The Entrez Gene ID to Gene Ontology mapping was downloaded from http://www.biomart.org.org
Syntenic maps were downloaded from the Genoscope database (http://www.genoscope.cns.fr/externe/English/Projets/Projet_C/data/synteny/TN_HS_SYNT)[36] and Ensembl's BioMart data mining tool (http://www.ensembl.org/multi/martview)[74], [75].
Prunus sequences that are anchored to the TxE Prunus reference map were downloaded from GDR.
Kyoto Encyclopedia for Genes and Genomes (KEGG) maps were downloaded and gene lists were extracted from associated KGML files.
Climatic and topographic variables were obtained from the Worldclim source [ 94], whose raster maps were downloaded at the EDIT Geoplatform http://edit.csic.es/.
Both species-specific probe-set annotation file and the corresponding probe-gene maps were downloaded from the Affymetrix site (http://www.affymetrix.com).
For this purpose, H3k36me3, H3k4me2, H3k4me3, H3k09me3, H3k27ac, H3k27me3, H3k4me1, H3k79me2, H3k9ac, H4k20me1, Ezh2, H2az and Pol2b maps were downloaded from The Encyclopedia of DNA Elements (ENCODE) [ 27].
The empirical estimates of the sex-averaged human recombination rates in 1 Mbp intervals based on Genethon [ 9], Marshfield [ 10] and deCODE [ 11] maps were downloaded from [ 12].
The marker sequences from the respective maps were downloaded from the National Center for Biotechnology Information and aligned with the A. thaliana genome using BLAST analysis, and crucifer building blocks containing important trait QTL were defined.
Graphical pathway maps were downloaded from the KEGG FTP server, and DEGs were then highlighted in them according to the coordinate description in the XML files at the KEGG FTP server, using Perl GD, XML Parser and XML LibXML modules.
