Table S1. Sequences of 5' and 3' flanking primers Primer name 3D7 chromosomal location TM Sequence 5' -3' 5' oligos Tel4.2 (upsB, upsC) Sub-teleomeric, central 48 TGATAGATARTATRGATAGAGAGA UpsB 5.1(upsB) Sub-telomeric 49 CRGAAGAASATATTTGYCTC Cen2.1 (upsC, upsB) central, subtelomeric 1 44 ATATGRTAGATAATAYAGATAGA UpsC5.1 (upsC) central 44 GTGATAACYAYTATATMATATAC var gr2 5p 5.1 (upsA) Sub-telomeric 50 ATKTATTAYATTTGTTGTAGGTGA Type3 5p 5.1 Sub-telomeric 46 GGATAAGTGATRACATAATRT 3' oligos exon2 3.2end 51 TTATATATYCYAYAYATCYSMTATAGG exon2 3.3 54 CCADYTCTTCATAYTCACTTTC 3ptel type13.1 (downsB) Sub-telomeric 45 GTTATACTRYTAATTACTACTTC 3ptel type23.1 (downsA) Sub-telomeric 

-B2STc(2b)-A1SSTt(3) 6 Cen <C1C(5) C1C(11b) 6 RTel B1Tc(1a)-B1STc(6) 7 LTel B1Tc(1a) A1Tt(10b)-A1SSTt(10aψ) 7 Cen <C1C(1a)<C1C(1b)<B1C(1b)<B3C(15)< C1C(1a)<B1C(1b)<C2C(1a) B1C(29)-?C(1b)-C1C(1a) -B1C(11b)- C2C(1b) B1C(1)-B1C(5)- B2C(11a) 7 RTel B1Tc(14) 8 LTel B1Tc(1a)-A1STt(2c)-B1SSTc(11a) 8 Cen C1C(1b)>B1C(1a)>B3C(1a)> C1C(27aψ)-B3C(27a)-B3C(27b)- B1C(28)-C1C(1b) 8 RTel B1Tc(1a)-A1STt(4) 9 LTel B1Tc(1b) B1C(1a) 9 RTel B1Tc(1b)-A1STt(3) B1C(1a)-A1STt(8b) LTel B1Tc(1b) B1Tc(u) [ST (17) on either Left or Right tel] 10 RTel B1Tc(1a) B1Cc(1a) 11 LTel B1Tc(1a)-A1STt(10a) ?-A1Tt(7b) 11 RTel A1Tt(9) B1Tc(1a) 12 LTel B1Tc(1a)-STc(2a)-ESSTt(13) ?-ETt(13) STc(5) L or R? 12 Cen1 B1C(1b) B1C(1b) 12 Cen2 B4C(5)-B1C(1a)-C1C(1a)-ψ B4C(27a)-C1C(1a)-A1C(26)- B3C ( 
Expected values were determined from the number of genes in each group assuming random likelihood of BLASTn similarity between any two genes. Type 3 var genes and var1csa were excluded from these calculations because these genes only had similarity to their homologs in other isolates. 

Table S2 .

