A highly contiguous genome assembly of Cyclamen persicum to accelerate functional genomics and breeding

Abstract

Cyclamen is an economically important ornamental plant widely cultivated for its diverse floral characteristics and adaptation to cool climates. Despite its horticultural significance, genomic resources for this species remain limited, hindering molecular studies and genomics-assisted breeding. Here, we report the first highly contiguous nuclear genome assembly of C. persicum generated using high-fidelity long-read sequencing. The assembled genome spans 1.48 Gb, consisting of 126 contigs with an N50 length of 52.3 Mb. Telomeric repeat analysis identified eight contigs containing telomeric sequences at both ends, suggesting the presence of near-complete chromosome assemblies. Genome completeness assessment using BUSCO indicated 98.1% completeness. Repetitive sequences occupied 82.9% of the assembly, with long terminal repeat retrotransposons accounting for 42.1% of the genome. A total of 40,223 protein-coding genes were predicted, with a complete BUSCO score of 95.7%. Comparative orthogroup analysis with five representative eudicot species identified 430 orthogroups specific to C. persicum and 363 orthogroups shared exclusively between C. persicum and Primula kwangtungensis, indicating the presence of both lineage-specific and Primulaceae-conserved gene families. These findings provide critical insights into gene family evolution within Primulaceae and establish an essential comparative framework for future genomic studies. The genome resource presented here provides an invaluable foundation for investigating genome evolution, gene function, and trait-associated loci in cyclamen, effectively facilitating molecular breeding and genetic improvement in this ornamental species.