Please use this identifier to cite or link to this item: http://repository.li.mahidol.ac.th/dspace/handle/123456789/43272
Title: A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes
Authors: Sarah Auburn
Ulrike Böhme
Sascha Steinbiss
Hidayat Trimarsanto
Jessica Hostetler
Mandy Sanders
Qi Gao
Francois Nosten
Chris I. Newbold
Matthew Berriman
Ric N. Price
Thomas D. Otto
Menzies School of Health Research
Wellcome Trust Sanger Institute
Eijkman Institute for Molecular Biology
National Institute of Allergy and Infectious Diseases
Jiangsu Institute of Parasitic Diseases
Mahidol University
Nuffield Department of Clinical Medicine
Weatherall Institute of Molecular Medicine
Keywords: Biochemistry, Genetics and Molecular Biology
Issue Date: 1-Jan-2016
Citation: Wellcome Open Research. Vol.1, (2016)
Abstract: © 2016 Auburn S et al. Plasmodium vivax is 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 continuous ex vivo culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite's biology and epidemiology. To date, molecular studies of P. vivax have 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 1200 Plasmodium interspersed 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.
URI: https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85014557853&origin=inward
http://repository.li.mahidol.ac.th/dspace/handle/123456789/43272
ISSN: 2398502X
Appears in Collections:Scopus 2016-2017

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