Additional file 21: of Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

Table S10. Synteny analysis of inversion breakpoints. Provided is breakpoint information for 12 inversions, including six from pseudochromosome A (h1, h2, h3, h4, 5 and 6), one from J (ST), two from U (1 and 2), two from E (g1 and ST), and one from O (ms). The MS Excel file contains six spreadsheets, including one for this title, and one for each of the five major pseudochromosomes (i.e., A, J, U, E and O). For each pseudochromosome, inversions are listed in column “A”. For each inversion, information about the three protein coding genes flanking each side of each breakpoint in three species, including D. melanogaster, D. guanche and D. subobscura is provided in subsequent columns, from “B” to “Q”. This information includes species names, names and pseudochromosome coordinates of the three coding gene markers on both sides of each distal and proximal breakpoint, and the size of the pseudochromosome segment spanned by the breakpoints in Mb. Also provided is, for each breakpoint, its cytological and estimated pseudochromosome coordinates, and its hypothetical originating mechanism with the length of the associated duplication where it applies. Cells color background indicate contiguity (brown) or altered (yellow) order of the markers relative to the outgroup (D. melanogaster/D. pseudoobscura). For example, in the case of hypothetical inversion 1 of the A chromosome (i.e., h1) in D. subobscura, the three markers downstream the proximal breakpoint and upstream the distal breakpoint are in reverse order relative to D. guanche, which shows the markers ordered as in D. melanogaster. Reciprocal BLASTn searches with each breakpoint did not detect evidence of duplication, suggesting that the most likely originating mechanism of inversion Ah1 (depicted in yellow) is simple, or nearly straight breaks. (XLSX 31 kb)