 S2 IT4 var tags for partial and full-length genes A4 


					A4	ItG2	FCR3S1.2	R29R	e	GenBank Accession
	IT4 var			Alias	DBLα a	DBLα b	DBLα c	DBLα d	DBLb DBLg DBLd whole or partial gene
	var1				43	ee	52	b11	g9	AY248889
	var2							b2, 9
	Var3			Type 3 var			
	var 4			var2csa			
								AJ007941, FCR3-
	var5				25	dd		g13	CD36 (partial)
	var6				5	P	C27	d21
	var7				34			4	b1	g5	d1
	var8				27	F	45	b6
	var 9			It-R29	9	j		1	Y13402
	var10 (p)	e		15	s	50	b5
	var11				18		44	b12	d9
								U67959, U31083(ItG
	var 12			FCR3varT11-1		d.1	4, 10	3	var)
	var13					bb	58	g12	L40609 (2	nd gene in
	var 15			FCR3 var2	16	Q	3	contig)
								AY578326 (IT-ICAM
	var16				17	aa	9p	g10	or FCR3-ICAM)
	var17				26		z	b10	g8
	var18							g2	d16
	var19					i	29	b14	g4	d22
								L40609 (first gene in
	var 20			FCR3var3				contig)
	var21			FCR S1.2 var1			1	AF003473
	var24						12	d4
	var25				32	b	49	d13
	var26				21	R	
								orthologous to
	var 27				14	cc	C27	d7	Dd2var1 (L40608)
	var28				22			d24
	var29				10			2	d2
	var30 (p)	f		1	L	46	d20
	var31			It A4tres	13			AF193424
	var 32			It-CS2varcsa	41	U		d23	AF134154, CS2-CSA
	var33				31	E		d14
	var34 (p)				11 f	d8
	var35			FCR3var CSA	8	k		AJ133811
	var36				30	ff		d6
	var39				12	O	C22	d5
	var40 (p)				65	d10
	var41					C		d18
	var43 (p)					d25
	var44 (p)		11	H		d19
	var45 (p)		29		71
	var46 (p)		24			d27	U67960, FCR3-T3-1
	var47						70	d28
	var51 (p)					d12
	var53 (p)		6		
	var54				2	A		d11
	var55 (p)	A4var	41	U		d29	L42244, A4varICAM
	var60				19		
	var64					W	
	a CAC41284-CAC41316			

b [1] c [2] d [3] e [4] f (p) denotes partial gene sequenced 
Table S3 .

 S3 Orphan Tags 


	Orphan	A4 DBLα	a	ItG2 DBLα	b	FCR3S1.2 DBLα c	chromosome location	notes
	1			b2				
	2			m		57	4	
	3	38						
	4					13	4	related to FCR3S1.2
	5			n		6	9	
	6	7				48	4	
	7			c.1				
	8			v				
	9	20		y				
	10	4						
	11			x				89% identical to IT4var28
	a CAC41284-CAC41316				
	b [1]							
	c [2]							

Table S4 . Var Gene chromosomal locations and domain types

 S4 
	Chromosome	Location	3D7	HB3	IT4
	1	LTel B1Tc(1a)-A1STt(3)		
	1	RTel B1Tc(1a)			
	2	LTel B1Tc(16)			
	2	RTel B1Tc(1a)			
	3	LTel B1Tc(1a)			
	3	RTel B1Tc(1a)			
	4	LTel B1Tc(12)-A1STt(8)		
	4	Cen1 <C1C(1a)<C1C(1a)<C1C(1b)<B3C(1b)	[B3C(1a)>C1C(1a)>C1C(1a)>]	
	4	Cen2 <C1C(1b)<C1C(1b)<B1C(1b)<C1C(1a)	C1C(1b)	
	4	RTel B1Tc(1)-A1STt(4)		B1Tc(1a)	
	5	LTel B1Tc(1a)		A2Tt(10a)	
	5	RTel A2Tt(17ψ)			
	6	LTel Tψ			

