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

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

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)

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.

ISSN: 1471-2164