SVEVO REFERENCE GENOME 2.0: A CHROMOSOME-LEVEL DE NOVO ASSEMBLY TO SUPPORT THE DURUM WHEAT COMMUNITY

We present the chromosome level assembly of the reference durum wheat (Triticum turgidum L. ssp. durum, cv. Svevo) genome, produced using high-quality long reads technology and optical mapping. The new genome (Svevo Rel. 2.0) includes 259 hybrid scaffolds (N50 = 112.3 Mb) organized by Hi-C data into 14 contiguous pseudomolecules spanning 10.4 Gb. The new assembly was compared with the previous short-read based assembly (Svevo Rel. 1.0) and discrepancies were manually resolved. The new release represents a significant improvement in assembly integrity and in terms of BUSCO and OMArk annotation quality parameters. The Svevo Rel. 2.0 was annotated using expression data from samples representing most tissues and developmental stages and plant response to biotic (Fusarium Head Blight), abiotic, and nutrient stress. The expression of 68,154 high-confidence genes was integrated into a transcriptome atlas. Annotation of leucine rich repeat-containing receptors and storage protein gene families was manually curated leading to the identification of 3,630 LRR-CR loci, 68% of them classified as nonsense mutation-containing genes (NsMCG). The accuracy and completeness of the assembly were demonstrated through the physical map of Tg1-B (Tenacious glumes 1), a locus controlling the free threshing trait located on the short arm of chromosome 2B, which was not present in Svevo Rel. 1.0. A wealth of 6,621 previously mapped QTLs for a comprehensive list of phenotypic trait categories were anchored onto Svevo Rel. 2.0 assembly and coupled with the expression atlas to define and refine genomic regions for specific traits. We demonstrated with several examples that for small hotspots encompassing few HC genes, new candidate genes might be suggested. The new reference genome, enhanced with advanced annotation, expression atlas, and QTLome data, represents the most comprehensive tool for durum wheat genomics and breeding.