Additional file 2: 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 S2. Genetic markers used for validation, and physical anchoring, ordering and orientation of scaffolds. In total, 683 markers were considered, of which 621 were used. 62 markers were not used because they showed inconsistencies as to their localization with respect to markers from other studies and our own data. The MS Excel file contains eight spreadsheets, including one for this title, one for each of the five major pseudochromosomes (i.e., A, J, U, E and O), one with a summary, and one with the references for the marker data. For each pseudochromosome, markers are listed in column “A”, including used cytological (numbered, black), used linkage (numbered, blue), and nonused (nonnumbered, red) markers. For each marker, information relative to its name, cytological localization, authors, corresponding D. pseudoobscura “GA” gene model name, inconsistency where it applies, coordinates in the pseudochromosome, scaffold name, scaffold orientation and cytological span, and BLASTn statistics is provided in subsequent columns, from “B” to “Y”. Column “X” provides the number of used marker per scaffold. Alternating color in the background denotes different scaffolds. Cytological coordinates are always relative to the Kunze-Mühl and Müller [12] standard reference map. From the summary spreadsheet, most of the inconsistencies (72%) come from one (Laayouni et al. 2007) out of the total 26 cited works. Excluding that study, the total percent of inconsistencies is only 2.85% (i.e, 17 out of 638 markers). (XLSX 168 kb)