Patterns of Intron Gain and Loss in Fungi (original) (raw)
Figure 3
Positional Biases in Intron Gain and Loss
Relative intron positions were defined as the number of bases in the coding sequence upstream of the intron divided by the total length of the coding sequence. These relative positions were binned into five categories (quintiles), each representing one-fifth of the coding sequence length (quintiles numbered 1–5 on the x-axis).
(A) Introns passing quality filter (light blue, back) and introns adjacent to gaps in the protein alignment that were removed by our quality filter (orange, front).
(B) Raw and inferred gains. Raw gains (green, back) are those introns present in exactly one organism (excluding the outgroup, A. nidulans). Inferred gains (blue, front) are corrected for the estimated number of cases that arose by other combinations of gain and loss events. Inferred gains are thus slightly lower than raw gains.
(C) Raw and inferred losses. Raw losses (green, front) are those introns absent in the organism in question but present in at least one of its siblings (descendants of its parent in the phylogenetic tree) and one of its cousins (non-descendants of its parent). Inferred losses (red, back) are corrected for the estimated number of introns lost along multiple lineages, or gained and then lost. Inferred losses are thus slightly higher than raw losses.
(D) Number of introns gained (blue) and lost (red) since last common ancestor (losses shown as negative numbers).
(E) Intron loss rate at each position since last common ancestor (introns lost per ancestral intron). Error bars represent binomial standard deviation.