The haplotype-resolved and chromosome-level reference genome assembly of Diospyros deyangensis provides insights into the evolution and juvenile growth of persimmon

IF 8.7 1区 农林科学 Q1 Agricultural and Biological Sciences
Changfei Guan, Yunxiao Liu, Zhongxing Li, Yangxin Zhang, Zhiguang Liu, Qinggang Zhu, Pingxian Zhang, Xiaoxia Shen, Jing Fang, Jiayan Li, Qingling Zhang, Qingmei Guan, Zhengrong Luo, Yong Yang, Tao Zhao
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Abstract

The Diospyros genus, which includes both wild and cultivated species such as Diospyros lotus and Diospyros kaki, represents a diverse genetic pool with significant agricultural value. In this study, we present a high-quality, haplotype-resolved, chromosome-level genome assembly for D. deyangensis (hereinafter referred to as “Deyangshi”), an autotetraploid wild species notable for its short juvenile phase, by integrating high-fidelity single-molecule, nanopore sequencing, and high-throughput chromosome conformation capture techniques. The assembled genome size is approximately 3.01 Gb, anchored onto 60 pseudo-chromosomes. Comparative genomic analysis revealed that the D. deyangensis genome underwent an additional whole-genome duplication event following the eudicots shared ancient hexaploidy event. Resequencing and clustering on 63 samples representing 11 geographically diverse Diospyros accessions revealed significant genetic differentiation between D. deyangensis and D. kaki, as well as between D. kaki and other Diospyros species using population genomic analyses, suggesting that D. kaki followed an independent evolutionary pathway. Additionally, we identified DdELF4 (EARLY FLOWERING 4) from the “Deyangshi” backcross population using bulked segregant RNA sequencing (BSR-seq) with 50 early flowering and 50 non-early flowering individuals. Overexpression of DdELF4 in Arabidopsis resulted in delayed flowering and down-regulation of FT gene expression, indicating its role as a flowering repressor. This high-quality genome assembly of “Deyangshi” provides an essential genomic resource for the Diospyros genus, particularly for breeding programs focused on developing early-flowering persimmon varieties.
deyangdiospyros的单倍型解析和染色体水平的参考基因组组装为柿的进化和幼年生长提供了新的思路
Diospyros属包括野生和栽培品种,如Diospyros lotus和Diospyros kaki,代表了一个具有重要农业价值的多样化基因库。在这项研究中,我们通过整合高保真的单分子、纳米孔测序和高通量染色体构象捕获技术,为德阳石南(以下简称“德阳石”)这一以幼年期短而着称的同源四倍体野生物种提供了高质量的、单倍型解析的染色体水平基因组组装。组装的基因组大小约为3.01 Gb,锚定在60条伪染色体上。比较基因组分析显示,德扬古猿基因组在同源物种共享古代六倍体事件之后,又经历了一次全基因组复制事件。对11个地理上不同的薯蓣种质资源的63个样本进行重测序和聚类分析,发现德阳薯蓣与卡基薯蓣之间存在显著的遗传分化,卡基薯蓣与其他薯蓣物种之间存在显著的遗传分化,表明卡基薯蓣遵循独立的进化途径。此外,利用BSR-seq技术,从“德阳石”回交群体中鉴定了50个早花和50个非早花个体的DdELF4 (EARLY开花4)基因。DdELF4在拟南芥中过表达导致开花延迟和FT基因表达下调,表明其作为开花抑制因子的作用。这个高质量的“德阳柿”基因组组合为薯蓣属提供了重要的基因组资源,特别是为培育早花柿子品种提供了重要的基因组资源。
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来源期刊
Horticulture Research
Horticulture Research Biochemistry, Genetics and Molecular Biology-Biochemistry
CiteScore
11.20
自引率
6.90%
发文量
367
审稿时长
20 weeks
期刊介绍: Horticulture Research, an open access journal affiliated with Nanjing Agricultural University, has achieved the prestigious ranking of number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2022. As a leading publication in the field, the journal is dedicated to disseminating original research articles, comprehensive reviews, insightful perspectives, thought-provoking comments, and valuable correspondence articles and letters to the editor. Its scope encompasses all vital aspects of horticultural plants and disciplines, such as biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.
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