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

Figure 6. Synteny in ‘Russian doll’ loci in Oxytricha and Tetmemena.

(A) Schematic comparison of the Russian doll gene cluster on Oxytricha germline micronucleus (MIC) contig OXYTRI_MIC_87484 vs. Tetmemena MIC contig TMEMEN_MIC_21461. Boxes of the same color represent clusters of macronuclear destined sequences (MDSs) for orthologous genes (detailed map in Figure 6—figure supplement 1 and Figure 6—figure supplement 2). Numbers in brackets indicate the number of MDSs in each cluster, grouped by somatic macronucleus (MAC) chromosome. One nested gene (green) in Oxytricha is absent from Tetmemena. A two-gene chromosome (orange) that derives from seven MDSs in Oxytricha is processed as two single-gene chromosomes in Tetmemena instead (indicated by black border around orange boxes). The purple gene in Oxytricha has two paralogs in Tetmemena. Black triangles represent conserved, orthologous, and nonscrambled gene loci inserted between nested Russian doll genes. Empty triangle represents scrambled MDSs for other loci. Gray triangles, complete nonscrambled MAC loci embedded between gene layers in one species with no orthologous gene detected in the other species. Black star, a complete telomere-bearing element (TBE) transposon insertion. Gray star, a partial TBE insertion. (B) Oxytricha MIC contig OXYTRI_MIC_69233 vs. Tetmemena MIC contig TMEMEN_MIC_22886. Pointer sequences bridging the nested MDSs of orange and green genes are highlighted. The underlined pointer portions are conserved between species, e.g., the last 8 bp of the Oxytricha pointer, TAAGTTCAAAGTAG, is identical to the first 8 bp of CAAAGTAGCTCAATC in Tetmemena, illustrating pointer sliding (DuBois and Prescott, 1995), or gradual shifting of MDS/IES boundaries. White star indicates a decayed TBE with no open reading frame identified.

Figure 6.

Figure 6—figure supplement 1. Detailed illustration of both Russian doll regions in Figure 6.

Figure 6—figure supplement 1.

Macronuclear destined sequence (MDS) indices are annotated here for each somatic macronucleus (MAC) locus. Overlined numbers represent inverted MDSs. MAC contig numbers for the MDSs are listed below and shown in corresponding color patterns (the Oxytricha loci were previously characterized in Braun et al., 2018).
Figure 6—figure supplement 2. Details of the Russian doll region in Tetmemena (TMEMEN_MIC_21461, Figure 6A).

Figure 6—figure supplement 2.

The whole region (~50 kb) was validated by 11 PCRs. The two black arrows indicate the absence of a Russian doll gene (green in Figure 6A) that is present in Oxytricha. Legend lists the 20 Tetmemena somatic macronucleus contigs that contain the corresponding macronuclear destined sequences.