Additional file 1 of qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)

Additional file 1: Table S1. Metadata for RNA-seq datasets integrated in EucGenIE. In total 355 transcriptome datasets were integrated: 42 exAtlas datasets, 30 biotic interactions datasets and 283 transcriptomes from different F2 backcross individuals. Table S2. The 44 laccase genes detected in Eucalyptus with their corresponding BLASTP, HMMER and SignalP results. Genes encoding proteins with the three truncated domains of a canonical LAC and predicted to have a signal peptide were considered for analysis in this study. Table S3. Expression values in transcripts per million (TPM) of the 59 LAC/PRX genes, in the E. grandis exAtlas [35] and across biotic stress conditions [36–38]. Table S4. Secondary cell wall-related genes that were used for co-expression analysis. Table S5. Nine trait QTLs that co-locate with the eight LAC/PRX candidate genes from subnetwork 2 (Fig. 2, Table S3) or their eQTL positions. Table S6. Genes sharing eQTLs at the eleven eQTL positions associated with the eight LAC/PRX candidate genes from subnetwork 2 (Fig. 2, Additional file 1: Table S3). Table S7. Fisher's Exact Test results for enrichment of cell wall-related genes with eQTLs located at each of eleven eQTL positions, respectively, associated with the eight LAC/PRX candidate genes from subnetwork 2 (Fig. 2, Additional file 1: Table S3). Table S8. Transcription factors underlying the eleven eQTL peak positions associated with the eight LAC/PRX candidate genes from subnetwork 2 (Fig. 2, Additional file 1: Table S3). Table S9. Final score for ranking the eight LAC/PRX candidate genes from subnetwork 2 (Fig. 2, Additional file 1: Table S3) using multiple lines of evidence.