Table S34: Characteristics of the 138 P. falciparum-specific intrasyntenic genes.

A list of 138 P. falciparum-specific genes located in indels within SBs (intrasyntenic genes) including all intrasyntenic pseudogenes. Groups of genes forming a cluster (82 indels) are separated by a black line. Proteins with a TM domain in the first 100 amino acids (TM-N) as well as var and rif genes are considered proteins potentially targeted to the surface membrane of the parasite or erythrocyte (78 of 126 genes and 11 of 12 pseudogenes marked with an asterisk, genes with a PEXEL/VTS (Marti et al. 2004; Hiller et al. 2004) are marked with two asterisks).

Pf gene

Product

pf-fam^a or homologue

Size indel (bp)

trans.

exp.

SP

AP

TM-N

TM

PFA0360c **

hypothetical protein

PFA0365c

2,246

S,G

-

X

X

X

X

PFA0365c *

hypothetical protein

PFA0360c

2,246

-

-

X

X

X

X

PFB0140w *

hypothetical protein

-

1,237

LT-LS

-

-

-

X

X

PFB0225c

hypothetical protein

-

1,526

G

S

-

-

-

-

PFB0300c *

merozoite surface protein 2 precursor

msp

2,805

ES-M

M

X

X

X

X

PFB0305c *

merozoite surface protein 5

msp

2,805

LS-M

-

X

-

X

X

PFB0340c *

cysteine protease, putative

proteases

22,130

ES-LS

M

X

-

X

X

PFB0345c *

cysteine protease, putative

proteases

22,130

LT-LS

S

X

-

X

X

PFB0350c *

cysteine protease, putative

proteases

22,130

LT-LS

G,T

X

-

X

X

PFB0355c

cysteine protease, putative

proteases

22,130

ES-LS,S

-

-

-

-

X

PFB0360c *

cysteine protease, putative

proteases

22,130

ES-LS

-

X

-

X

X

PFB0540w

hypothetical protein

-

5,534

LT-ES

S

-

-

-

-

PFB0650w

hypothetical protein

-

7,502

LT-M

-

-

-

-

-

PFB0695c *

acyl-CoA synthetase

acyl-CoA

2,666

M-LR

-

X

X

X

X

PFC0110w *

cytoadherence linked asexual protein

clag

21,201

ES-M

-

X

-

X

X

PFC0115w **

pseudo var gene

var

21,201

PFC0120w *

cytoadherence linked asexual protein

clag

21,201

ES-M

M

X

-

X

X

PFC0215c *

hypothetical protein

-

1,856

-

-

X

X

X

X

PFC0440c

helicase, putative

-

6,809

LR-ES

S,T

-

-

-

X

PFD0765w

RING finger protein, putative

-

2,627

M

M,S

-

-

-

X

PFD0995c **

erythrocyte membrane protein 1 (PfEMP1)

var

52,417

*

vicar pseudogene

vicar

52,417

PFD1000c **

erythrocyte membrane protein 1 (PfEMP1)

var

52,417

*

vicar pseudogene

vicar

52,417

PFD1005c **

erythrocyte membrane protein 1 (PfEMP1)

var

52,417

PFD1010w **

rifin

rif

52,417

PFD1015c **

erythrocyte membrane protein 1 (PfEMP1)

var

52,417

chr4.phat_229 *

var internal cluster associated repeat gene 4b

vicar

52,417

-

-

X

-

X

X

PFD1020c **

rifin

rif

52,417

PFD1025c **

var pseudogene

var

52,417

PFE0080c *

rhoptry-associated protein 2

PFE0075c

1,196

ES-M

M

X

-

X

X

PFE0125w *

hypothetical protein

-

1,784

M,G

-

X

-

X

X

PFE0805w *

cation-transporting ATPase 1

-

7,375

LR-ES,G

S

-

-

X

X

PFE1055c

hypothetical protein

-

1,690

ER-ES,G

-

-

-

-

-

PFE1325w

hypothetical protein

-

13,574

-

-

-

-

-

X

PFE1455w *

sugar transporter, putative

-

2,359

S

-

-

-

X

X

MAL6P1.49

DNA helicase, putative

-

5,493

ET

M,T

-

-

-

X

MAL6P1.71 *

hypothetical protein

-

899

-

-

X

-

X

X

MAL6P1.99

hypothetical protein

-

3,961

-

M

-

-

-

X

MAL6P1.108

calcium-dependent protein kinase

-

1,907

ET-LS,G

-

-

-

-

X

MAL6P1.252 **

erythrocyte membrane protein 1 (PfEMP1)

