Haplotype-resolved genome assembly and clonal variation of the Italian almond cultivar ‘Filippo Cea’

‘Filippo Cea’ (FC) is a widely grown Italian cultivar, combining self-compatibility, high yield, and excellent organoleptic quality. Here we report the generation of a haplotype-resolved de novo assembly of the FC genome, using PacBio HiFi sequencing, and whole-genome resequencing of nine FC clones sampled from orchards of different origin. The two haplotype genomes, FC_Hap1 and FC_Hap2, have an estimated size of 306 Mb and 285 Mb and N50 values exceeding 31 Mb, indicating high level of contiguity. Gene prediction, based on UniProt protein clusters and RNA-seq libraries from different tissues, captured more than 98% of the BUSCO gene set, indicating high completeness and accuracy. Variant calling on the FC clones revealed as few as 563 single nucleotide polymorphisms (SNPs), indicating overall genetic uniformity. Nonetheless, the genetic profile of clones originating from Apulia could be clearly discriminated from the one of clones of other origin, such as the Sardinian clone FC10. Sensory evaluations showed overall homogeneity among clones, with minor but consistent differences. In particular, the clone FC10 displayed higher seed elasticity, adhesiveness, and aftertaste intensity. Clustering of sensory traits did not correlated with the genetic structure, indicating that environment and orchard management strongly influence almond sensory attributes. The results of this study add important genomic resources to the scientific community working on almond. In addition, they are expected to be of high value for the consolidation of FC in the agrifood industry, its valorization through a Protected Origin Declaration mark, and its use in breeding programs.