Fig. 4.

A TE divergence landscape. Distribution of the divergence (Kimura two parameters, K2P) between TE copies and their consensus, aggregated by TE class reported in percent of the genome. The less divergent superfamilies are distributed to the left and suggest recent activity. Strikingly, most of the TE copies have less than 10% divergence to their consensus, with a large number of copies under 5% (dotted line). The distribution of the “unknown” class overlaps with the leftmost mode of the TIR distribution, suggesting that many more TIR families are yet to be described in S. oryzae. Strikingly, LTR elements are the least diverged altogether with the mode of the distribution on the 0–1% divergence bin. B Mean K2P distributions within TE superfamilies. Left panel depicts Class II families, and all Class I (retrotransposons) and unknown families are on the right panel. LTR superfamilies harbor some of the least divergent TE families, suggesting that this class may host some of the youngest TE