Fig. 3

Structural variations (SVs) and lineage specific regions (LSRs) between U. virens UV8b and UVP1. a The circos figure illustrates the conserved sequences and SVs between UV8b and UVP1. The circular layers from outside to inside are: separate solid bar colors for each chromosome, predicted genes (orange), repetitive elements (blue) and LSRs (purple). The black, blue and red stripes indicate the interchromosomal translocations, intrachromosomal translocations and inversions, respectively. b Alignment analysis of DNA sequences at the ends of chromosome 2 between UV8b and UVP1. Syntenic alignments are indicated by orange stripes, while the inversion or translocation events are indicated by purple. Repetitive elements are indicated by blue boxes. c More complete LTR-retrotransposons were found in the LSRs than those in randomly selected non-conserved regions with the same size as LSRs. Intact LTR-retrotransposons were defined with 80, 90 and 95% coverage levels. The percentages of intact LTR-retrotransposons were counted in the LSRs of UV8b relative to UVP1, in the LSRs of UVP1 relative to UV8b, and in randomly selected non-conserved regions. d The nucleotide diversities in long terminal repeats (LTRs) at flanking regions of LTR-retrotransposons in SVs, LSRs and other regions of UV8b genome. The LTRs at both flanking regions of LTR-retrotransposons were aligned to each other and the nucleotide diversities were calculated. LTR-RTs, LTR-retrotransposons