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Fig. 8 | BMC Genomics

Fig. 8

From: Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: patterns of repeated sequences and physicochemical signatures

Fig. 8

GC and AT base composition skews in EXT repeats and SUB regions are associated to transcription and replication. a E. cuniculi chromosome Iα extremity containing EXT1 repeat. Terminal regions (EXT and rDNA) present accumulation of G. The inversion of the AT skew takes place at R02 recombination site. This observation suggests that the region between R01 and R02 sites is related to the SUB region despite the presence of an interD gene close to R01. The accumulation of A is strongly associated with the presence of interAE and interB genes. The curve is in fact doing the revers in the gene poor region upstream of ECU01_0130 interAE gene. The G enrichment starts after the dhfr-ts gene cluster in EXT1-2 repeat. These knee points on the curve do not match with recombination sites. b E. cuniculi chromosome IIα extremity containing EXT2 repeat. R01 and R02 recombination site are not present in the consensus sequence of chromosome II actually present. The accumulation of A in EXT2 repeat is strongly associated with the presence of interAE and interB genes. It is also associated to interD genes in EXT2-4 but not in EXT2-1 sub-sequence. The interC gene in EXT2-2 displays a frame shift. It is therefore encoded by two putative CDS which may be two parts of a pseudogene. As all interC members, these CDSs are not associated to any base composition biases. The coding core region outside EXT2 also exhibits an accumulation of A up to CDS ECU02_0150. The inflexion of the curve between ECU02_0150 and ECU02_0160 CDS is marked by the inversion of both GC and AT skew. The same phenomenon is observed between ECU02_0190 and ECU02_0200 CDS. In both case genes are all transcribed in the same orientation. This suggests that origins of replication are present at these points in the IIα extremity. c E. cuniculi chromosome XIα extremity containing EXT4 repeat. An A + G accumulation is detected all over the EXT4 repeat starting at R015 recombination site. However, the curve shows several inflexion points due to local inversion of AT skew. The two interB genes present in this repeat are associated with these knee points. CDS names have been reduced to the last four digit numbers for a matter of space

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