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Make a Manhattan plot from a VCF file

5 minute read


A friend recently asked me to make her a Manhattan plot from a VCF (Variant Call Format) for some Plasmodium berghei SNPs. I was familiar with neither Manhattan plots nor VCFs, but we ended up with a decent-looking plot. This is far from the most sophisticated solution, but this post might help the SNP-naive (like me) looking for a simple way to go from VCF to Manhattan.

CRISPR-Cas9 editing in Plasmodium falciparum

4 minute read


This is my protocol for using a commercial Cas9 nuclease and custom synthesised guide RNA for CRISPR editing in P. falciparum. I don’t go into how I design the repair template, but to see some examples for HA-tagging and gene disruption, check out my lab book on Benchling.


McHugh E, Batinovic S, Hanssen E, McMillan PJ, Kenny S, Griffin MD, Crawford S, Trenholme KR, Gardiner DL, Dixon MW, Tilley L. 2015. "A repeat sequence domain of the ring-exported protein-1 of Plasmodium falciparum controls export machinery architecture and virulence protein trafficking." Mol Microbiol. 98(6):1101-14.

Chisholm SA, McHugh E, Lundie R, Dixon MW, Ghosh S, O'Keefe M, Tilley L, Kalanon M, de Koning-Ward TF. 2016. "Contrasting Inducible Knockdown of the Auxiliary PTEX Component PTEX88 in P. falciparum and P. berghei Unmasks a Role in Parasite Virulence." PLOS One 17;11(2):e0149296.

Batinovic S, McHugh E, Chisholm SA, Matthews K, Liu B, Dumont L, Charnaud SC, Schneider MP, Gilson PR, de Koning-Ward TF, Dixon MWA, Tilley L. 2017. "An exported protein-interacting complex involved in the trafficking of virulence determinants in Plasmodium-infected erythrocytes." Nat Commun. 10;8:16044.

Parkyn Schneider M, Liu B, Glock P, Suttie A, McHugh E, Andrew D, Batinovic S, Williamson N, Hanssen E, McMillan P, Hliscs M, Tilley L, Dixon MWA. 2017. "Disrupting assembly of the inner membrane complex blocks Plasmodium falciparum sexual stage development." PLOS Pathog. 6;13(10):e1006659.

Charnaud SC, Jonsdottir TK, Sanders PR, Bullen HE, Dickerman BK, Kouskousis B, Palmer CS, Pietrzak HM, Laumaea AE, Erazo AB, McHugh E, Tilley L, Crabb BS, Gilson PR. 2018. "Spatial organization of protein export in malaria parasite blood stages." Traffic 19(8):605-623.

Kennedy K, Cobbold SA, Hanssen E, Birnbaum J, Spillman NJ, McHugh E, Brown H, Tilley L, Spielmann T, McConville MJ, Ralph SA. 2019. "Delayed death in the malaria parasite Plasmodium falciparum is caused by disruption of prenylation-dependent intracellular trafficking." PLOS Biol. 18;17(7):e3000376.

Yeoh LM, Goodman CD, Mollard V, McHugh E, Lee VV, Sturm A, Cozijnsen A, McFadden GI, Ralph SA. 2019. "Alternative splicing is required for stage differentiation in malaria parasites." Genome Biol. 20(1):151.

McHugh E+, Carmo OMS+, Blanch A, Looker O, Liu B, Tiash S, Andrew D, Batinovic S, Low AJY, Cho H-J, McMillan P, Tilley L, Dixon MWA. 2020. "Role of Plasmodium falciparum protein GEXP07 in Maurer’s cleft morphology, knob architecture, and P. falciparum EMP1 trafficking." mBio 11:e03320-19.
+ Equal contribution.

Cobbold SA, V Tutor M, Frasse P, McHugh E, Karnthaler M, Creek DJ, Odom John A, Tilley L, Ralph SA, McConville MJ. 2021. "Non-canonical metabolic pathways in the malaria parasite detected by isotope-tracing metabolomics." Mol Syst Biol. Apr;17(4):e10023.

McHugh E, Bulloch MS, Batinovic S, Sarna DK, Ralph SA. 2021. "A divergent nonsense-mediated decay machinery in Plasmodium falciparum is inefficient and non-essential." bioRxiv. (Preprint).

Sinha A, Baumgarten S, Distiller A, McHugh E, Chen P, Singh M, Bryant JM, Liang J, Cecere G, Dedon PC, Preiser PR, Ralph SA, Scherf A. 2021. "Functional Characterization of the m6A-Dependent Translational Modulator PfYTH.2 in the Human Malaria Parasite." mBio. 12 (2) e00661-21