Fig. 4.

TE expansions in M. oryzae experienced complex histories that differ between various lineages. Columns correspond to MAG_Ty3, Copia_elem, Grasshopper, and MGRL3 (from left to right, for each row of the figure). (A–D) Divergence between flanking LTR sequences of LTR-retrotransposons. (E–H) The Jukes–Cantor distance calculated using a separate consensus for each lineage. (I–L) The Jukes–Cantor distance calculated using one consensus for all lineages. (M–P) Schematic diagrams representing our hypothesis for the history of TE expansion events for each of the families. The representation of the current population for each TE is highlighted in yellow, and these expansions occurred either by one or multiple copies from an older population of TEs with sequence differences (highlighted in gray) proliferating recently. We indicate that TEs from different lineages might have proliferated from the same original copy for Copia_elem and MGRL3. Blue and red outlined Grasshopper rectangles correspond to the two labeled peaks in G. MGRL3 is an example of an old expansion. The tree in the bottom right corner serves as a key for color-coding of the lineages for all parts of the figure.