Widespread genome duplications throughout the history of flowering plants
Widespread genome duplications throughout the history of flowering plants
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DOI：
10.1101/gr.4825606
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发表时间：
2006-06-01
期刊：
影响因子：
7
通讯作者：
dePamphilis, Claude W.
中科院分区：
文献类型：
--
作者：
Cui, Liying;Wall, P. Kerr;dePamphilis, Claude W.
基因组比较为各种动植物的古老基因组复制提供了证据。我们开发了一个出生-死亡模型，以确定EST数据中基因组重复的证据，并应用混合模型来估计代表最基本的现存开花植物谱系的物种的EST集中确定的旁系同源对的年龄分布。我们发现了基础被子植物谱系中古代全基因组重复事件的证据，包括Nuphar advena（黄睡莲：睡莲科）和木兰科植物Persea americana（鳄梨：樟科）、北美鹅掌楸（郁金香白杨：木兰科）和Saruma henryi（马兜铃科）。此外，我们检测到独立的基因组重复的基础真双子叶植物calculscholzia californica（加州罂粟：罂粟科）和基础单子叶植物Acorus americanus（菖蒲科），这两者都是不同的复制记录祖先草（禾本科）和核心真双子叶植物谱系。在裸子植物中，我们发现了在Welwitschia mirabilis（买麻藤目）的古代多倍性的模棱两可的证据，并没有在松树的多倍性的证据，虽然裸子植物通常有更大的基因组比被子植物调查。跨物种序列分歧的估计表明，在基础被子植物的同义替换率不到一半，以前报道的核心真双子叶植物和成员的禾本科。这些较低的替代率允许推断较旧的重复事件。我们推测，在Nuphar数据中观察到的古代重复的证据可能代表了所有或大多数现存被子植物的共同祖先中的基因组重复，除了Amborella。
Genomic comparisons provide evidence for ancient genome-wide duplications in a diverse array of animals and plants. We developed a birth-death model to identify evidence for genome duplication in EST data, and applied a mixture model to estimate the age distribution of paralogous pairs identified in EST sets for species representing the basal-most extant flowering plant lineages. We found evidence for episodes of ancient genome-wide duplications in the basal angiosperm lineages including Nuphar advena (yellow water lily: Nymphaeaceae) and the magnoliids Persea americana (avocado: Lauraceae), Liriodendron tulipifera (tulip poplar: Magnoliaceae), and Saruma henryi (Aristolochiaceae). In addition, we detected independent genome duplications in the basal eudicot Eschscholzia californica (California poppy: Papaveraceae) and the basal monocot Acorus americanus (Acoraceae), both of which were distinct from duplications documented for ancestral grass (Poaceae) and core eudicot lineages. Among gymnosperms, we found equivocal evidence for ancient polyploidy in Welwitschia mirabilis (Gnetales) and no evidence for polyploidy in pine, although gymnosperms generally have much larger genomes than the angiosperms investigated. Cross-species sequence divergence estimates suggest that synonymous substitution rates in the basal angiosperms are less than half those previously reported for core eudicots and members of Poaceae. These lower substitution rates permit inference of older duplication events. We hypothesize that evidence of an ancient duplication observed in the Nuphar data may represent a genome duplication in the common ancestor of all or most extant angiosperms, except Amborella.