Gene copy number variation in natural populations of Plasmodium falciparum in Eastern Africa

Simam, Joan; Rono, Martin; Ngoi, Joyce; Nyonda, Mary; Mok, Sachel; Marsh, Kevin; Bozdech, Zbynek; Mackinnon, Margaret

doi:10.1186/s12864-018-4689-7

BMC Genomics

Table 3 CNVs showing evidence of population-specific adaptation. Only those CNVs that either had F_ST greater than 0.30 or which showed significant transmission intensity-related clines in population frequency are shown

From: Gene copy number variation in natural populations of Plasmodium falciparum in Eastern Africa

CNV name	CNV type	F_ST^a	Cline^b	Annotations^c
cnv5_101	Amplification	0.64	- ***	6-cysteine protein (P38) SET domain protein, putative (SET9)
cnv12_413	Amplification	0.64	-*
cnv9_242	Amplification	0.44		P1 nuclease, putative
cnv13_478	Deletion	0.46	- †	E1-E2 ATPase, putative
cnv9_254	Deletion	0.41		protein phosphatase-beta thioredoxin-like protein 2 (TLP2) zinc binding protein (Yippee), putative histone deacetylase 1 (HDAC1)
cnv3_051	Amplification	0.34		circumsporozoite- and TRAP-related protein (CTRP)
cnv3_036	Amplification	0.32	-†	Plasmodium exported protein (hyp1), unknown function (GEXP21)
				Plasmodium exported protein, unknown function
				Plasmodium exported protein, unknown function
cnv6_129	Deletion	0.30		ubiquitin-conjugating enzyme E2, putative polypyrimidine tract binding protein, putative
cnv4_078	Amplification	0.30	-†
cnv11_354	Deletion	0.27		Plasmodium exported protein (PHISTc), unknown function (GEXP12)
				Plasmodium exported protein (hyp11), unknown function
				Plasmodium exported protein, unknown function
cnv11_355	Deletion	0.18	-***	antigen 332, DBL-like protein (Pf332)
cnv9_269	Deletion	0.27	-***	gametocyte development protein 1 (GDV1)
				Plasmodium exported protein, unknown function (GEXP22)
				gametocytogenesis-implicated protein (GIG)
				Plasmodium exported protein, unknown function
				cytoadherence linked asexual protein 9 (CLAG9)
				ring-exported protein 1 (REX1)
				ring-exported protein 2 (REX2)
				early transcribed membrane protein (ETRAMP9)
				ring-exported protein 4 (REX4)
				virulence-associated protein 1 (VAP1)
				Plasmodium exported protein (PHISTc), unknown function
				(GEXP05)
				lysophospholipase, putative
				Plasmodium exported protein (PHISTc), unknown function
				Plasmodium exported protein (PHISTb), unknown function
				Plasmodium exported protein, unknown function
				lysophospholipase, putative
cnv1_007	Amplification	0.26	-**	tubulin-specific chaperone a, putative N-acetyltransferase, putative
cnv14_549	Amplification	0.21	-***	thioredoxin peroxidase 1 (Trx-Px1) copper transporter
cnv11_355	Deletion	0.18	- ***	antigen 332-DBL-like protein (Pf332)
cnv2_023	Deletion	0.14	-*	conserved Plasmodium membrane protein, unknown function
cnv12_368	Deletion	0.07	-*	glycerol-3-phosphate dehydrogenase, putative

^aMaximum of pairwise population F_ST values
^bSignificance of transmission intensity cline in CNV frequency after Benjamini-Hochberg correction for multiple testing. (†, P < 0.10;*, P < 0.05;**, P < 0.01;***, P < 0.001; +, positive association; −, negative association). Four further CNVs had clines with adjusted P < 0.10 but F_ST < 0.3 and so are not shown (three amplifications, cnv9_262, − †; cnv5_109, + †; cnv14_573, − †, and one deletion, cnv7_193, − †)
^cExcluding genes with no known or putative function

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ISSN: 1471-2164

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