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The persimmon (Diospyros oleifera Cheng) genome provides new insights into the inheritance of astringency and ancestral evolution.
Horticulture Research ( IF 7.6 ) Pub Date : 2019-12-18 , DOI: 10.1038/s41438-019-0227-2 Qing-Gang Zhu 1, 2 , Yang Xu 3 , Yong Yang 4 , Chang-Fei Guan 4 , Qiu-Yun Zhang 1, 2 , Jing-Wen Huang 1, 2 , Don Grierson 1, 5 , Kun-Song Chen 1, 2 , Bang-Chu Gong 3 , Xue-Ren Yin 1, 2
Horticulture Research ( IF 7.6 ) Pub Date : 2019-12-18 , DOI: 10.1038/s41438-019-0227-2 Qing-Gang Zhu 1, 2 , Yang Xu 3 , Yong Yang 4 , Chang-Fei Guan 4 , Qiu-Yun Zhang 1, 2 , Jing-Wen Huang 1, 2 , Don Grierson 1, 5 , Kun-Song Chen 1, 2 , Bang-Chu Gong 3 , Xue-Ren Yin 1, 2
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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.
中文翻译：
柿子（Diospyros oleifera Cheng）基因组为涩味遗传和祖先进化提供了新的见解。
柿子（Diospyros kaki）是一种东方多年生木本果树，其受欢迎的水果在世界各地生产和消费。柿子果实的独特之处在于，在果实发育过程中原花青素的过度积累，导致大多数品种的成熟果实具有涩味。在本研究中，我们通过整合 Illumina 测序、单分子实时测序和高通量技术，获得了柿子二倍体物种“油柿”（Diospyros oleifera，2n = 2x = 30）的染色体规模基因组组装。染色体构象捕获技术。组装的油茶基因组由 849.53 Mb 组成，其中 94.14%（799.71 Mb）被分配给 15 条假染色体，并且是 Ebenaceae 任何成员的第一个组装基因组。比较基因组分析表明，油茶基因组经历了古老的γ全基因组复制事件。我们研究了涩味产生（原花青素生物合成）和去除（原花青素不溶）的潜在遗传基础。原花青素生物合成基因主要分布在1号染色体上，这些基因的聚集负责涩味遗传的遗传稳定性。基于基因组的RNA-seq鉴定出去涩味基因，启动子分析显示其大部分启动子含有大量低氧响应基序，这与高CO2处理去除涩味的高效工业应用相一致。以油柿基因组为参考，SLAF-seq表明“油石”是栽培柿的祖先之一（2n = 6x = 90）。 我们的研究为柿子进化的遗传基础以及柿子涩味的发育和去除提供了重要的见解，并将有助于柿子果实育种的改进。
更新日期：2019-12-18
中文翻译：
柿子（Diospyros oleifera Cheng）基因组为涩味遗传和祖先进化提供了新的见解。
柿子（Diospyros kaki）是一种东方多年生木本果树，其受欢迎的水果在世界各地生产和消费。柿子果实的独特之处在于，在果实发育过程中原花青素的过度积累，导致大多数品种的成熟果实具有涩味。在本研究中，我们通过整合 Illumina 测序、单分子实时测序和高通量技术，获得了柿子二倍体物种“油柿”（Diospyros oleifera，2n = 2x = 30）的染色体规模基因组组装。染色体构象捕获技术。组装的油茶基因组由 849.53 Mb 组成，其中 94.14%（799.71 Mb）被分配给 15 条假染色体，并且是 Ebenaceae 任何成员的第一个组装基因组。比较基因组分析表明，油茶基因组经历了古老的γ全基因组复制事件。我们研究了涩味产生（原花青素生物合成）和去除（原花青素不溶）的潜在遗传基础。原花青素生物合成基因主要分布在1号染色体上，这些基因的聚集负责涩味遗传的遗传稳定性。基于基因组的RNA-seq鉴定出去涩味基因，启动子分析显示其大部分启动子含有大量低氧响应基序，这与高CO2处理去除涩味的高效工业应用相一致。以油柿基因组为参考，SLAF-seq表明“油石”是栽培柿的祖先之一（2n = 6x = 90）。 我们的研究为柿子进化的遗传基础以及柿子涩味的发育和去除提供了重要的见解，并将有助于柿子果实育种的改进。
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