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. 2022 Nov 24;11:e82979. doi: 10.7554/eLife.82979

Figure 1. Genome rearrangements in representative ciliate species.

Figure 1.

(A) Diagram of genome rearrangement in Oxytricha. Each ciliate cell contains a somatic macronucleus (MAC) and a germline micronucleus (MIC). During development, the MAC genome rearranges from a copy of the MIC genome. (1) Nonscrambled genes rearrange simply by joining consecutive macronuclear destined sequences (MDSs, blue boxes) and removing internal eliminated sequences (IESs, thin lines). (2) Rearrangement of scrambled genes requires MDS translocation and/or inversion. Pointers are microhomologous sequences (colored vertical bars) present in two copies in the MIC and only one copy in the MAC where consecutive MDSs recombine. (B) Comparison of genome rearrangement features of representative ciliates and the non-ciliate Plasmodium falciparum as an outgroup (phylogenetic information is based on Parfrey et al., 2011; Bracht et al., 2013). Conclusions from this study are shown in bold. * indicates that some scrambled pointers in Euplotes woodruffi are much longer, as discussed in the results. Statistics for pointers ≤30 bp in E. woodruffi are shown. Table information derives from the following sources: 1 - Swart et al., 2013; 2 - Lindblad et al., 2019; 3 - Chen et al., 2014; 4 - Chen et al., 2015; 5 - Sheng et al., 2020; 6 - Eisen et al., 2006; 7 - Hamilton et al., 2016; 8 - Aury et al., 2006; 9 - Guérin et al., 2017; 10 - Arnaiz et al., 2012; 11 - Riley and Katz, 2001; 12 - Maurer-Alcalá et al., 2018a; 13 - Katz and Kovner, 2010; 14 - Gao et al., 2014.