var

19,289

MAL6P1.251 **

rifin

rif

19,289

MAL6P1.250 **

rifin

rif

19,289

MAL6P1.170

hypothetical protein

-

1,928

S

-

-

-

-

X

MAL6P1.156 *

troponin c-like protein, putative

-

1,248

-

-

-

-

X

X

MAL7P1.97 *

hypothetical protein

-

904

-

-

-

-

X

X

MAL7P1.167

hypothetical protein

-

8,321

LS

S

-

-

-

-

MAL8P1.97

hypothetical protein

-

4,830

S,G,M

-

-

-

-

X

MAL8P1.111

hypothetical protein

-

4,204

B,G

G

-

-

-

X

MAL8P1.126 *

serine protease, putative

-

3,139

S

-

X

-

X

X

MAL8P1.155 *

hypothetical protein

-

1,292

S

-

-

-

X

X

PFI0405w *

hypothetical protein

-

10,089

LT-LS

-

X

X

X

X

PFI0410c

hypothetical protein

-

10,089

ES-LS

T

-

-

-

X

PFI0510c *

hypothetical protein

-

5,093

LS

S

-

-

X

X

PF10_0309

hypothetical protein (helicase, putative)

-

3,616

S,B,G

-

-

-

-

X

PF10_0342 *

hypothetical protein

-

19,110

ES-M,G

-

X

-

X

X

PF10_0343 *

S-antigen

-

19,110

ES-M

-

X

-

X

X

PF10_0344 *

glutamate-rich protein

-

19,110

ES-M

G,S

X

X

X

X

PF10_0345 *

merozoite surface protein 3

msp

19,110

ES-M

M,T

X

-

X

X

PF10_0346 *

merozoite surface protein 6

msp

19,110

LS-M

M

-

-

X

X

PF10_0347 *

hypothetical protein

msp

19,110

ES-M

-

-

-

X

X

PF10_0362 *

DNA polymerase zeta catalytic subunit, putative

msp

7,204

LT-LS

-

-

-

X

X

PF11_0161 *

falcipain-2 precursor, putative

proteases

1,448

ER-LT

T

X

X

X

X

PF11_0165 *

hypothetical protein

proteases

5,073

LR-LT

T

X

X

X

X

PF11_0166

hypothetical protein

-

5,073

LS-LR

M,T

-

-

-

-

PF11_0186 *

hypothetical protein

-

756

B,G

S

-

-

X

X

PF11_0211 *

hypothetical protein, conserved

-

1,348

M-LR

-

-

-

X

X

PF11_0326

hypothetical protein

-

8,291

-

S

-

-

-

X

PF11_0357

hypothetical protein

-

5,168

G

M

-

-

-

-

PFL0105w

hypothetical protein

-

2,136

G

M,G,T

-

-

-

-

PFL0305c

hypothetical protein

-

2,422

G,S

G

-

-

-

-

PFL0360c

hypothetical protein

-

8,171

LT

-

-

-

-

X

PFL0935c **

erythrocyte membrane protein 1 (PfEMP1)

var

16,848

PFL0940c **

var fragment, pseudogene

var

16,848

PFL0945w **

var fragment, pseudogene

var

16,848

PFL1060c **

hypothetical protein, conserved

-

1,709

-

-

X

X

X

X

PFL1075w

Apicomplexan AP2-integrase DNA binding domain containing protein

apiap2

7,676

ET-LS,G

G,S

-

-

-

X

PFL1265c

hypothetical protein

-

1,751

G

-

-

-

-

-

PFL1945c *

hypothetical protein

etramp

58,313

M

-

X

X

X

X

PFL1950w **

erythrocyte membrane protein 1 (PfEMP1)

