Pipeline publication

[…] ite., We anchored the genome into eight pseudomolecules with the aid of the genetic linkage map and synteny with the A. lyrata genome25. Markers on the genetic linkage map are already linked to genomic scaffolds as a consequence of using the draft sequence as a reference for SNP discovery. In order to take advantage of synteny with A. lyrata we identified gene pairs between B. vulgaris gene predictions and those from A. lyrata. To do this we only selected 1:1 orthologs from an OrthoMCL analysis between proteins from the two species. We identified gene pairs that we were able to use for anchoring. The final pseudomolecule assembly was generated from the genetic map and synteny evidence using ALLMAPS64, where higher weighting was given to evidence from the genetic map. The macrosynteny between B. vulgaris and A. lyrata was compared by anchoring the genetic markers to the A. lyrata genome using gene-pairs identified with the OrthoMCL analysis (linking a gene in a mapped contig with the physical position of its putative ortholog in A. lyrata). Comparisons for each linkage group are shown in Supplementary Figs 20–27. Images were generated using AutoGRAPH65. We also evaluated the microsynteny between B. vulgaris and A. lyrata using SimpleSynteny66 for several B. vulgaris contigs (Supplementary Figs 28–30). B. vulgaris contigs with sequence homology to A. lyrata chromosome 1 were selected and genes within these were used in BLAST searches against the complete sequence of A. lyrata chromosome 1 using a minimum evalue of 0.0001 and a minimum coverage cutoff of 40%. Annotations were lifted from the scaffolds onto the pseudomolecule assembly and can be visualized at http://plen.ku.dk/Barbarea., QTL analysis for the traits analysed here was previously carried out in this population using a linkage map developed on a limited set of SSR markers, and dominant AFLP markers10. We used the less redundant genetic map (355 markers) for QTL analy […]

Pipeline specifications

Software tools ALLMAPS, AutoGRAPH, SimpleSynteny
Organisms Beta vulgaris, Plutella xylostella
Chemicals Glucosides, Thioglycosides, Saponins