The Chromosome Level Genome and Genome-wide Association Study for the Agronomic Traits of Panax Notoginseng.
The Chromosome Level Genome and Genome-wide Association Study for the Agronomic Traits of Panax Notoginseng.
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DOI：
10.1016/j.isci.2020.101538
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发表时间：
2020-09-25
期刊：
影响因子：
5.8
通讯作者：
Lee SM
中科院分区：
文献类型：
--
作者：
Fan G;Liu X;Sun S;Shi C;Du X;Han K;Yang B;Fu Y;Liu M;Seim I;Zhang H;Xu Q;Wang J;Su X;Shao L;Zhu Y;Shao Y;Zhao Y;Wong AK;Zhuang D;Chen W;Zhang G;Yang H;Xu X;Tsui SK;Liu X;Lee SM
人参三七是一种具有重要药用价值和经济价值的驯化中草药。在这里，我们报告了一个染色体水平三七基因组组装与高（约79%）重复序列的内容。与广泛分布的、密切相关的高丽参（Panax ginseng）基因组的并列揭示了三七基因组中植物防御基因（特别是R基因）的收缩。我们还调查了人参属植物基因组较大的原因，揭示了两个人参特异性全基因组复制事件和转座因子扩增的贡献。转录组数据和比较基因组分析揭示了参与β-内酰胺酶合成途径的候选基因。我们还对240个栽培三七个体进行了全基因组关联研究，并确定了与根干重（63个基因）和茎粗（168个基因）相关的基因。三七基因组代表了利用一种经济上重要且神秘的植物的全部潜力的关键一步。三七染色体水平的基因组组装通过人参特异性WGD事件和TE扩增实现了三七基因组的大规模组装，揭示了三七合成途径中的候选基因，利用GWAS数据对与农艺性状相关的基因进行了鉴定。
The Chinese ginseng Panax notoginseng is a domesticated herb with significant medicinal and economic value. Here we report a chromosome-level P. notoginseng genome assembly with a high (∼79%) repetitive sequence content. The juxtaposition with the widely distributed, closely related Korean ginseng (Panax ginseng) genome revealed contraction of plant defense genes (in particular R-genes) in the P. notoginseng genome. We also investigated the reasons for the larger genome size of Panax species, revealing contributions from two Panax-specific whole-genome duplication events and transposable element expansion. Transcriptome data and comparative genome analysis revealed the candidate genes involved in the ginsenoside synthesis pathway. We also performed a genome-wide association study on 240 cultivated P. notoginseng individuals and identified the associated genes with dry root weight (63 genes) and stem thickness (168 genes). The P. notoginseng genome represents a critical step toward harnessing the full potential of an economically important and enigmatic plant. A chromosome-level P. notoginseng genome assembly is provided Panax-specific WGD events and TE expansion contribute to the larger genome size Candidate genes involved in the ginsenoside synthesis pathway are revealed The associated genes with agronomic traits were identified using GWAS data Biological Sciences; Plant Biology; Genomics; Transcriptomics
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影响因子：
4.6
作者：
Bakshi A;Zhu Z;Vinkhuyzen AA;Hill WD;McRae AF;Visscher PM;Yang J
通讯作者：
Yang J
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影响因子：
11.6
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Guo, Dongshu;Zhang, Jinzhe;Qin, Genji
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Qin, Genji
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Durand NC;Shamim MS;Machol I;Rao SS;Huntley MH;Lander ES;Aiden EL
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Aiden EL
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12.3
作者：
Haas, Brian J.;Salzberg, Steven L.;Zhu, Wei;Pertea, Mihaela;Allen, Jonathan E.;Orvis, Joshua;White, Owen;Buell, C. Robin;Wortman, Jennifer R.
通讯作者：
Wortman, Jennifer R.
影响因子：
3
作者：
Alexander DH;Lange K
通讯作者：
Lange K