var

58,313

PFL1955w **

erythrocyte membrane protein 1 (PfEMP1)

var

58,313

chr12.phat_410/

chr12.glm_457 *

var internal cluster associated repeat gene 12

vicar

58,313

-

-

X

-

X

X

PFL1960w **

erythrocyte membrane protein 1 (PfEMP1)

var

58,313

PFL1965w **

rif pseudogene

rif

58,313

*

vicar pseudogene

vicar

58,313

PFL1970w **

var pseudogene

var

58,313

*

vicar pseudogene

vicar

58,313

PFL2085w

hypothetical protein

-

1,331

LT-M

S

-

-

-

-

PFL2255w

hypothetical protein

-

1,819

G,S

-

-

-

-

-

PF13_0071

hypothetical protein

-

1,688

ET-LT,G

S

-

-

-

X

MAL13P1.58

hypothetical protein

-

30,826

ER-LT

-

-

-

-

-

PF13_0073 **

hypothetical protein

-

30,826

ER-ET

T

X

-

X

X

MAL13P1.59 *

hypothetical protein

pf-fam-f

30,826

-

-

-

-

X

X

MAL13P1.60 *

erythrocyte binding antigen 140

dbl-ebp

30,826

LS-M

M,T

X

-

X

X

MAL13P1.61 **

hypothetical protein

-

30,826

M-LR

-

X

X

X

X

PF13_0074

hypothetical protein

pf-fam-b

30,826

M

-

-

-

-

X

PF13_0075

hypothetical protein, conserved in Pf

pf-fam-b

30,826

M-ER

-

-

-

-

-

MAL13P1.62 *

hypothetical protein

-

30,826

-

-

X

X

X

X

PF13_0076 **

hypothetical protein

-

30,826

M-ET

-

X

-

X

X

MAL13P1.106 *

hypothetical protein

-

21,907

G

G

X

-

X

X

MAL13P1.107 *

hypothetical protein

-

21,907

ET-LT

G,S

X

-

X

X

PF13_0115 *

frameshifted ebl1, pseudogene

dbl-ebp

21,907

LS-M

-

X

X

X

X

MAL13P1.109 **

pftstk13

tstk

21,907

-

-

X

-

X

X

MAL13P1.110 *

hypothetical protein

-

21,907

LR-LT

-

X

-

X

X

MAL13P1.122

hypothetical protein

-

8,478

S,B,G

T

-

-

-

-

PF13_0127

hypothetical protein

-

1,538

LT-LS

-

-

-

-

X

PF13_0153

hypothetical protein

-

3,014

S,B,G

M

-

-

-

X

PF13_0191 *

hypothetical protein

msp

10,811

ET-LT

S

X

X

X

X

PF13_0192 *

hypothetical protein

msp

10,811

ET-ES

-

X

-

X

X

PF13_0193 *

MSP7-like protein

msp

10,811

ES-LS

-

X

-

X

X

PF13_0194 *

hypothetical protein

-

10,811

M-LR

T

X

-

X

X

PF13_0195

MSP7 fragment, pseudogene

msp

10,811

S,B,G

-

-

-

-

-

MAL13P1.176

reticulocyte binding protein 2 homologue b

PF13_0198

14,894

LS-M

-

-

-

-

X

PF13_0198 *

reticulocyte binding protein 2 homologue a

MAL13P1.176

14,894

LS-M

S,T

-

-

X

X

MAL13P1.197

hypothetical protein

-

1,092

-

-

-

-

-

-

MAL13P1.214

phosphoethanolamine N-methyltransferase, putative

-

1,219

S,B,G

M

-

-

-

-

MAL13P1.235 *

hypothetical protein

-

1,227

-

-

-

-

X

X

PF13_0295

hypothetical protein

-

1,870

G,S

-

-

-

-

-

MAL13P1.295

hypothetical protein

-

6,149

ET-ES,G

S

-

-

-

X

MAL13P1.303 *

polyadenylate binding protein, putative

-

2,259

ET-LS,G

G,T,M

-

-

X

X

MAL13P1.306

hypothetical protein

-

2,491

ES-M

-

-

-

-

-

PF13_0338 *

hypothetical protein