Table S5 Homologs and duplicated genes in all genomes

 S5 
	isolates	var1	var2	Ups var1	Ups var2	% ID B	Match length C
	Duplicated gene				
	3d7x3d7	PFD1235w	MAL8P1.207	A1	A1	100	9441
	Type3					
	var						
	3d7x3d7	PFF0020c	PFA0015c	A1	A1	98.98	1866
	3d7x3d7	PFI1820w	PFA0015c	A1	A1	99.41	1866
	3d7x3d7	PFA0015c	PFF0020c	A1	A1	98.66	2020
	ITx3D7	PFA0015c	IT4var3	A1	A1	98.6	2006
	ITx3D7	PFF0020x	IT4var3	A1	A1	98.45	1866
	ITx3D7	PFI1820w	IT4var3	A1	A1	99.3	1866
	var1csa					
	3d7xHB3	HB3var1csa	PFE1640w-ps	A2	A2	96.8	1909
	HB3xIT	FCR3var1csa A	HB3var1csa	A2	A2	96.18	680
	HB3xIT	FCR3var1csa A	HB3var1csa	A2	A2	96.76	4689
	HB3xIT	FCR3var1csa A	HB3var1csa	A2	A2	94.3	2367
	ITx3D7	PFE1640w-ps	FCR3var1csa	A2	A2	95.69	743
	ITx3D7	PFE1640w-ps	FCR3var1csa	A2	A2	94.33	1657
	var2csa					
	3d7xHB3	HB3var2csaA	PFL0030c	E	E	92.34	522
	3d7xHB3	HB3var2csaA	PFL0030c	E	E	93.03	932
	3d7xHB3	HB3var2csaA	PFL0030c	E	E	96.08	1839
	3d7xHB3	HB3var2csaB	PFL0030c	E	E	91.1	854
	3d7xHB3	HB3var2csaB	PFL0030c	E	E	95.76	566
	3d7xHB3	HB3var2csaB	PFL0030c	E	E	95.25	547
	3d7xHB3	HB3var2csaB	PFL0030c	E	E	96.87	511
	HB3xHB3	HB3var2csaB	HB3var2csaA	E	E	97.69	1298
	HB3xHB3	HB3var2csaB	HB3var2csaA	E	E	93.74	671
	HB3xHB3	HB3var2csaB	HB3var2csaA	E	E	96.09	1814
	HB3xHB3	HB3var2csaB	HB3var2csaA	E	E	97.53	527
	HB3xHB3	HB3var2csaB	HB3var2csaA	E	E	98.61	1799
	HB3xIT	IT4var4	HB3var2csaA	E	E	93.26	742
	HB3xIT	IT4var4	HB3var2csaA	E	E	95.57	1016
	HB3xIT	IT4var4	HB3var2csaA	E	E	96.08	944
	HB3xIT	IT4var4	1817	E	E	92.18	1253
	HB3xIT	IT4var4	1817	E	E	95.1	1307
	ITx3D7	PFL0030c	IT4var4	E	E	92.08	1754
	ITx3D7	PFL0030c	IT4var4	E	E	94.26	592
	ITx3D7 12 RTel B1Tc(1a) PFL0030c ITx3D7 PFL0030c ITx3D7 PFL0030c	IT4var4 IT4var4 IT4var4	E E B1Cc(27aψ)-?STt(27a) E 92.31 1a)-C1C(1a) E 95.98 E E 94.65	754 547 1440	B1Tc(18)-A1STc(20)
	13	LTel B1Tc(1a)-A1STt(7)					L or R?
	13	RTel B1Tc(1a)-STψ		B1Tt(5)		
	14	LTel Tψ				
	14	RTel					

Ltel: left telomere, Rtel: right telomere, Cen: Central chromosomal location Ups types are listed first as A1-2, B1-4, C1-2, and E (when known) T, ST, SST: first, second, and third var genes from the telomere respectively. C: internal var genes. t: transcribed towards telomere, c: transcribed towards centromere Ψ: pseudogene A Highlighted rows indicate multiple hits of high sequence similarity, shared between homologous (or duplicated) gene pairs. B Percent identity for each match, from blastn (word length 90 nucleotides) C Length of each match, in nucleotides 
Table S6 . BLASTn similarity between var groups

 S6 
		A	B1	B2-4	C
	A	7.3,5.9	0.4,0.7	0.0,2.3	0.0,0.6
	B1		0.5,0.7	0.4,2.6	0.5,1.3
	B2-4			8.6,4.2	2.6,2.8
	C				0.4,1.7
	Observed/expected (O/E) ratios of BLASTn similarities
	were calculated for the different var groups. The first
	number in each cell represents the O/E ratio for gene
	similarities greater than 510 nucleotides (n = 42) and
	the second number represents O/E ratio for gene
	similarities greater than 90 nucleotides (n = 183).

Table S7

 S7 Order and color-coding of var exon1 sequences in ACT diagram, with Ups type (Ups) and Chromosomal location/direction of transcription, where known [Location: T, first gene after telomere associated repeats; ST, subtelomeric (not first open reading frame on chromosome, or pseudogene between var and telomere repeats); Cen, chromosomecentral; t, transcribed towards telomere; c, transcribed towards centromere]. 


