A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

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

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    Abstract

    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.
    Original languageEnglish
    Pages (from-to)1-12
    Number of pages12
    JournalWellcome Open Research
    Volume1
    Issue number4
    DOIs
    Publication statusPublished - 15 Nov 2016

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    Plasmodium vivax
    Plasmodium
    Parasites
    South America
    Genes
    Vivax Malaria
    Indonesia
    Thailand
    Scaffolds
    Malaria
    Haplorhini
    China
    Epidemiology
    Genome

    Cite this

    Auburn, Sarah ; Böhme, Ulrike ; Steinbiss, Sascha ; Trimarsanto, Hidayat ; Hostetler, Jessica ; Sanders, Mandy ; Gao, Qi ; Nosten, Francois ; Newbold, Chris I. ; Berriman, Matthew ; Price, Ric N. ; Otto, Thomas D. / A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes. In: Wellcome Open Research. 2016 ; Vol. 1, No. 4. pp. 1-12.
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    title = "A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes",
    abstract = "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.",
    author = "Sarah Auburn and Ulrike B{\"o}hme and Sascha Steinbiss and Hidayat Trimarsanto and Jessica Hostetler and Mandy Sanders and Qi Gao and Francois Nosten and Newbold, {Chris I.} and Matthew Berriman and Price, {Ric N.} and Otto, {Thomas D.}",
    year = "2016",
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    doi = "10.12688/wellcomeopenres.9876.1",
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    Auburn, S, Böhme, U, Steinbiss, S, Trimarsanto, H, Hostetler, J, Sanders, M, Gao, Q, Nosten, F, Newbold, CI, Berriman, M, Price, RN & Otto, TD 2016, 'A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes', Wellcome Open Research, vol. 1, no. 4, pp. 1-12. https://doi.org/10.12688/wellcomeopenres.9876.1

    A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes. / Auburn, Sarah; Böhme, Ulrike; Steinbiss, Sascha; Trimarsanto, Hidayat; Hostetler, Jessica; Sanders, Mandy; Gao, Qi; Nosten, Francois; Newbold, Chris I.; Berriman, Matthew; Price, Ric N.; Otto, Thomas D.

    In: Wellcome Open Research, Vol. 1, No. 4, 15.11.2016, p. 1-12.

    Research output: Contribution to journalArticleResearchpeer-review

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    AU - Böhme, Ulrike

    AU - Steinbiss, Sascha

    AU - Trimarsanto, Hidayat

    AU - Hostetler, Jessica

    AU - Sanders, Mandy

    AU - Gao, Qi

    AU - Nosten, Francois

    AU - Newbold, Chris I.

    AU - Berriman, Matthew

    AU - Price, Ric N.

    AU - Otto, Thomas D.

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