D. Oleifera Genome

Abstract

Diospyros oleifera is closely related to the hexaploid cultivated persimmon, making it a promising model system for research D. kaki. As such, efforts to develop genomic resources for D. oleifera have the potential to enable hexaploidy persimmon genome assembly and to clarify the molecular basis for key developmental or agronomic traits of interest. The integration of Illumina sequencing, single-molecule real-time sequencing, and high-throughput chromosome capture has enabled the assembly of two D. oleifera genome versions (DOL_v1.0 and DOL_v2.0). The DOL_v1.0 and DOL_v2.0 genomes were 849.53 Mb and 812.32 Mb in length, respectively with an N50 scaffold length of 1.42 Mb and 3.36 Mb, respectively, of which 94.1% (799.71 Mb) and 88.81% (721.45 Mb) were anchored to 15 pseudochromosomes, respectively. In total, 64.96% and 54.8% of the DOL_v1.0 and DOL_v2.0 genomes, respectively, were composed of identified repeat sequences. Through de novo sequencing and comparisons with other species of plants, 32,516 gene candidates (average length: 6773.92 bp) were identified within the DOL_v1.0, of which 95.95% were functionally annotated. Similarly, 30,530 candidate protein-coding genes (average length: 7105.40 bp) were identified within the DOL_v2.0 genome, of which (93.61%) harbored conserved functional motifs or annotated terms. Through a 4DTv analysis, the DOL_v1.0 genome was found to have undergone only an evolutionarily ancient γ whole-genome duplication (WGD) event, while both the DOL_v2.0 and D. lotus (4dtv = 0.36 ~ 0.27–0.42) genomes have undergone a second WGD event. Based on the DOL_v2.0 genome, phylogenetic analyses suggested that the split between D. oleifera and D. lotus likely arose ~9.0 million years ago. Furthermore, these two genome versions were predicted to encode 57 and 171 respective genes associated with proanthocyanidin biosynthesis and insolubilization, with chalcone synthase (CHS) genes having undergone expansion in the DOL_v2.0 genome in comparison to the D. lotus genome, and with chalcone isomerase (CHI) gene having undergone positive selection. Overall, the assembly of a high-quality D. oleifera draft genome offers new insight regarding the evolution of persimmon species, and provides a promising foundation for future efforts to develop germplasm resources and to decrease the astringency of cultivated fruits.