title: A newPlasmodium vivaxreference sequence with improved assembly of the subtelomeres reveals an abundance ofpirgenes.
abstract: Plasmodium vivaxis now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuousex vivoculture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite's biology and epidemiology. To date, molecular studies ofP. vivaxhave relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds.  Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres.  An extensive repertoire of over 1200Plasmodiuminterspersed repeat (pir) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality.
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia.
authors.forename: Sarah
authors.initials: S
authors.lastname: Auburn
authors.affiliation: Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Böhme
authors.affiliation: Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Sascha
authors.initials: S
authors.lastname: Steinbiss
authors.affiliation: Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
authors.forename: Hidayat
authors.initials: H
authors.lastname: Trimarsanto
authors.affiliation: Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK.|Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, USA.
authors.forename: Jessica
authors.initials: J
authors.lastname: Hostetler
authors.affiliation: Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Mandy
authors.initials: M
authors.lastname: Sanders
authors.affiliation: Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Jiangsu, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Gao
authors.affiliation: Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.|Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
authors.forename: Francois
authors.identifier: 0000-0002-7951-0745
authors.initials: F
authors.lastname: Nosten
authors.affiliation: Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK.|Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
authors.forename: Chris I
authors.initials: CI
authors.lastname: Newbold
authors.affiliation: Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Matthew
authors.initials: M
authors.lastname: Berriman
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia.|Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
authors.forename: Ric N
authors.initials: RN
authors.lastname: Price
authors.affiliation: Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Thomas D
authors.identifier: 0000-0002-1246-7404
authors.initials: TD
authors.lastname: Otto
keywords: Plasmodium; genome; pir; reference; subtelomere; vir; vivax