BACKGROUND Diospyros oleifera Cheng, of the family Ebenaceae, is an economically important tree. Phylogenetic analyses indicate that D. oleifera is closely related to Diospyros kaki Thunb. 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 elucidate the molecular mechanisms of important traits. FINDINGS The D. oleifera genome was assembled with 443.6 Gb of raw reads using the Pacific Bioscience Sequel and Illumina HiSeq X Ten platforms. The final draft genome was ∼812.3 Mb and had a high level of continuity with N50 of 3.36 Mb. Fifteen 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. 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 tannin synthesis and deastringency in persimmon were identified; of these chalcone synthase (CHS) genes were expanded in the D. oleifera genome compared with Diospyros lotus, Camellia sinensis, and Vitis vinifera. Moreover, 186 positively selected genes were identified, including chalcone isomerase (CHI) gene, 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. CONCLUSIONS 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.

中文翻译：

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高质量的油柿染色体基因组组装。


背景技术 油橄榄（Diospyros oleifera Cheng）属于 Ebenaceae 科，是一种重要的经济树种。系统发育分析表明D. oleifera 与Diospyros kaki Thunb 密切相关。可作为柿树研究的模式植物。因此，开发油柿基因组资源将有利于六倍体柿基因组的辅助组装，阐明重要性状的分子机制。结果 使用 Pacific Bioscience Sequel 和 Illumina HiSeq X Ten 平台将油茶基因组与 443.6 Gb 的原始读数组装在一起。最终的基因组草案约为 812.3 Mb，具有高度连续性，N50 为 3.36 Mb。使用332个支架将对应于15条染色体的15个支架组装成最终大小721.5Mb，占基因组的88.81%。重复序列占基因组的54.8%。通过从头测序和与其他植物物种的同源性分析，注释了30,530个蛋白质编码基因，平均转录本大小为7,105.40 bp；其中，28,580 个蛋白质编码基因（93.61%）具有保守的功能基序或术语。此外，还鉴定了171个与柿子单宁合成和脱涩相关的候选基因；与黑枣、茶树和葡萄相比，这些查尔酮合酶 (CHS) 基因在油橄榄基因组中得到了扩展。此外，还鉴定了186个正选基因，其中包括查耳酮异构酶（CHI）基因，这是类黄酮-花青素途径中的关键酶。系统发育树分析表明，油茶和莲花的分裂可能发生在 900 万年前。除了古γ事件外，油茶和莲花中还发生了第二次全基因组重复事件。 结论我们生成了高质量的油柿染色体水平草图基因组，这将有助于六倍体柿基因组的组装以及柿属主要经济性状的进一步研究。