Fig. 2.

A Proportion of repeat content in S. oryzae’s genome. The majority of repeats detected in S. oryzae are represented by Class II (TIR) elements, LINEs (Class I), and unclassified repeats (unknown). NR: non repetitive. B Variation of genome size and TE content in 62 insect species from [40] and S. oryzae. Coleopteran species are depicted in dark blue, and S. oryzae in light blue. S. oryzae is clearly a TE-rich genome. C TE proportion across 11 insect species, including six coleoptera. In agreement with the data used for comparison [40], PLEs are included in the LINE superfamilies, DIRS in LTRs, and RC, CRY, MAV and TIR in the DNA superfamilies. NR: non repetitive. S. oryzae harbors the largest TE content among Coleopterans and most insect species studied to date. Within Coleoptera, there is a large variation in TE content and type, with A. planipennis, L. decemlineata, and O. taurus carrying an abundant LINE content, while S. oryzae, T. castaneum, and A. glabripennis show larger DNA content. Cladogram based on [246]. D Classification of the 570 Mbs of TEs present in the S. oryzae genome. Most TIR families detected were not classified into known superfamilies. RTE LINE and Gypsy LTR elements are the most abundant superfamilies among retrotransposons. Around 21% of repeats in S. oryzae’s genome were not classified by our pipeline, and remain unknown (gray). E Distribution of TIR length sequences (right) detected by einverted and the internal region present between both TIRs (left) for complete consensus of TIR superfamilies (color) and unknown TIR families (gray)