This study presents the transcriptome analysis of 13 elite durum wheat varieties representatives of the worldwide cultivated germplasm. cDNA libraries were produced from roots, seedling leaves and developing grains. Based on the reference genome sequence assembly of durum wheat cv. Svevo, 75.0, 70.5 and 74.5% of high-confidence Svevo genes were expressed in grain, leaf and root, respectively. Principal Component Analysis (PCA) showed a gene expression clustering led by tissues and varietal ancestry. Differentially up- and down-regulated gene clusters based on tissues and varieties were identified. Functional enrichment analysis for three Gene Ontology terms showed that differentially expressed genes were significantly enriched in transport, kinase activity, binding, enzyme activity and protein metabolism. Variance expression analysis projected on the Svevo assembly revealed the chromosome regions that drove the major expression variation patterns. Clustering the gene expression profiles and the cultivar\u2019s expression profiles evidenced several gene expression patterns related to their co-ancestry, particularly for the grain. Towards a more complete assembly of a pan-transcriptome in durum, the cultivar-specific reads that could not be mapped on the Svevo genome (4-30% referred to Svevo Illumina sequencing data) are being de novo assembled. Further, using the transcriptome of the 13 varieties in relation to bread wheat reference genome (cv. Chinese Spring IWGSC RefSeq) we are currently investigating the gene loss/deletion during the polyploidisation events. Moreover, the availability of the genome assemblies of the 10+ Wheat Genomes Project, which includes cultivars that represent genetic diversity, will allow us to infer strong allele fixation events (allopolyploidisation bottleneck)
