A reference genome and methylome for the Plasmodium knowlesi A1-H.1 line

Ernest Diez Benavente; Paola Florez de Sessions; Robert W. Moon; Munira Grainger; Anthony A. Holder; Michael J. Blackman; Cally Roper; Christopher J. Drakeley; Arnab Pain; Colin J. Sutherland; Martin L. Hibberd; Susana Campino; Taane G. Clark

doi:10.1016/j.ijpara.2017.09.008

A reference genome and methylome for the Plasmodium knowlesi A1-H.1 line

Ernest Diez Benavente, Paola Florez de Sessions, Robert W. Moon, Munira Grainger, Anthony A. Holder, Michael J. Blackman, Cally Roper, Christopher J. Drakeley, Arnab Pain, Colin J. Sutherland, Martin L. Hibberd, Susana Campino, Taane G. Clark

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Abstract

Plasmodium knowlesi, a common parasite of macaques, is recognized as a significant cause of human malaria in Malaysia. The P. knowlesi A1H1 line has been adapted to continuous culture in human erythrocytes, successfully providing an in vitro model to study the parasite. We have assembled a reference genome for the PkA1-H.1 line using PacBio long read combined with Illumina short read sequence data. Compared with the H-strain reference, the new reference has improved genome coverage and a novel description of methylation sites. The PkA1-H.1 reference will enhance the capabilities of the in vitro model to improve the understanding of P. knowlesi infection in humans.

Original language	English (US)
Pages (from-to)	191-196
Number of pages	6
Journal	International Journal for Parasitology
Volume	48
Issue number	3-4
DOIs	https://doi.org/10.1016/j.ijpara.2017.09.008
State	Published - Dec 16 2017

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: TGC is funded by the Medical Research Council (MRC), UK (Grant no. MR/K000551/1, MR/M01360X/1, MR/N010469/1). SC and CR are funded by the MRC (Grant no. MR/M01360X/1). RWM is supported by an MRC Career Development Award jointly funded by the MRC and UK Department for International Development. This work was supported in part by the Francis Crick Institute, UK which receives its core funding from Cancer Research, UK (FC001097, FC001043), the MRC (FC001097, FC001043), and the Wellcome Trust, UK (FC001097, FC001043) We gratefully acknowledge the Scientific Computing Group for data management and computer infrastructure at Genome Institute of Singapore for their help. Bioinformatic analysis was performed on the MRC, UK, funded eMedLab computing resource.

UN SDGs

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

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10.1016/j.ijpara.2017.09.008

https://repository.kaust.edu.sa/bitstream/10754/626402/1/1-s2.0-S0020751917303466-main.pdf

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Benavente, E. D., de Sessions, P. F., Moon, R. W., Grainger, M., Holder, A. A., Blackman, M. J., Roper, C., Drakeley, C. J., Pain, A., Sutherland, C. J., Hibberd, M. L., Campino, S., & Clark, T. G. (2017). A reference genome and methylome for the Plasmodium knowlesi A1-H.1 line. International Journal for Parasitology, 48(3-4), 191-196. https://doi.org/10.1016/j.ijpara.2017.09.008

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title = "A reference genome and methylome for the Plasmodium knowlesi A1-H.1 line",

abstract = "Plasmodium knowlesi, a common parasite of macaques, is recognized as a significant cause of human malaria in Malaysia. The P. knowlesi A1H1 line has been adapted to continuous culture in human erythrocytes, successfully providing an in vitro model to study the parasite. We have assembled a reference genome for the PkA1-H.1 line using PacBio long read combined with Illumina short read sequence data. Compared with the H-strain reference, the new reference has improved genome coverage and a novel description of methylation sites. The PkA1-H.1 reference will enhance the capabilities of the in vitro model to improve the understanding of P. knowlesi infection in humans.",

author = "Benavente, {Ernest Diez} and {de Sessions}, {Paola Florez} and Moon, {Robert W.} and Munira Grainger and Holder, {Anthony A.} and Blackman, {Michael J.} and Cally Roper and Drakeley, {Christopher J.} and Arnab Pain and Sutherland, {Colin J.} and Hibberd, {Martin L.} and Susana Campino and Clark, {Taane G.}",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: TGC is funded by the Medical Research Council (MRC), UK (Grant no. MR/K000551/1, MR/M01360X/1, MR/N010469/1). SC and CR are funded by the MRC (Grant no. MR/M01360X/1). RWM is supported by an MRC Career Development Award jointly funded by the MRC and UK Department for International Development. This work was supported in part by the Francis Crick Institute, UK which receives its core funding from Cancer Research, UK (FC001097, FC001043), the MRC (FC001097, FC001043), and the Wellcome Trust, UK (FC001097, FC001043) We gratefully acknowledge the Scientific Computing Group for data management and computer infrastructure at Genome Institute of Singapore for their help. Bioinformatic analysis was performed on the MRC, UK, funded eMedLab computing resource.",

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doi = "10.1016/j.ijpara.2017.09.008",

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AU - Benavente, Ernest Diez

AU - de Sessions, Paola Florez

AU - Moon, Robert W.

AU - Grainger, Munira

AU - Holder, Anthony A.

AU - Blackman, Michael J.

AU - Roper, Cally

AU - Drakeley, Christopher J.

AU - Pain, Arnab

AU - Sutherland, Colin J.

AU - Hibberd, Martin L.

AU - Campino, Susana

AU - Clark, Taane G.

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: TGC is funded by the Medical Research Council (MRC), UK (Grant no. MR/K000551/1, MR/M01360X/1, MR/N010469/1). SC and CR are funded by the MRC (Grant no. MR/M01360X/1). RWM is supported by an MRC Career Development Award jointly funded by the MRC and UK Department for International Development. This work was supported in part by the Francis Crick Institute, UK which receives its core funding from Cancer Research, UK (FC001097, FC001043), the MRC (FC001097, FC001043), and the Wellcome Trust, UK (FC001097, FC001043) We gratefully acknowledge the Scientific Computing Group for data management and computer infrastructure at Genome Institute of Singapore for their help. Bioinformatic analysis was performed on the MRC, UK, funded eMedLab computing resource.

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N2 - Plasmodium knowlesi, a common parasite of macaques, is recognized as a significant cause of human malaria in Malaysia. The P. knowlesi A1H1 line has been adapted to continuous culture in human erythrocytes, successfully providing an in vitro model to study the parasite. We have assembled a reference genome for the PkA1-H.1 line using PacBio long read combined with Illumina short read sequence data. Compared with the H-strain reference, the new reference has improved genome coverage and a novel description of methylation sites. The PkA1-H.1 reference will enhance the capabilities of the in vitro model to improve the understanding of P. knowlesi infection in humans.

AB - Plasmodium knowlesi, a common parasite of macaques, is recognized as a significant cause of human malaria in Malaysia. The P. knowlesi A1H1 line has been adapted to continuous culture in human erythrocytes, successfully providing an in vitro model to study the parasite. We have assembled a reference genome for the PkA1-H.1 line using PacBio long read combined with Illumina short read sequence data. Compared with the H-strain reference, the new reference has improved genome coverage and a novel description of methylation sites. The PkA1-H.1 reference will enhance the capabilities of the in vitro model to improve the understanding of P. knowlesi infection in humans.

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A reference genome and methylome for the Plasmodium knowlesi A1-H.1 line

Abstract

Bibliographical note

UN SDGs

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