Chromosome-level genomes of seeded and seedless date plum based on third-generation DNA sequencing and Hi-C analysis

Abstract

Diospyros lotus L. (Date plum) is an important tree species that produces fruit with a high nutritional value. An accurate chromosomal assembly of a species facilitates research on chromosomal evolution and functional gene mapping. In this study, we assembled the first chromosome-level genomes of seeded and seedless D. lotus using Illumina short reads, PacBio long reads, and Hi-C technology. The assembled genomes comprising 15 chromosomes were 617.66 and 647.31 Mb in size, with a scaffold N50 of 40.72 and 42.67 Mb for the seedless and seeded D. lotus, respectively. A BUSCO analysis revealed that the seedless and seeded D. lotus genomes were 91.53% and 91.60% complete, respectively. Additionally, 20,689 (95.4%) and 22,844 (98.5%) protein-coding genes in the seedless and seeded D. lotus genomes were annotated, respectively. Comparisons of the chromosomes between genomes revealed inversions and translocations on chromosome 8 and inversions on chromosome 11. We identified 490 and 424 gene families that expanded in the seedless and seeded D. lotus, respectively. The enriched pathways among these gene families included the estrogen signaling pathway, the MAPK signaling pathway, and biosynthetic pathways for flavonoids, monoterpenoids, and glucosinolates. Moreover, we constructed the first Diospyros genome database (http://www.persimmongenome.cn). On the basis of our data, we developed the first high-quality annotated D. lotus reference genomes, which will be useful for genomic studies on persimmon and for clarifying the molecular mechanisms underlying important traits. Comparisons between the seeded and seedless D. lotus genomes may also elucidate the molecular basis of seedlessness.