Cargando…

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

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...

Descripción completa

Detalles Bibliográficos
Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000Research 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5172418/
https://www.ncbi.nlm.nih.gov/pubmed/28008421
http://dx.doi.org/10.12688/wellcomeopenres.9876.1
_version_ 1782484126038753280
author 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.
author_facet 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.
author_sort Auburn, Sarah
collection PubMed
description 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.
format Online
Article
Text
id pubmed-5172418
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher F1000Research
record_format MEDLINE/PubMed
spelling pubmed-51724182016-12-20 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. Wellcome Open Res Data Note 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. F1000Research 2016-11-15 /pmc/articles/PMC5172418/ /pubmed/28008421 http://dx.doi.org/10.12688/wellcomeopenres.9876.1 Text en Copyright: © 2016 Auburn S et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The author(s) is/are employees of the US Government and therefore domestic copyright protection in USA does not apply to this work. The work may be protected under the copyright laws of other jurisdictions when used in those jurisdictions.
spellingShingle Data Note
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
title A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes
title_full A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes
title_fullStr A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes
title_full_unstemmed A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes
title_short A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes
title_sort new plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes
topic Data Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5172418/
https://www.ncbi.nlm.nih.gov/pubmed/28008421
http://dx.doi.org/10.12688/wellcomeopenres.9876.1
work_keys_str_mv AT auburnsarah anewplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT bohmeulrike anewplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT steinbisssascha anewplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT trimarsantohidayat anewplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT hostetlerjessica anewplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT sandersmandy anewplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT gaoqi anewplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT nostenfrancois anewplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT newboldchrisi anewplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT berrimanmatthew anewplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT pricericn anewplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT ottothomasd anewplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT auburnsarah newplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT bohmeulrike newplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT steinbisssascha newplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT trimarsantohidayat newplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT hostetlerjessica newplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT sandersmandy newplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT gaoqi newplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT nostenfrancois newplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT newboldchrisi newplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT berrimanmatthew newplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT pricericn newplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes
AT ottothomasd newplasmodiumvivaxreferencesequencewithimprovedassemblyofthesubtelomeresrevealsanabundanceofpirgenes