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Our analysis shows that the E. histolytica genome has three times more transposable elements than previously reported (20% of the genome and mean repeat density of 4 TEs every 10 Kb), and twice as much as its closest relative, E. dispar.
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We divided the Abp gene family region into 50 kilobase (kb) non-overlapping bins to capture the mean and median repeat densities and their variability within the Abp regions.
Three very similar repeat types, (AAAAGTTCAACTTTATG with 273.0 bp/Mbp, mean length 318.5 bp, AAAAGTAGAACTTTTCT with 209.8 bp/Mbp, mean length 739.62 bp, AAAAGTTCTACTTTGAC with 88.9 bp/Mbp, mean length 705.3 bp) contribute 88% to the total repeat density of 17 bp repeats.
Whereas for the three vertebrate species a high TR density is correlated with a high value of the mean repeat length, no similar correlation can be observed for the three arthropods.
An analysis of TE dispersion along the scaffolds revealed that 90% of the genomic sequence in E. histolytica has a repeat density of less than 4 repeats every 10 Kb, the mean value for this genome (Fig. 8).
Related to Figure S3 To confirm that the different repeat elements (mouse and rat, B3; dog, SINEC_Cf2 and SINEC_Cf3; and opossum, MAR1_Mdo) are indeed bound by CTCF in vivo, we plotted the mean read count per base centered around CTCF PWM matches inside bound repeats, as well as the repeat density (repeats per position) at the same genomic locations.
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Only strain 26695 has a remarkably higher repeat density of 5.9% (207 repeats).
The bulk gene/repeat density is modelled as two overlapping populations that are better distinguished in terms of gene density than repeat density.
The mean repeat number was 9 and the mean repeat length was 23 bp.
Similar to the repeat densities, the mean lengths of TRs show remarkable differences among the three arthropods.
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