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Table 2 Established and novel evolutionary links between Plasmodium variant gene families predicted by hierarchical clustering

From: Variant surface antigens of malaria parasites: functional and evolutionary insights from comparative gene family classification and analysis

Cluster A Size A Cluster B Size B MP# MP% Avg. Evalue Avg. PID(Stddev)
Established links        
  rif 161 stevor 31 281,244 74.8% 0.016 26.4(3.1)
  vir/kir 385 yir/bir/cir 1,192 2,087 0.4% 9.7 28.2(5.2)
  surfin 15 Pvstp1 2 90 93.8% 3.9e-15 38.3(6.6)
  var 67 dbl 18 707 42.8% 1.7e-10 25.0(2.9)
  phist-c 80 rad 58 718 15.5% 0.38 23.9(3.7)
  phist-c/rad 138 phist-b 21 241 8.3% 2.4 25.2(4.2)
  phist-c/rad/phist-b 168 phist-a 29 273 4.0% 1.6 26.4(5.3)
  ab_hydb 10 pst-a 77 787 99.6% 1.7e-11 33.1(6.2)
  ab_hydb/pst-a 87 ab_hyda 17 231 10.4% 3.8 28.4(5.5)
  surfin/Pvstp1 17 SICAvar 31 2,003 35.7% 0.013 37.8(8.4)
  surfin/Pvstp1/SICAvar 51 var 67 435 1.8% 1.9 37.9(6.8)
Novel links        
  surfin/Pvstp1/SICAvar/var 149 pir 1,814 772 0.1% 14 30.5(6.5)
  Pfmc-2TM 12 hyp8 2 24 100.0% 1.6 27.9(2.4)
  Pfmc-2TM/hyp8 14 hyp2 2 23 76.7% 5.6 32.6(2.8)
  hyp4 9 hyp6 5 40 80.0% 1.9 26.7(1.5)
  hyp15 4 hyp5 9 44 100.0% 0.082 31.0(5.5)
  pk-fam-a 9 pk-fam-b 13 38 16.2% 2.3e-06 55.7(18.4)
  pk-fam-a/pk-fam-b 22 pv-fam-d 38 137 11.6% 0.048 30.6(7.9)
  pyst-a/pc-fam-1/pb-fam-1 328 PcEMA1 16 90 1.5% 7.7e-32 50.6(8.9)
  pv-fam-h* 12 hyp16 2 16 80.0% 7.8e-12 33.7(6.8)
  hyp16/pv-fam-h 12 pk-fam-c 5 22 30.6% 0.72 38.1(5.5)
  TSP_1 53 P25/28 13 29 1.1% 18 32.0(11.2)
  hyp11 19 rbp/235 kDa 47 13 1.1% 31 30.4(6.0)
  phist-c/rad/phist-b* 168 pk-fam-e 3 30 4.5% 1.9e-06 67.5(14.3)
  vir/kir* 385 pv-fam-c 7 94 2.9% 1.3 27.0(5.2)
  pir* 1,814 pyst-d 10 179 0.9% 0.11 64.2(14.6)
  1. The hierarchical tree was searched for neighboring and parental clusters where both clusters (denoted A and B) map to variant gene families as identified in Table 1. Such cluster pairs are shown if (a) their BLAST match pair percentage (MP%) is ≥ 1% or (b) they share at least 100 BLAST match pairs (MP#). Avg. E-value and Avg. PID denote the average E-value and percent identity of all BLAST match pairs between the two clusters. Size A and Size B indicate numbers of genes in respective clusters, excluding annotated pseudogenes and gene fragments. An asterisk next to cluster A indicates that it is a parental cluster of cluster B, i.e. cluster B is fully contained in cluster A. Our search predicts both previously established (top) and novel evolutionary links (bottom) between Plasmodium variant gene families.