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Table 3 CNVs showing evidence of population-specific adaptation. Only those CNVs that either had FST 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 FSTa Clineb Annotationsc
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
  1. aMaximum of pairwise population FST values
  2. 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 FST < 0.3 and so are not shown (three amplifications, cnv9_262, − †; cnv5_109, + †; cnv14_573, − †, and one deletion, cnv7_193, − †)
  3. cExcluding genes with no known or putative function