High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height.
High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height.
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DOI：
10.1186/s13059-021-02522-9
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发表时间：
2021-11-04
期刊：
影响因子：
12.3
通讯作者：
Luo J
中科院分区：
文献类型：
--
作者：
Wang S;Xiao Y;Zhou ZW;Yuan J;Guo H;Yang Z;Yang J;Sun P;Sun L;Deng Y;Xie WZ;Song JM;Qamar MTU;Xia W;Liu R;Gong S;Wang Y;Wang F;Liu X;Fernie AR;Wang X;Fan H;Chen LL;Luo J
椰子是一种重要的热带油料和水果作物，其进化地位使其成为研究单子叶植物染色体进化和古植物分化的理想物种。在这里，我们报告的参考级基因组的Cn的组装和注释。高和Cn。矮秆型，基因组大小分别为2.40 Gb和2.39 Gb。比较分析表明，两个椰子亚种的遗传距离约为2-8 Mya，而槟榔科特有的全基因组重复（ω WGD）发生在47-53 Mya。它还使我们能够重建10个古代单子叶植物染色体的祖先核型和16个现代椰子染色体的进化轨迹。纤维合成基因在Cn.与木质素和纤维素合成相关的高大椰子的拷贝数和表达水平高于矮小椰子。综合多组学分析表明，椰子株高的差异是赤霉素代谢改变的结果，GA 20 ox拷贝数和启动子中的单核苷酸变化一起导致Cn之间株高的差异。高和Cn。矮人我们提供高质量的椰子基因组，通过多组学分析揭示两种椰子性状差异的遗传基础。我们还发现，数百万年来，株高的选择一直针对同一个基因，不仅在古代植物的自然选择中，如椰子，而且在栽培作物如水稻和玉米的人工选择中。在线版本包含补充材料，可通过10.1186/s13059-021-02522-9获得。
Coconut is an important tropical oil and fruit crop whose evolutionary position renders it a fantastic species for the investigation of the evolution of monocot chromosomes and the subsequent differentiation of ancient plants. Here, we report the assembly and annotation of reference-grade genomes of Cn. tall and Cn. dwarf, whose genome sizes are 2.40 Gb and 2.39 Gb, respectively. The comparative analysis reveals that the two coconut subspecies diverge about 2–8 Mya while the conserved Arecaceae-specific whole-genome duplication (ω WGD) occurs approximately 47–53 Mya. It additionally allows us to reconstruct the ancestral karyotypes of the ten ancient monocot chromosomes and the evolutionary trajectories of the 16 modern coconut chromosomes. Fiber synthesis genes in Cn. tall, related to lignin and cellulose synthesis, are found at a higher copy number and expression level than dwarf coconuts. Integrated multi-omics analysis reveals that the difference in coconut plant height is the result of altered gibberellin metabolism, with both the GA20ox copy number and a single-nucleotide change in the promoter together leading to the difference in plant height between Cn. tall and Cn. dwarf. We provide high-quality coconut genomes and reveal the genetic basis of trait differences between two coconuts through multi-omics analysis. We also reveal that the selection of plant height has been targeted for the same gene for millions of years, not only in natural selection of ancient plant as illustrated in coconut, but also for artificial selection in cultivated crops such as rice and maize. The online version contains supplementary material available at 10.1186/s13059-021-02522-9.
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影响因子：
4.9
作者：
Bao W;Kojima KK;Kohany O
通讯作者：
Kohany O
影响因子：
7.4
作者：
Davidson, SE;Smith, JJ;Reid, JB
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Reid, JB
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7.4
作者：
Davidson, SE;Elliott, RC;Reid, JB
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Reid, JB
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64.8
作者：
Jaillon, Olivier;Aury, Jean-Marc;Wincker, Patrick
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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.