Fig. S1 Microarray experimental design.

Fig. S2 Transcriptome divergence and nonadditive gene expression between Coffea arabica cv T18141 and parental diploid species.

Table S1 Monitoring selection of differential responses of 66 unigenes in two growth temperature conditions

Table S2 Blast2GO annotation for genes differentially expressed in the ‘dominance’ and ‘transgression’ categories

Table S3 The missing genes

Table S4 Oligonucleotides that may cross-hybridize with several sequences

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