# Read_me on methods used to define correspondances between Darmor v5 et v10 (from Rousseau-Gueutin et al. 2020. Long-read assembly of the Brassica napus reference genome Darmor-bzh. Gigascience.)


Correspondence between the genes of the v5 and v10 assemblies. We calculated a correspondence table between the predicted genes on the v5 and v10 assemblies. To that purpose, we aligned all the v5 proteins against all the v10 proteins using diamond (DIAMOND, RRID:SCR 016071) (version 0.9.24 with the following parameters: “–more-sensitive -e 0.00001”). The best reciprocal hits were selected if they came from the same chromosome in both assemblies, and used as anchors. We then enriched the anchored genes using synteny and by filtering hits on the basis of percent identity (>80%) and sequence coverage (>80% of the target or the query). Using this strategy (M1), we were able to find a correspondence for 73,560 of the 101,040 genes of the v5 assembly (72.8%). Owing to the importance of such information for the Brassica community, we decided to use a second method (M2) to increase the number of genes with a correspondence. For this latter method, we first performed a reciprocal BlastP (NCBI BLAST, RRID:SCR 004870) (blastp v2.9.0 with the parameters “evalue 1e-20”) between the v5 and v10 proteins, then only conserved the blast hits with a minimum percentage of identity of 95%, an alignment length of 50%, and if they were on the same chromosome (scaffolds accepted). Using this second method, we identified approximately the same number of genes with a correspondence (72,314 v5 proteins). When comparing the results from these 2 methods, we observed that 85% were similar to both methods (62,514), ∼14% were found in only 1 method (11,032 and 9,800 specific to the first and second method, respectively), and 0.6% were discordant (450). In this article, we decided to provide the most complete correspondence table that derives from both analyses (82,441 proteins after removal of the 450 discordant results). In this supplementary table (Supplementary Table S18), we indicate which method(s) (M1 and/or M2) allowed us to identify the correspondence between v5 and v10 proteins. Any updates to this table will be available at Genoscope [60].