A chromosome-scale, haplotype-resolved genome assembly of Tragopogon dubius Scop. (Asteraceae)

Objectives: Tragopogon dubius (yellow salsify or yellow goats beard; Asteraceae) is native to Eurasia and has been introduced to all continents except Antarctica. It is the common diploid parent of two allotetraploid species, T. mirus (involving hybridization with diploid T. porrifolius) and T. miscellus (involving hybridization with diploid T. pratensis). These two polyploids originated repeatedly within the last century in the northwestern USA. Tragopogon mirus and T. miscellus are important systems for the study of neopolyploidy in plants. We assembled the genome of T. dubius to facilitate bioinformatic studies that address the evolution of neopolyploid genomes. This genome is part of a larger effort to assemble high-quality genomes for all parental species of T. mirus and T. miscellus, including T. pratensis and T. porrifolius. Data description: We produced 116.7 Gb of PacBio long reads and 135.5 Gb of Dovetail Omni-C short reads from genomic DNA. The genomic reads were assembled with hifiasm and scaffolded using YaHS, yielding a phased, 2.0-Gb genome with six chromosomes. Transcriptomic reads and predicted proteins from closely-related reference genomes were used to annotate the genome using BRAKER3. BUSCO estimates of genome completeness were 97.5-97.6% for the scaffolded haplotype assemblies and 97.4% for the BRAKER3 predicted proteins.