[DOI] 10.5524/100687 [Title] Supporting data for "A high-quality chromosomal genome assembly of Diospyros oleifera" [Release Date] 2019-12-20 [Citation] Suo, Y; Sun, P; Cheng, H; Han, W; Diao, S; Li, H; Mai, Y; Zhao, X; Li, F; Fu, J (2019): Supporting data for "A high-quality chromosomal genome assembly of Diospyros oleifera" GigaScience Database. http://dx.doi.org/10.5524/100687 [Data Type] Genomic [Dataset Summary] Diospyros oleifera, a member of the genus Diospyros of the family Ebenaceae, is an economically important tree. Phylogenetic analyses have indicated that D. oleifera is closely related to D. kaki, and could be used as a model plant for studies of D. kaki. Therefore, development of genomic resources of D. oleifera will facilitate auxiliary assembly of the hexaploid persimmon genome and provide insight into the molecular mechanisms of major economic traits.
The D. oleifera genome was assembled into 443.6 Gb of raw reads using the Pacific Bioscience Sequel and Illumina HiSeq X Ten platforms. The final draft genome was approximately 812.3 Mb and had a high level of continuity with the 3.36 Mb N50. Using the Hi-C data and the draft genome assembly, 15 scaffolds corresponding to the 15 chromosomes were assembled to a final size of 721.5 Mb using 332 scaffolds, accounting for 88.81% of the genome. The identified repeat sequences accounted for 54.8% of the genome. By de novo sequencing and analysis of homology with other plant species, 30,530 protein-coding genes with an average transcript size of 7,105.40 bp were annotated; of these, 28,580 protein-coding genes (93.61%) had conserved functional motifs or terms. In addition, 171 candidate genes involved in the tannin synthesis and deastringency in persimmon were identified; of these chalcone synthase (CHS) genes expanded in the D. oleifera genome compared with D. lotus, C. sinensis, and V. vinifera. Moreover, 186 positively selected genes were identified, including chalcone isomerase (CHI) gene, which is a key enzyme in the flavonoid-anthocyanin pathway. Phylogenetic tree analysis indicated that the split of D. oleifera and D. lotus likely occurred 9.0 million years ago. In addition to the ancient γ event, a second whole-genome duplication event occurred in D. oleifera and D. lotus (4dtv = 0.36 ~ 0.27-0.42).
We generated a high-quality chromosome-level draft genome for D. oleifera, which will facilitate assembly of the hexaploid persimmon genome and further studies of major economic traits in the genus Diospyros. [File Location] ftp://parrot.genomics.cn/gigadb/pub/10.5524/100001_101000/100687/ [File name] - [File Description] tree.nwk - Phylogenetic tree files (newick) Dol.snRNA.gff3 - snRNAs annotations  of Diospyros oleifera Dol.tRNA.gff3 - tRNAs annotations  of Diospyros oleifera Dol.rpkm.csv - Expression levels  of Diospyros oleifera single-copy.pep.phy - Gene family alignments (multi-fasta) Dol.trinity.fasta.gz - De novo transcriptome assembly  of Diospyros oleifera readme_100687.txt - None Dol.genome.fa.gz - Genome assembly of  Diospyros oleifera Dol.gff3 - Coding gene annotations of  Diospyros oleifera Dol.cds.fa - Coding gene nucleotide sequences of  Diospyros oleifera Dol.pep.fa - Coding gene translated sequences of  Diospyros oleifera Dol.genome.full_table_BUSCO.tsv - BUSCO output file(s) (text) of  Diospyros oleifera Dol.genome.short_summary_BUSCO.txt - BUSCO output file(s) (text) of  Diospyros oleifera Dol.CEGMA.species.completeness_report - CEGMA output file(s) (text) of  Diospyros oleifera Dor.repeat.gff - Repeatsannotations of  Diospyros oleifera Dol.miRNA.gff3 - miRNAs annotations of  Diospyros oleifera Dol.rRNA.gff3 - rRNAs annotations of Diospyros oleifera Dol_repeat.gff - Repeats annotations of Diospyros oleifera [License] All files and data are distributed under the Creative Commons Attribution-CC0 License unless specifically stated otherwise, see http://gigadb.org/site/term for more details. [Comments] [End]