Genome variation and evolution of the malaria parasite Plasmodium falciparum

Daniel C. Jeffares; Arnab Pain; Andrew Berry; Anthony V. Cox; James Stalker; Catherine E. Ingle; Alan Thomas; Michael A. Quail; Kyle Siebenthall; Anne Catrin Uhlemann; Sue Kyes; Sanjeev Krishna; Chris Newbold; Emmanouil T. Dermitzakis; Matthew Berriman

doi:10.1038/ng1931

Genome variation and evolution of the malaria parasite Plasmodium falciparum

Daniel C. Jeffares, Arnab Pain, Andrew Berry, Anthony V. Cox, James Stalker, Catherine E. Ingle, Alan Thomas, Michael A. Quail, Kyle Siebenthall, Anne Catrin Uhlemann, Sue Kyes, Sanjeev Krishna, Chris Newbold, Emmanouil T. Dermitzakis^*, Matthew Berriman

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

165 Scopus citations

Abstract

Infections with the malaria parasite Plasmodium falciparum result in more than 1 million deaths each year worldwide. Deciphering the evolutionary history and genetic variation of P. falciparum is critical for understanding the evolution of drug resistance, identifying potential vaccine candidates and appreciating the effect of parasite variation on prevalence and severity of malaria in humans. Most studies of natural variation in P. falciparum have been either in depth over small genomic regions (up to the size of a small chromosome) or genome wide but only at low resolution. In an effort to complement these studies with genome-wide data, we undertook shotgun sequencing of a Ghanaian clinical isolate (with fivefold coverage), the IT laboratory isolate (with onefold coverage) and the chimpanzee parasite P. reichenowi (with twofold coverage). We compared these sequences with the fully sequenced P. falciparum 3D7 isolate genome. We describe the most salient features of P. falciparum polymorphism and adaptive evolution with relation to gene function, transcript and protein expression and cellular localization. This analysis uncovers the primary evolutionary changes that have occurred since the P. falciparum-P. reichenowi speciation and changes that are occurring within P. falciparum.

Original language	English (US)
Pages (from-to)	120-125
Number of pages	6
Journal	Nature Genetics
Volume	39
Issue number	1
DOIs	https://doi.org/10.1038/ng1931
State	Published - Jan 2007
Externally published	Yes

Bibliographical note

Funding Information:
In the original version of this paper, the authors failed to acknowledge that sequencing of the P. falciparum IT laboratory isolate was funded by a European Union 6th Framework Program grant to the BioMalPar Consortium (contract number LSHP-LT-2004-503578). This error has been corrected in the PDF version of the article.

Funding Information:
We thank the Pathogen Sequencing teams for producing the sequence data used in this study, P. Horrocks and B. Pinches for the supply of DNA from the IT isolate and M. Marti for the list of PEXEL motif–containing genes. This study was funded by the Wellcome Trust through its support of the Pathogen Sequencing Unit and E.T.D.’s group at the Wellcome Trust Sanger Institute. Sequencing of the P. falciparum IT isolate was funded by a European Union 6th Framework Program grant to the BioMalPar Consortium (contract number LSHP-LT-2004-503578).

ASJC Scopus subject areas

Genetics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1038/ng1931

Cite this

@article{1dbadd37deff4eeea9f383d27b886ad8,

title = "Genome variation and evolution of the malaria parasite Plasmodium falciparum",

abstract = "Infections with the malaria parasite Plasmodium falciparum result in more than 1 million deaths each year worldwide. Deciphering the evolutionary history and genetic variation of P. falciparum is critical for understanding the evolution of drug resistance, identifying potential vaccine candidates and appreciating the effect of parasite variation on prevalence and severity of malaria in humans. Most studies of natural variation in P. falciparum have been either in depth over small genomic regions (up to the size of a small chromosome) or genome wide but only at low resolution. In an effort to complement these studies with genome-wide data, we undertook shotgun sequencing of a Ghanaian clinical isolate (with fivefold coverage), the IT laboratory isolate (with onefold coverage) and the chimpanzee parasite P. reichenowi (with twofold coverage). We compared these sequences with the fully sequenced P. falciparum 3D7 isolate genome. We describe the most salient features of P. falciparum polymorphism and adaptive evolution with relation to gene function, transcript and protein expression and cellular localization. This analysis uncovers the primary evolutionary changes that have occurred since the P. falciparum-P. reichenowi speciation and changes that are occurring within P. falciparum.",

author = "Jeffares, {Daniel C.} and Arnab Pain and Andrew Berry and Cox, {Anthony V.} and James Stalker and Ingle, {Catherine E.} and Alan Thomas and Quail, {Michael A.} and Kyle Siebenthall and Uhlemann, {Anne Catrin} and Sue Kyes and Sanjeev Krishna and Chris Newbold and Dermitzakis, {Emmanouil T.} and Matthew Berriman",

