The persimmon (Diospyros oleifera Cheng) genome provides new insights into the inheritance of astringency and ancestral evolution

Qing-Gang Zhu,Qiu-Yun Zhang,Yong Yang,Bang-Chu Gong,Xue-Ren Yin,Chang-Fei Guan,Don Grierson,Kun-Song Chen,Jing-Wen Huang,Yang Xu

doi:10.1038/s41438-019-0227-2

Abstract

Persimmon (Diospyros kaki) is an oriental perennial woody fruit tree whose popular fruit is produced and consumed worldwide. The persimmon fruit is unique because of the hyperaccumulation of proanthocyanidins during fruit development, causing the mature fruit of most cultivars to have an astringent taste. In this study, we obtained a chromosome-scale genome assembly for ‘Youshi’ (Diospyros oleifera, 2n = 2x = 30), the diploid species of persimmon, by integrating Illumina sequencing, single-molecule real-time sequencing, and high-throughput chromosome conformation capture techniques. The assembled D. oleifera genome consisted of 849.53 Mb, 94.14% (799.71 Mb) of which was assigned to 15 pseudochromosomes, and is the first assembled genome for any member of the Ebenaceae. Comparative genomic analysis revealed that the D. oleifera genome underwent an ancient γ whole-genome duplication event. We studied the potential genetic basis for astringency development (proanthocyanidin biosynthesis) and removal (proanthocyanidin insolublization). Proanthocyanidin biosynthesis genes were mainly distributed on chromosome 1, and the clustering of these genes is responsible for the genetic stability of astringency heredity. Genome-based RNA-seq identified deastringency genes, and promoter analysis showed that most of their promoters contained large numbers of low oxygen-responsive motifs, which is consistent with the efficient industrial application of high CO2 treatment to remove astringency. Using the D. oleifera genome as the reference, SLAF-seq indicated that ‘Youshi’ is one of the ancestors of the cultivated persimmon (2n = 6x = 90). Our study provides significant insights into the genetic basis of persimmon evolution and the development and removal astringency, and it will facilitate the improvement of the breeding of persimmon fruit.

Highlights

Introduction DiospyrosL. belongs to the Ebenaceae, a plant genus that includes over 500 species that are distributed worldwide[1] and is one of the largest angiosperm genera[2]
The final genome assembly was 849.53 Mb in size, very close to the predicted size of 853.3 Mb based on nuclear weight measurements performed via flow cytometry (Supplementary Fig. 3), and it consisted of 4728 scaffolds (≥1 kb) with an N50 of 42.43 Mb and 5919 contigs (≥1 kb) with an N50 of 890.84 kb (Supplementary Table 3)
The results showed that D. oleifera is relatively closely related to Actinidia chinensis and Solanum lycopersicum (Fig. 2b)

Summary

Introduction

L. belongs to the Ebenaceae, a plant genus that includes over 500 species that are distributed worldwide[1] and is one of the largest angiosperm genera[2]. In ancient China, persimmon was first described in ‘Li Ji·Nei Ze’ (circa 450 BC, written by Ji Kong, grandson of Confucius), and it began to be considered an important food during the Warring States Period (475–221 B.C.)[6]. The persimmon was widely cultivated in China during the Tang Dynasty (618–907 A.D.). Persimmon has been cultivated mainly in oriental countries (e.g., China, Japan, and Korea) but is widely distributed in other areas (e.g., China, Japan, and Korea). The most recent statistical data indicate that persimmon fruit production in China has reached 400 million tons annually (FAO, 2016)

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Results

Conclusion