Chromosome-level genome assembly of the red mutant of Chinese chestnut (Castanea mollissima) provides new insights into anthocyanin accumulation

The Chinese chestnut cultivar ‘Hongli-1’ is a unique germplasm resource with red spines and leaves in Castanea plants. To investigate the origin, evolution and inheritance of this natural wild mutant, we sequenced and assembled its genome, and combined transcriptome and metabolome analysis to identify the key sites associated with this trait. The final assembly contained two haplotypes: hapA (708.83 Mb) and hapB (702.81 Mb), which contained 416.78 Mb and 419.20 Mb of repeat sequences, respectively. BUSCO analyses revealed complete gene coverage of 97.4 % for hapA and 98.3 % for hapB. The genome annotation of hapA and hapB predicted 51,183 and 50,517 genes, respectively. Whole-genome duplication event analysis suggested that ‘Hongli-1’ may have undergone only one WGD event. Gene family analysis revealed that the expanded genes of ‘Hongli-1’ included 28 structural genes and 95 transcription factor-encoding genes involved in flavonoid synthesis and metabolism. Transcriptional and metabolic analysis revealed that cyanidin and peonidin accounted for approximately 99 % of the anthocyanin contents in the spines and leaves of ‘Hongli-1’; the levels of cyanidin, peonidin and pelargonidin were significantly increased in the leaves and spines of ‘Hongli-1’; and the expression of PAL, 4CL, C4H, CHS, F3′5′H, BZ1 and LAR was significantly upregulated. The expanded and differentially expressed genes related to anthocyanin synthesis may be important causes of color development in the leaves and spines of ‘Hongli-1’; it is speculated that the red color is caused mainly by differences in gene expression.