A high-quality chromosomal genome assembly of Diospyros oleifera Cheng

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.

Phytohormone and integrated mRNA and miRNA transcriptome analyses and differentiation of male between hermaphroditic floral buds of andromonoecious Diospyros kaki Thunb

“…To determine the OGI expression level, small RNAs reads were mapped to the D. lotus OGI sequence [ 75 ], the MeGI sequence from the D. oleifera genome [ 76 ], and the ‘ Kali ’ sequence cloned from ‘Longyanyeshi 1’ persimmon (Fig. 4 ).…”

Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding

“…We scaffolded the Vmac_v1 genome into chromosomes leveraging the high contiguity of the chromosomes and the synteny with haplotype1 of blueberry, and then validated the order and orientation of the Vmac scaffolds (chromosomes) reported here using high-density genetic map markers [26]. The resulting Vmac chromosome-scale assembly was contiguous with other closely related species that have chromosome-scale assemblies such as rhododendron ( Rhododendron williamsianum ) [27], persimmon ( Diospyros lotus ) [28], tea ( Camellia sinensis ) [29] and kiwi ( Actinidia chinensis ) [30] (Figure 2B).…”

A high-quality genome of the mangroveAegiceras corniculatumaids investigation of molecular adaptation to intertidal environments

“…We compared the complexity of gene families between A. corniculatum and other species (P. veris, D. oleifera, V. corymbosum, R. delavayi, A. chinensis, C. sinensis, and M. guttatus) (Colle et al, 2019;Hellsten et al, 2013;Huang et al, 2013;Nowak et al, 2015;Suo et al, 2020;Xia et al, 2019;Zhang et al, 2017). We identified 8291 gene families common among these species.…”

“…We used Augustus (v3.3.1) (Stanke et al, 2006) and GlimmerHMM (Majoros et al, 2004) to perform de novo gene prediction based on the masked genome. Protein sets were collected and chosen as homology-based evidence from sequenced plants Ericales (Actinidia chinensis (Huang et al, 2013), Camellia sinensis (Xia et al, 2019), Diospyros oleifera (Suo et al, 2020), Primula veris (Nowak et al, 2015), Rhododendron delavayi (Zhang et al, 2017), Vaccinium corymbosum (Colle et al, 2019)), and model plants (Arabidopsis thaliana (Lamesch et al, 2012) and Oryza sativa (Ouyang et al, 2007)). Clean RNA-seq reads were used as RNA-seq-based evidence; gene structure was estimated using Tophat2 (v2.1.1) and Cufflinks (v2.2.1) (Kim et al, 2013;Langmead and Salzberg, 2012;Trapnell et al, 2012).…”

“…We used OrthoFinder (Emms and Kelly, 2019) to identify orthologous genes from A. corniculatum and ten other angiosperms species: Primula veris (Nowak et al, 2015), Diospyros oleifera (Suo et al, 2020), Vaccinium corymbosum (Colle et al, 2019), Rhododendron delavayi (Zhang et al, 2017), Actinidia chinensis (Huang et al, 2013), Camellia sinensis (Xia et al, 2019), Mimulus guttatus (Hellsten et al, 2013), Vitis vinifera (Jaillon et al, 2007), Nelumbo nucifera (Shi et al, 2020), Oryza sativa (Ouyang et al, 2007). We also used the reciprocal BLASTP best-hit method for the 11 angiosperm proteins and single-copy genes from the BUSCO dataset.…”