	ACT order	3D7	Ups	Location	ACT order	IT4	Ups	Loc	ACT order	HB3	Ups	Loc
	1 PFL0030c	E	STt	1 IT4var4	E		1 HB3var2csaA	E	STt
						FCR3						
	2 PFE1640w-ps	A2	STt	2	var1csa	A2	ST	2 HB3var2csaB	E	STt
	3 PFA0015c	A1	STt	3 IT4var3	A1		3 HB3var1csa	A2	STt
	4 PFF0020c	A1	STt	4 R29var1	A1	STt	4 HB3var1	A1	STt
	5 PFI1820w	A1	STt	5 IT4var18	A1		5 HB3var2	A1	STt
	6 PF08_0141	A1	STt	6 IT4var22	A1		6 HB3var4	A1	STt
	7 MAL8P1.207	A1	STt	7 IT4var2	A1		7 HB3var5	A2	STt
	8 PF11_0008	A1	STt	8 IT4var60	A1		8 HB3var3	A1	STt
	9 PFD0020c	A1	STt	9 IT4var64	A1		9 HB3var6	A1	Cen
	10 PF13_0003	A1	STt	10 IT4var7	A1		10 HB3var30	C1	Cen
	11 PF11_0521	A1	STt	11 IT4var8	A1		11 HB3var31	C1	Cen
	12 PFD1235w	A1	STt	12 IT4var1	C1	Cen	12 Hb3var33	C1	Cen
	13 PFD0615c	C1	Cen	13 IT4var5	C1		13 HB3var28	C1	Cen
	14 PFD0625c	C1	Cen	14 IT4var28	C2		14 HB3var29	C1	Cen
	15 PFD0630c	C1	Cen	15 IT4var47	C1		15 HB3var32	C1	Cen
	16 PFD0995c	C1	Cen	16 IT4var16	B2		16 HB3var34	C1	Cen
	17 PFD1000c	C1	Cen	17 IT4var27	B3	Cen	17 HB3var36	C2	Cen
						FCR3						
	18 PFD1015c	C1	Cen	18	var3	B2	Cen	18 HB3var35	C1	Cen
						FCR3						
	19 PFF0845c	C1	Cen	19	var2	B1	Cen	19 HB3var27	B3	Cen
	20 PF07_0048	C1	Cen	20 IT4var11	B1		20 HB3var23	B4	Cen
	21 PF07_0049	C1	Cen	21 IT4var13	B1		21 HB3var26	B3	Cen
	22 PF07_0051	C1	Cen	22 IT4var17	B1		22 HB3var24	B3	Cen
	23 MAL7P1.56	C2	Cen	23 IT4var19	B1		23 HB3var25	B3	Cen
	24 PF08_0107	C1	Cen	24 IT4var25	B1		24 HB3var22	B1	Cen
	25 PFL1960w	C1	Cen	25 IT4var26	B1		25 HB3var21	B1	Cen
	26 PF07_0050	B3	Cen	26 IT4var29	B1		26 HB3var20	B1	STc
	27 PFD0635c	B3	Cen	27 IT4var33	B1		27 HB3var17	B1	Cen
	28 PFL1950w	B4	Cen	28 IT4var41	B1		28 HB3var19	B1	Cen
	29 PF08_0103	B3	Cen	29 IT4var54	B1		29 HB3var18	B1	Tc
	30 PFD1005c	B1	Cen	30 ITGvar	B1		30 HB3var12	B1	Tc
						A4var						
	31 MAL7P1.50	B1	Cen	31	tres	B1	T	31 HB3var13	B1	Tc
						A4var						
	32 MAL7P1.55	B1	Cen	32	ICAM	B1	Tc	32 HB3var14	B1	Tc
	33 PF08_0106	B1	Cen	33 CS2var	U	T	33 HB3var8	B1	Tc
	34 PFL1955w	B1	Cen					34 HB3var9	B1	Tc
	35 PFL0935c	B1	Cen					35 HB3var15-inc	B1	Tc
	36 PFF0010w	B2	STc					36 HB3var11	B1	Tc
	37 PF08_0140	B1	STc					37 HB3var10	B1	Tc