Reference genome assembly of the tetraploid tuber crop Tropaeolum tuberosum

Abstract

Tropaeolum tuberosum is a tuber-forming crop native to the Andes, valued for its nutritional content, pest resistance and adaptation to high-altitude environments. Despite its contribution to food security and sustainable agriculture, it remains an underutilized species with scarce genomic resources, limiting genetic and functional studies. To address this gap, we generated a reference genome assembly for a European ex situ tetraploid accession of T. tuberosum using PacBio HiFi sequencing. The assembly spans 1.3 Gb in 1,805 contigs (contigs N50 = 32.2 Mb, longest contig = 60 Mb) and recovers 87% of the estimated genome size. We assessed assembly completeness and accuracy using Benchmarking Universal Single-Copy Orthologs, which detected 98.5% complete genes (21.7% single-copy, 76.8% duplicated), 0.7% fragmented, and 0.7% missing, demonstrating near-complete gene space recovery consistent with a high-quality tetraploid genome. To evaluate transferability, we resequenced a field-collected Colombian genotype of economic relevance using Oxford Nanopore technology. Read mapping showed 99.7% of primary alignments to the reference (weighted mean coverage = 16.4x, 96.1% at [≥]5x), confirming broad sequence conservation between accessions and validating the suitability of the ex situ reference as an anchor for in situ germplasm. Repetitive elements accounted for 71.3% of the genome. Using ANNEVO, we annotated 56,354 high-confidence protein-coding genes, achieving 98.3% complete BUSCOs, a PSAURON score of 97.2, and 90.5% taxonomic consistency with the rosid lineage (OMArk). This high-quality reference genome establishes a foundational resource for comparative genomics, population genomics and functional analyses on T. tuberosum, supporting future breeding and conservation of this important food resource. Significance statementT. tuberosum is an underutilized Andean tuber crop that combines highly nutritious tubers with remarkable disease resistance and UV tolerance, supporting Andean smallholder livelihoods under harsh high-altitude conditions. Beyond its role as a food crop, it is cultivated widely as an ornamental due to its abundant, brightly colored flowers closely resembling those of its relative nasturtium. Despite this dual relevance, genomic resources have been entirely lacking, limiting efforts to understand its domestication history, adaptation, and potential as a climate-resilient alternative to potato with higher nutraceutical properties. Our reference genome assembly provides the first genome-scale resource for T. tuberosum, creating a foundation for dissecting polyploid genome organization, key agronomic and nutritional traits, and interactions with biotic and abiotic stress. By enabling evolution, domestication, comparative genomics, breeding, conservation, and functional studies, this resource unlocks T. tuberosum as a model for resilient, diversified cropping systems globally.