B. Stewart , Susana Campino , Mihir Kekre , William L. Hamilton , Antoine Claessens , Sarah K. Volkman , Daouda Ndiaye , Alfred Amambua-Ngwa , Mahamadou Diakite , Rick M. Fairhurst , David J. Conway , Matthias Franck , Chris I. Newbold , Matt Berriman 1 Wellcome Sanger Institute, Hinxton, UK Centre of Immunobiology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany London School of Hygiene and Tropical Medicine, London, UK Department of Pathology, University of Cambridge, Cambridge, UK Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, UK KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya Harvard T.H. Chan School of Public Health, Boston, MA, USA The Broad Institute of MIT and Harvard, Cambridge, MA, USA Simmons College, Boston, MA, USA Faculty of Medicine and Pharmacy, Université Cheikh Anta Diop, Dakar, Senegal Medical Research Council Unit, Fajara, The Gambia Malaria Research and Training Center, University of Bamako, Bamako, Mali Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK Abstract : Although thousands of clinical isolates of Background Plasmodium falciparum are being sequenced and analysed by short read technology, the data do not resolve the highly variable subtelomeric regions of the genomes that contain polymorphic gene families involved in immune evasion and pathogenesis. There is also no current standard definition of the boundaries of these variable subtelomeric regions. : Using long-read sequence data (Pacific Biosciences SMRT Methods technology), we assembled and annotated the genomes of 15 P. falciparum isolates, ten of which are newly cultured clinical isolates. We performed comparative analysis of the entire genome with particular emphasis on the subtelomeric regions and the internal genes clusters. var : The nearly complete sequence of these 15 isolates has enabled us to Results 1,2 1 1 1 3 4 5 1,6 7 3 4 1,4 1 1 1 8-10 11 12 13 14 4 3 1,15 1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Referee Status: Invited Referees version 1 published 03 May 2018 1 2 3 report report report , University of Maryland David Serre School of Medicine, USA 1 03 May 2018, :52 (doi: ) First published: 3 10.12688/wellcomeopenres.14571.1 03 May 2018, :52 (doi: ) Latest published: 3 10.12688/wellcomeopenres.14571.1 v1 Page 1 of 24 Wellcome Open Research 2018, 3:52 Last updated: 23 MAY 2018