note = "Funding Information: In the original version of this paper, the authors failed to acknowledge that sequencing of the P. falciparum IT laboratory isolate was funded by a European Union 6th Framework Program grant to the BioMalPar Consortium (contract number LSHP-LT-2004-503578). This error has been corrected in the PDF version of the article. Funding Information: We thank the Pathogen Sequencing teams for producing the sequence data used in this study, P. Horrocks and B. Pinches for the supply of DNA from the IT isolate and M. Marti for the list of PEXEL motif–containing genes. This study was funded by the Wellcome Trust through its support of the Pathogen Sequencing Unit and E.T.D.{\textquoteright}s group at the Wellcome Trust Sanger Institute. Sequencing of the P. falciparum IT isolate was funded by a European Union 6th Framework Program grant to the BioMalPar Consortium (contract number LSHP-LT-2004-503578).",

year = "2007",

month = jan,

doi = "10.1038/ng1931",

language = "English (US)",

volume = "39",

pages = "120--125",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Publishing Group",

number = "1",

}

TY - JOUR

T1 - Genome variation and evolution of the malaria parasite Plasmodium falciparum

AU - Jeffares, Daniel C.

AU - Pain, Arnab

AU - Berry, Andrew

AU - Cox, Anthony V.

AU - Stalker, James

AU - Ingle, Catherine E.

AU - Thomas, Alan

AU - Quail, Michael A.

AU - Siebenthall, Kyle

AU - Uhlemann, Anne Catrin

AU - Kyes, Sue

AU - Krishna, Sanjeev

AU - Newbold, Chris

AU - Dermitzakis, Emmanouil T.

AU - Berriman, Matthew

N1 - Funding Information: In the original version of this paper, the authors failed to acknowledge that sequencing of the P. falciparum IT laboratory isolate was funded by a European Union 6th Framework Program grant to the BioMalPar Consortium (contract number LSHP-LT-2004-503578). This error has been corrected in the PDF version of the article. Funding Information: We thank the Pathogen Sequencing teams for producing the sequence data used in this study, P. Horrocks and B. Pinches for the supply of DNA from the IT isolate and M. Marti for the list of PEXEL motif–containing genes. This study was funded by the Wellcome Trust through its support of the Pathogen Sequencing Unit and E.T.D.’s group at the Wellcome Trust Sanger Institute. Sequencing of the P. falciparum IT isolate was funded by a European Union 6th Framework Program grant to the BioMalPar Consortium (contract number LSHP-LT-2004-503578).

PY - 2007/1

Y1 - 2007/1

N2 - Infections with the malaria parasite Plasmodium falciparum result in more than 1 million deaths each year worldwide. Deciphering the evolutionary history and genetic variation of P. falciparum is critical for understanding the evolution of drug resistance, identifying potential vaccine candidates and appreciating the effect of parasite variation on prevalence and severity of malaria in humans. Most studies of natural variation in P. falciparum have been either in depth over small genomic regions (up to the size of a small chromosome) or genome wide but only at low resolution. In an effort to complement these studies with genome-wide data, we undertook shotgun sequencing of a Ghanaian clinical isolate (with fivefold coverage), the IT laboratory isolate (with onefold coverage) and the chimpanzee parasite P. reichenowi (with twofold coverage). We compared these sequences with the fully sequenced P. falciparum 3D7 isolate genome. We describe the most salient features of P. falciparum polymorphism and adaptive evolution with relation to gene function, transcript and protein expression and cellular localization. This analysis uncovers the primary evolutionary changes that have occurred since the P. falciparum-P. reichenowi speciation and changes that are occurring within P. falciparum.

AB - Infections with the malaria parasite Plasmodium falciparum result in more than 1 million deaths each year worldwide. Deciphering the evolutionary history and genetic variation of P. falciparum is critical for understanding the evolution of drug resistance, identifying potential vaccine candidates and appreciating the effect of parasite variation on prevalence and severity of malaria in humans. Most studies of natural variation in P. falciparum have been either in depth over small genomic regions (up to the size of a small chromosome) or genome wide but only at low resolution. In an effort to complement these studies with genome-wide data, we undertook shotgun sequencing of a Ghanaian clinical isolate (with fivefold coverage), the IT laboratory isolate (with onefold coverage) and the chimpanzee parasite P. reichenowi (with twofold coverage). We compared these sequences with the fully sequenced P. falciparum 3D7 isolate genome. We describe the most salient features of P. falciparum polymorphism and adaptive evolution with relation to gene function, transcript and protein expression and cellular localization. This analysis uncovers the primary evolutionary changes that have occurred since the P. falciparum-P. reichenowi speciation and changes that are occurring within P. falciparum.

UR - http://www.scopus.com/inward/record.url?scp=33845905179&partnerID=8YFLogxK

U2 - 10.1038/ng1931

DO - 10.1038/ng1931

M3 - Article

C2 - 17159978

AN - SCOPUS:33845905179

SN - 1061-4036

VL - 39

SP - 120

EP - 125

JO - Nature Genetics

JF - Nature Genetics

IS - 1

ER -

Genome variation and evolution of the malaria parasite Plasmodium falciparum

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this