Table 2.

LCR Data Summary.

PlasmoDB ID	Gene Annotation (Abbreviation)	Heterozygosity	Plasmodium reichenowi Divergencea	LCR Family	AT-content (%)
PFE0305w	Transcription initiation factor Tfiid, TATA-binding protein (PfTfiid)	0	Deletion	Heterogeneous	76.1
MAL7P1.91	Exported serine/threonine protein kinase (PfSTPK)	0	Deletion	Heterogeneous	74.5
PFL0950c	P-type ATPase2 (PfATPase2)	0	Deletion	Heterogeneous	81.7
MAL13P1.148	Myosin II (PfMyo)	0	Deletion	Heterogeneous	84.1
PFB0500c	Rab5.1 protein, putative (PfRab5)	0	Insertion	Heterogeneous	88.9
PFD0950w	Ran-binding protein 1 (PfRanB1)	0	Insertion	Heterogeneous	70.5
PFE0120c	Merozoite surface protein 8.I (PfMSP8)	0	None	Heterogeneous	86.9
PFE0805w	Cation-transporting ATPase 1.I (PfCTA)	0	None	Heterogeneous	80.9
PFE0805w	Cation-transporting ATPase 1.II (PfCTA)	0	None	Heterogeneous	94.8
MAL7P1.91	Exported serine/threonine protein kinase (PfSTPK)	0	None	Heterogeneous	73.3
PF10_0345	Merozoite surface protein 3 (PfMSP3)	0	None	Heterogeneous	64.9
PFL2140c	ADP-ribosylation factor GTPase-activating protein (PfARF)	0	None	Heterogeneous	83.2
MAL13P1.148	Myosin I (PfMyo)	0	None	Heterogeneous	83.7
MAL13P1.301	Guanylyl cyclase II (PfGCyII)	0	None	Heterogeneous	68.3
PFD0590c	DNA polymerase alpha (PfPolA)	0	Not found	Heterogeneous	79.8
PFL1700c	Vacuolar-type H+-translocating inorganic pyrophosphatase (PfTIPP)	0	Not found	Heterogeneous	82.5
PF13_0257	Glutamate-tRNA ligase (PftRNAlig)	0	Unknown	Heterogeneous	86.9
PFB0685c	Acyl CoA synthetase (PfACS9)	0.734	Deletion	HighGC	61.9
PFD0085c	Acyl-CoA synthetase, putative (PfACS6)	0.648	Deletion	HighGC	73.6
PFD0865c	Cdc2-related protein kinase 1 (Pfcdc2)	0.8	Deletion	HighGC	72.6
PF07_0030	Heat shock protein 86 family protein (PfHSP86)	0.56	Deletion	HighGC	72.3
MAL13P1.176	Reticulocyte-binding protein 2 homolog B (PfRBP2b)	0.633	Insertion	HighGC	70.9
PF13_0198	Reticulocyte-binding protein 2 homolog A (PfRBP2a)	0.695	NA	HighGC	70.8
PFA0675w	RESA-like protein with DNAJ domain (PfRLP)	0.764	Not found	HighGC	68.5
PFE0120c	Merozoite surface protein 8.III (PfMSP8)	0.716	Not found	HighGC	73.9
PFL1370w	NIMA-related protein kinase (Pfnek-1)	0.914	Not found	HighGC	61.8
PFI0925w	Gamma-glutamylcysteine synthetase (PfGGS)	0.833	Unknown	HighGC	65.5
PF10_0071	RhoGAP protein (PfrhoGap)	0.75	Unknown	HighGC	71.2
PFL1880w	Acyl CoA synthetase (PfACS11)	0.719	Deletion	PolyN	89.3
PFE0120c	Merozoite surface protein 8.II (PfMSP8)	0.531	Insertion/deletion	PolyN	88.3
PF11_0395	Guanylyl cyclase 1.I (PfGCy1)	0.806	Not found	PolyN	83.8
PF11_0395	Guanylyl cyclase 1.II (PfGCy1)	0.72	Not found	PolyN	82.1
PF13_0150	DNA-directed RNA polymerase 3 largest subunit (RNApol3)	0.8	Not found	PolyN	90.5
PFL0465c	Zinc finger transcription factor (Pfkrox1)	0.72	Unknown	PolyN	80.3

NOTE.—Sixteen loci used in the first portion of the study comparing 16 different isolates are given in bold and loci used in the second part of the study comparing sequence from 5 isolates are not in bold. “None” indicates no size difference and no divergence. “Insertion” or “deletion” represents the P. reichenowi sequence size difference, for example, “deletion” indicating a shorter sequence in P. reichenowi than that of P. falciparum or any of its alleles (the one “insertion/deletion” represents a single instance in which the P. reichenowi sequence was an intermediate size compared with P. falciparum alleles). “Unknown” indicated that only part of the P. reichenowi sequence was found and “not found” indicates unsuccessful searches for a P. reichenowi ortholog for this gene. Unsuccessful searches likely result from the incomplete nature of P. reichenowi genome data (rather than the absence of the locus in the P. reichenowi genome) because in all cases sequence data were successfully found from regions up- and downstream and/or from known orthologs from multiple, more divergent, Plasmodium species.

^aDivergence as measured by size difference of P. falciparum loci with orthologous P. reichenowi sequence.