The first two chromosome-scale genome assemblies of American hazelnut enable comparative genomic analysis of the genusCorylus

Abstract

SummaryThe native, perennial shrub American hazelnut (Corylus americana) is cultivated in the Midwestern U.S. for its significant ecological benefits, as well as its high-value nut crop. Implementation of modern breeding methods and quantitative genetic analyses ofC. americanarequires high-quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome-scale assemblies for this species using the accessions ‘Rush’ and ‘Winkler’. Genomes were assembled using HiFi PacBio reads and Arima Hi-C data, and Oxford Nanopore reads and a high-density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for ‘Rush’ and ‘Winkler’, respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. ‘Rush’ has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while ‘Winkler’ had corresponding scores of 96.9 and 96.5, indicating high-quality assemblies. These two independent assemblies enable unbiased assessment of structural variation withinC. americana, as well as patterns of syntenic relationships across theCorylusgenus. Furthermore, we identified high-density SNP marker sets from genotyping-by-sequencing data using 1,343C. americana, C. avellana, andC. americanaxC. avellanahybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently publishedCorylusgenomes, were utilized to perform phylogenetic analysis of sporophytic self-incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self-incompatibility inCorylus.