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A Draft Genome of Prunus avium ‘Karina’: A Foundational Resource for Sweet Cherry Genomics

Sweet cherry (Prunus avium) is one of the most valuable fruit crops in the Rosaceae family, yet historically it has lacked the genomic resources available for related species such as peach, strawberry, or Prunus mume. To help close this gap, our team contributed to the development of a partial draft genome for the cultivar ‘Karina’, a mid‑to‑late blooming sweet cherry known for its large fruit, dark-red color, firmness, and moderate resistance to cracking.

As described in the publication — “Here we present the construction of a partial draft genome of the sweet cherry Prunus avium ‘Karina’…” — this project represents one of the earliest genome‑level resources available for Chilean sweet cherry breeding and molecular research.

Genome Assembly Overview

Using next‑generation sequencing (NGS) technologies and a de novo assembly strategy, the team generated a draft genome with the following characteristics:

  • Estimated genome size: 352.5 Mb

  • Contigs: 904,813 (N50 = 9,188 bp)

  • Scaffolds: 898,488 (N50 = 13,235 bp)

  • Maximum scaffold length: 419,819 bp

  • Coverage: ~100×

K‑mer analysis revealed a heterozygosity level of 2–5%, consistent with the highly heterozygous nature of sweet cherry genomes.

Although the assembly is fragmented compared to later long‑read assemblies, it provides a robust foundation for gene discovery, comparative genomics, and marker development.

Agronomically Relevant Gene Discovery

The draft genome was evaluated for key gene families associated with dormancy, phenology, and viral susceptibility:

Dormancy‑Associated MADS-box (DAM) Genes

Six putative DAM genes were identified in a tandem array, showing high sequence identity with Prunus persica (average 89.14%). These genes are central regulators of bud dormancy induction and release in Prunus species.

Eukaryotic Translation Initiation Factor 4G (eIF4G)

Two eIF4G homologs were detected, exhibiting:

  • 89.76% identity with P. persica

  • 60.36% identity with Arabidopsis thaliana

These factors are known to influence viral susceptibility and host–virus interactions in Prunus crops.

Assembly Validation and Completeness

Multiple validation strategies confirmed the biological relevance of the assembly:

  • Homology searches recovered full or partial sequences of known DAM and eIF4G genes.

  • Gene prediction using FGENESH produced peptide sequences with high identity to peach and Arabidopsis orthologs.

  • BUSCO analysis showed 93.5% complete single-copy orthologs, indicating strong coverage of core plant genes.

Together, these results demonstrate that the ‘Karina’ draft genome captures the essential gene space required for functional and comparative genomics.

Impact and Applications

This genome resource provides:

  • A baseline reference for sweet cherry genetics in Chile and internationally.

  • A tool for marker development, trait mapping, and comparative genomics.

  • Foundational support for functional genomics, including CRISPR target discovery.

  • A stepping stone toward high-contiguity assemblies using long-read technologies such as PacBio or Oxford Nanopore.

As the authors note, “we are hoping to obtain valuable data to perform genomic studies and to contribute to the better understanding of the genetic background of this cultivar.” This draft genome remains an important milestone in the molecular characterization of sweet cherry.

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