-

2,390

LT-LS,G

M

X

-

X

X

MAL13P1.325

hypothetical protein

-

1,094

ET-LT

-

-

-

-

-

PF14_0036 *

acid phosphatase, putative

-

1,728

S,B,G

G,T,M

-

-

X

X

PF14_0076 *

plasmepsin 1 precursor

Proteases

10,526

M-LR

T,G,M

X

X

X

X

PF14_0077 *

plasmepsin 2 precursor

Proteases

10,526

LR-LT

T,M,G

-

-

X

X

PF14_0078 *

HAP protein

Proteases

10,526

ER-ES

T,G,M

X

X

X

X

PF14_0119 *

hypothetical protein, conserved

PF14_0117

962

ES-M

G,S

X

-

X

X

PF14_0206

hypothetical protein

-

2,861

G

-

-

-

-

X

PF14_0236

hypothetical protein

-

5,345

G

S,M

-

-

-

-

PF14_0262 *

hypothetical protein

-

6,925

S

-

-

-

X

X

PF14_0263

hypothetical protein

-

6,925

-

G

-

-

-

X

PF14_0291

hypothetical protein

-

3,677

M-LR

-

-

-

-

X

PF14_0297 *

ecto-nucleoside triphosphate diphosphohydrolase 1, putative

-

2,846

ET-ES

-

X

X

X

X

PF14_0463

chloroquine resistance marker protein

-

11,385

LT,LS

S,M

-

-

-

X

PF14_0565

hypothetical protein

-

2,867

B,G

M

-

-

-

-

PF14_0594

hypothetical protein

-

9,968

M

S

-

-

-

-

PF14_0638 *

hypothetical protein

-

2,582

-

G

X

-

X

X

^a In the column pf-fam or homologue, various gene families are listed as well as the gene names of single homologous genes. References to the papers describing the gene families are as follows: msp, merozoite surface proteins (Cowman et al. 2000); proteases (Bourgon et al. 2004); acyl-CoA, acyl-CoA synthetases (Hall et al. 2005); clag, cytoadherence-linked asexual gene (Holt et al. 1999); var (Baruch et al. 1995; Smith et al. 1995; Su et al. 1995); vicar, var internal cluster associated repeat gene (this paper); rif (Kyes et al. 1999); apiap2 (Balaji et al. 2005); etramp (Spielmann et al. 2003); pf-fam-f, P. falciparum gene family f (Hall et al. 2005); dbl-ebp, Duffy-binding-like erythrocyte-binding proteins (Adams et al. 1992); pf-fam-b, P. falciparum gene family b (Hall et al. 2005); tstk, transforming growth factor β (TGF-β) receptor-like serine/threonine protein kinases (this paper).

Abbreviations: SB, synteny block; PEXEL, Plasmodium export element; VTS, vacuolar transport signal; Pf, P. falciparum; pf-fam, described P. falciparum gene family; SP, predicted signal peptide; AP, predicted apicoplast transit peptide; TM, transmembrane domain; TM-N, N-terminal TM-domain; trans., approximate stage of (highest) transcription for all genes except the var, rif and vicar genes based on transcriptome data (Le Roch et al. 2003; Bozdech et al. 2003; S, sporozoite; M, merozoite; ER, early ring; LR, late ring; ET, early trophozoite; LT, late trophozoite; ES, early schizont; LS, late schizont; B, asexual blood stages; G, gametocyte; exp., expression of those genes based on proteome data (Florens  et al. 2002; Lasonder et al. 2002); M, merozoite; T, trophozoite; G, gametocyte; S, sporozoite.