A high-quality chromosomal genome assembly of Diospyros oleifera Cheng

Author:

Suo Yujing123ORCID,Sun Peng123ORCID,Cheng Huihui4ORCID,Han Weijuan123ORCID,Diao Songfeng123ORCID,Li Huawei123ORCID,Mai Yini123ORCID,Zhao Xing4ORCID,Li Fangdong123ORCID,Fu Jianmin123ORCID

Affiliation:

1. Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, No. 3 Weiwu Road, Jinshui District, Zhengzhou 450003, China

2. Non-timber Forest Research and Development Center, Chinese Academy of Forestry, No. 3 Weiwu Road, Jinshui District, Zhengzhou 450003, China

3. National Innovation Alliance of Persimmon Industry, No. 3 Weiwu Road, Jinshui District, Zhengzhou 450003, China

4. Novogene Bioinformatics Institute, Zone A10 Jiuxianqiao North Road, Chaoyang District, Beijing 100083, China

Abstract

Abstract 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.

Funder

National Key Research and Development Program of China

Fundamental Research Funds for the Central Non-profit Research Institution of CAF

Publisher

Oxford University Press (OUP)

Subject

Computer Science Applications,Health Informatics

Reference61 articles.

1. Five complete chloroplast genome sequences from Diospyros: genome organization and comparative analysis;Fu;PLoS One,2016

2. Persimmon genetics and breeding;Yonemori,2000

3. Staminate flower production on shoots of ‘Fuyu’ and ‘Jiro’ persimmon (Diospyros kaki Thunb.);Yakushiji;J Jpn Soc Hortic Sci,1995

4. Comprehensive mapping of long-range interactions reveals folding principles of the human genome;Lieberman-Aiden;Science,2009

5. Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects;Liu;arXiv,2013

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