Reference genome assembly of the tetraploid tuber crop Tropaeolum tuberosum
Scheffler, I.; Greb, T.; Hunziker, P.
Show abstract
Tropaeolum tuberosum is a tetraploid tuber-forming crop with agroecological and agronomic potential, yet genomic resources for this species remain scarce and limit genetic and functional studies. To address this gap, we generated a reference genome assembly for T. tuberosum using PacBio HiFi reads with an estimated genome size of 418 Mb based on k-mer analysis. The final assembly spans 1.32 Gb with 2,189 contigs (contigs N50 = 32.2 Mb, longest contig = 60 Mb) and recovers 79 % of the estimated genome size. We assessed assembly completeness and accuracy using Benchmarking Universal Single-Copy Orthologs (BUSCO), which detected 98.8 % complete genes (21.6 % single-copy, 77.1 % duplicated), 0.5 % fragmented, and 0.7 % missing, demonstrating near-complete gene space recovery consistent with a high-quality tetraploid reference genome. Repetitive sequences account for 71.6 % of the genome, and we annotated 87,927 protein-coding genes using Helixer. This reference genome assembly represents the first genome-scale resource for T. tuberosum and will enable studies of evolution, domestication and comparative genomics, and support breeding, conservation, and functional genomics in this species and related taxa.
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