Chromosomal-scale genome assembly of parsnip (Pastinaca sativa) reveals genome evolution and carotenoid regulation

Parsnip (Pastinaca sativa), which belongs to the Apiaceae family, is a nutritious root vegetable consumed worldwide. Here, we report a 1.52 Gb chromosomal-scale assembly of the parsnip genome anchored on 11 chromosomes with a scaffold N50 of 135.6 Mb and containing 51,156 protein-coding genes. A total of 90.63% of the parsnip genome was composed of repetitive sequences, with transposon elements accounting for 84.07%. The continuous insertion of long terminal repeat (LTR) transposons led to the expansion of the parsnip genome, especially SIRE in LTR-Copia and Tekay in LTR-Gypsy. Whole genome duplication (WGD) and ancestral karyotype deduction revealed that chromosome variation was facilitated by the WGD events shared by Apiaceae species and has contributed to the diversity within Apiaceae. Transcriptome analyses, tissue structure observation, and enzyme activity assays suggested that ascorbate peroxidase gene (PsAPX) expression was significantly correlated with ascorbic acid (AsA) content. Furthermore, we explored the contributions of the carotenoid pathway to lack of pigment accumulation in the parsnip root by comparing gene expression patterns during carotenogenesis and the roles of carotenoid cleavage dioxygenase (CCD) proteins. The results indicated potential insufficient substrate flow within the carotenoid biosynthesis pathway and the obstructive effect of several PsCCDs on lycopene and β-carotene accumulation. Our findings offer resources for fundamental research on parsnip and genomics-assisted breeding of parsnip with enhanced nutritional quality.