Fig. 5

Chromosomal breakpoints were associated with transposable elements. Of the nine NA1 isolates carrying chromosomal aberrations, a total of seven independent chromosomal breakpoints were identified at four chromosomal locations (see Additional files 4, 5, 6 and 7 for details). Black vertical lines represent transposable elements visualized by Integrative Genomics Viewer [81]. Cyan and orange bars represent segments of homologous chromosomes. a In scaffold 12, chromosomal breakpoints resulted in a partial monosomy in Pr-140.9 and a cnLOH in Pr-16. Two LINE retrotransposons were located at the breakpoint (red asterisk). b In scaffold 34, the chromosomal breakpoints for the partial trisomy (Pr-102 and Pr-16) and cnLOH (MK516a) occurred at the same genomic location. Four gypsy retrotransposons were found at the breakpoint (red asterisk). c Another breakpoint for cnLOH in Pr-16 was found in scaffold 37. Two gypsy retrotransposons flank the breakpoint (red asterisks). d The third breakpoint for cnLOH in Pr-16 was located in scaffold 44. A MuDR DNA transposon was located at the breakpoint (red asterisk). Additional files. 4, 5, 6 and 7 show close up of breakpoints