Table S33: Characteristics of the 53 P. falciparum-specific intersyntenic genes.

 

A list of 53 P. falciparum-specific genes located in indels between SBs (intersyntenic genes) including all intersyntenic pseudogenes. Groups of genes forming a cluster (8 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 (37 of 42 genes and 11 of 11 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-fama

Size indel (bp)

trans.

exp.

SP

AP

TM-N

TM

PFD0615c **

erythrocyte membrane protein 1 (PfEMP1)

var

70,195

 

 

 

 

 

 

chr4.phat_143/

chr4.glm_148 *

var internal cluster associated repeat gene 4a

vicar

70,195

-

-

X

-

X

X

PFD0620c **

rifin--related protein

rif

70,195

 

 

 

 

 

 

PFD0625c **

erythrocyte membrane protein 1 (PfEMP1)

var

70,195

 

 

 

 

 

 

- *

vicar pseudogene

vicar

70,195

 

 

 

 

 

 

PFD0630c **

erythrocyte membrane protein 1 (PfEMP1)

var

70,195

 

 

 

 

 

 

- *

vicar pseudogene

vicar

70,195

 

 

 

 

 

 

PFD0635c **

erythrocyte membrane protein 1 (PfEMP1)

var

70,195

 

 

 

 

 

 

PFD0640c **

rifin

rif

70,195

 

 

 

 

 

 

PFD0645w **

rifin

rif

70,195

 

 

 

 

 

 

PFD0650w

hypothetical protein

-

70,195

-

-

-

-

-

-

PFD0655w **

var-related pseudogene

var

70,195

 

 

 

 

 

 

MAL7P1.39 *

var internal cluster associated repeat gene 7a

vicar

105,155

S,M

-

X

-

X

X

PF07_0048 **

erythrocyte membrane protein 1 (PfEMP1)

var

105,155

 

 

 

 

 

 

chr7.phat_103/

chr7.glm_101 *

var internal cluster associated repeat gene 7b

vicar

105,155

-

-

X

-

X

X

MAL7P1.43 **

rif pseudogene

rif

105,155

 

 

 

 

 

 

PF07_0049 **

erythrocyte membrane protein 1 (PfEMP1)

var

105,155

 

 

 

 

 

 

chr7.phat_108/

chr7.glm_105 *

var internal cluster associated repeat gene 7c

vicar

105,155

-

-

X

-

X

X

MAL7P1.47 **

rif pseudogene

rif

105,155

 

 

 

 

 

 

MAL7P1.50 **

erythrocyte membrane protein 1 (PfEMP1)

var

105,155

 

 

 

 

 

 

PF07_0050 **

erythrocyte membrane protein 1 (PfEMP1)

var

105,155

 

 

 

 

 

 

MAL7P1.52 **

rif pseudogene

rif

105,155

 

 

 

 

 

 

PF07_0051 **

erythrocyte membrane protein 1 (PfEMP1)

var

105,155

 

 

 

 

 

 

chr7.phat_114 *

vicar pseudogene

vicar

105,155

 

 

 

 

 

 

MAL7P1.55 **

erythrocyte membrane protein 1 (PfEMP1)

var

105,155

 

 

 

 

 

 

MAL7P1.56 **

erythrocyte membrane protein 1 (PfEMP1)

var

105,155

 

 

 

 

 

 

MAL7P1.57 **

rifin

rif

105,155

 

 

 

 

 

 

MAL7P1.58 *

hypothetical protein, conserved in Pf

pfmc-2tm

105,155

ET

-

-

-

X

X

MAL7P1.59

hypothetical protein, conserved in Pf

-

105,155

-

-

-

-

-

-

MAL7P1.60 **

var fragment, pseudogene

var

105,155

 

 

 

 

 

 

MAL7P1.62 **

var fragment, pseudogene

var

105,155

 

 

 

 

 

 

MAL7P1.63 **

var fragment, pseudogene

var

105,155

 

 

 

 

 

 

PF07_0107 *

hypothetical protein

-

13,799

M-LR

-

-

-

X

X

MAL7P1.144 **

pftstk7a

tstk

13,799

ER-LT,G

S

-

-

-

X

PF08_0103 **

erythrocyte membrane protein 1 (PfEMP1)

var

43,407

 

 

 

 

 

 

- *

vicar pseudogene

vicar

43,407

 

 

 

 

 

 

PF08_0104 **

rifin

rif

43,407

 

 

 

 

 

 

PF08_0105 **

rifin

rif

43,407

 

 

 

 

 

 

PF08_0106 **

erythrocyte membrane protein 1 (PfEMP1)

var

43,407

 

 

 

 

 

 

PF08_0107 **

erythrocyte membrane protein 1 (PfEMP1)

var

43,407

 

 

 

 

 

 

chr8.phat_232/

chr8.glm_253 *

var internal cluster associated repeat gene 8

vicar

43,407

-

-

X

-

X

X

PFI0330c

hypothetical protein

-

11,729

LR-LT

-

-

-

-

X

PF10_0159 **

glycophorin-binding protein 130 precursor

gbp

37,843

ER-LS

T

-

-

X

X

PF10_0160 **

3.8 protein - pftstk10a

tstk

37,843

ER-ES

T

-

-

X

X

PF10_0161

hypothetical protein

-

37,843

ER-LR

S

-

-

-

-

PF10_0162

hypothetical protein

-

37,843

ET,M

-

-

-

-

-

PF10_0163 **

hypothetical protein

-

37,843

LS-ER

-

X

X

X

X

PF10_0164 *

hypothetical protein

etramp

37,843

S,G

G

X

-

X

X

MAL13P1.268 *

hypothetical protein

-

18,712

M-ER

-

X

-

X

X

MAL13P1.269 *

hypothetical protein

-

18,712

B,G

T

-

-

X

X

PF13_0275 **

hypothetical protein

-

18,712

M-ET

T,G,M

-

-

X

X

PF13_0276 *

hypothetical protein

-

18,712

M-LR

-

-

-

X

X

PF14_0708 *

hypothetical protein

-

13,194

G

-

-

-

X

X

a References to the papers describing the gene families are as follows: 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); pfmc-2tm, P. falciparum Maurer’s cleft localized 2 transmembrane domain proteins (Sam-Yellowe et al. 2004); tstk, transforming growth factor β (TGF-β) receptor-like serine/threonine protein kinases (this paper); gbp, glycophorin-binding protein (Nolte et al. 1991; Perkins et al. 1984; Rudolph et al. 1994); etramp, early transcribed membrane proteins (Spielmann et al. 2003).

 

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); M, merozoite; ER, early ring; LR, late ring; ET, early trophozoite; LT, late trophozoite; ES, early schizont; LS, late schizont; G, gametocyte; S, sporozoite; B, asexual blood stages; 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.