A Plasmodium Whole-Genome Synteny Map: Indels and Synteny Breakpoints as Foci for Species-Specific Genes
Figure 2
A Whole-Genome Synteny Map of P. falciparum and Three RMPs
Synteny map of the core regions of all chromosomes of P. falciparum (left) and the RMPs (right), showing the 36 SBs, 22 SBPs, 14 CAT regions, P. falciparum-specific indels, and translocations in the RMP chromosomes. The 36 SBs, colored according to their chromosomal location in the cRMP genome, are named with a Roman and an Arabic number referring to the corresponding chromosome location in P. falciparum and the cRMP genome, respectively. Letters give the order in which the SBs are connected. Small arrows indicate the inverted orientation of a SB in P. falciparum relative to the cRMP genome. Indels containing P. falciparum-specific intrasyntenic genes are indicated through interruption of the colored SBs. P. falciparum telomeres are shown as white arrow heads (▹). SBs forming the cRMP chromosomes are linked by gray lines. In the cRMP genomes, the 23 coinciding subtelomeric linked ends are shown as white arrowheads (▹) and the five P. falciparum subtelomeric ends that are chromosomal internal in the cRMP chromosomes are indicated by small white arrowheads (▹). The 11 syntenic P. falciparum CAT regions [29] are shown as white circles (○), two inconsistent CAT regions as white circles with a cross (⊗), and three newly recognized CAT regions as white diamonds (⋄). Chromosome-internal var clusters are shown as white arrows (); stars and circles on sticks indicate rrna gene units (
) and tstk genes (
); black stars and circles represent nonsyntenic genes; while syntenic genes (three rrna gene units and one tstk gene) are colored according to their chromosomal location in the RMPs. Bars under the cRMP chromosomes represent the differences in the organization of the SBs of P. yoelii, P. chabaudi, and P. vinckei as a result of translocations. Colors indicate the cRMP chromosome with which recombination has taken place, while color gradients represent the ill-defined regions of the translocation breakpoints.