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

Figure 3. The three germline micronucleus genomes are interrupted by internally eliminated sequences (IESs) at different levels.

(A) Macronuclear destined sequences (MDSs) of Euplotes woodruffi are longer compared to Oxytricha or Tetmemena. (B) Positive correlation between the numbers of MDSs for orthologous genes in Tetmemena and in Oxytricha for 903 single-gene orthologs. Black line is the function of linear regression (R2=0.75). Red line is y=x. (C) Orthologs in E. woodruffi have fewer MDSs compared to Oxytricha, with no correlation (R2=0.003). Note that many highly discontinuous genes in Oxytricha are IES-less in E. woodruffi (present on one MDS). 917 single-gene orthologs are shown. (D) Distribution of pointers on single-gene somatic macronucleus (MAC) chromosomes in Oxytricha vs. (E) E. woodruffi, with MAC chromosomes oriented in gene direction. Pointers significantly accumulate at the 5’ end of single-gene MAC chromosomes in E. woodruffi. (F) Pointer positions on 3684 two-MDS MAC chromosomes demonstrate a preference upstream of the start codon.

Figure 3.

Figure 3—figure supplement 1. Lengths of orthologs in Oxytricha, Tetmemena and Euplotes woodruffi, and the distribution of pointers on Tetmemena chromosomes.

Figure 3—figure supplement 1.

(A and B) Coding sequence (CDS) lengths correlate for Oxytricha, Tetmemena, and E. woodruffi orthologs (related to Figure 3). (A) Tetmemena CDS length positively correlates with that of Oxytricha orthologs (R2=0.96). Black line is the linear regression fitting function. Red line shows y=x. (B) E. woodruffi CDS length positively correlates with that of Oxytricha orthologs (R2=0.83). (C) The distribution of pointers on single-gene somatic macronucleus (MAC) chromosomes in Tetmemena displays a weak 5’ bias (related to Figure 3).
Figure 3—figure supplement 2. Scrambled and nonscrambled loci have distinct length distributions of internally eliminated sequences (IESs) and pointers.

Figure 3—figure supplement 2.

(A–C) Length distribution of scrambled and nonscrambled pointers ≤30 bp in (A) Oxytricha, (B) Tetmemena, and (C) Euplotes woodruffi. (D–F) Length distribution of scrambled and nonscrambled IESs in (D) Oxytricha (≤100 bp), (E) Tetmemena (≤100 bp), and (F) E. woodruffi (≤300 bp).