Figure 7

Repeat elements are enriched in T2R, but not in V1R genomic neighborhood. Transposable elements (repeat elements) were identified using RepeatMasker in ten t2r and four v1r gene clusters with up to 100 kb flanking regions and ten reference genomic regions (12.2 Mb total). A) Genomic sequence containing class I transposons (SINEs, LINEs, LTRs) and class II transposons (DNA transposons), small RNA, and Satellites/simple/low complexity repeats is determined as percent of total sequence in T2R and V1R clusters (each including 10 kb flanking regions) and the reference regions. Color code as indicated. B) Average density of class I transposons in 20 kb genomic segments centering on 47 t2r (T2R) and 14 v1r genes (V1R) and in 11.3 Mb reference region (Ctrl). Significance was evaluated by students t test (two-sided; ***, p < 0.001; n.s., not significant). C, D) The frequency of class I transposable elements is given as number of elements per kb sequence. The position of the genes is indicated by triangles; dark magenta, ++ (5′- > 3′); light magenta,+- (3′- > 5′). C) Ten contigs with t2r gene clusters are shown, from left to right and top to bottom, JH128085, JH128916, JH129648, JH129303, JH129750, JH132239, JH129824, JH130976, JH130917, JH130784. D) Four contigs with v1r gene clusters are shown, from left to right and top to bottom, JH126562, JH129249, JH126576, JH1276167.