Figure 4. IE dynamics and genomic implications.

a, Presence-absence variation in a newer isolate of A. anophagefferens. *Non-reference IEs identified cannot be absent/absent. b, Sequences that can be co-opted to construct splice sites are biased with respect to codon phasing. For M. pusilla, IE introns should be biased by availability of AG sequences that can be co-opted as 3′ splice sites (3′ss). For A. anophagefferens, IE introns should be biased by availability of GY (Y is C or T) sequences that can be co-opted for 5′ splice sites (5′ss). IE introns indeed have phase biases more similar to the respectively co-opted sequence (bold). c, Nearby IE insertions generate nucleosome-sized segments. Distances between neighboring IE introns (solid) and between other neighboring introns (broken) are displayed as kernel density estimates. Nucleosome repeat lengths¹² of 206 bp for M. pusilla and 168 bp for A. anophagefferens show the expected sizes of integer numbers of nucleosomes (vertical lines).