Whole-genome assembly of Corylus avellana cv 'Tonda Gentile delle Langhe' using linked-reads (10X Genomics)

The European hazelnut (Corylus avellana L.; 2n=2x=22) is a worldwide economically important tree nut that, being an outbred species, displays a high rate of heterozygosity. In recent years, the interest in this crop has increased, due to a growing demand related to the recognized nut health benefits. C. avellana cv ‘Tonda Gentile delle Langhe’ (‘TGdL’) represents an excellence for the Italian economy thanks to high nut quality. 

High-quality genome assembly in many fruit tree species is a difficult task because of their high heterozygosity. Therefore, a chromosome-scale assembly of ‘TGdL’ was built up through a two-tier bioinformatic approach. The 10X Genomics Chromium Technology was firstly used to obtain a high-quality assembly, which was then implemented through a reference-guided scaffolding step using the cv ‘Tombul’ genome.

Eleven pseudomolecules were obtained, corresponding to 11 chromosomes. A total of 11,046 scaffolds remained unplaced, representing 11% of the genome (46,504,161 bp). Gene prediction, performed with Maker-P software, identified 27,791 genes (AED ≤ 0.4 and 92% of BUSCO completeness), whose function was analysed with BlastP and InterProScan software. In order to characterise ‘TGdL’ specific genetic mechanisms, Orthofinder was used to detect orthologs between hazelnut and close related species. The ‘TGdL’ genome sequence is expected to be a powerful tool to understand hazelnut genetics and makes the basis to detect markers/genes related to agronomic traits to be used in targeted breeding programs.