Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics
Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics
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DOI：
10.1073/pnas.0307901101
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发表时间：
2004-06-29
影响因子：
11.1
通讯作者：
Chapman, BA
中科院分区：
文献类型：
--
作者：
Paterson, AH;Bowers, JE;Chapman, BA
整合大量组装的水稻基因组序列的结构基因组数据，以及对许多其他分类群序列样本的系统发育分析，表明多倍体化事件发生在大约7000万年前，在主要谷类彼此分化之前，但在禾本科与百合目和禾本科分化之后。古代多倍化和随后的“二倍体化”（损失）的许多重复的基因拷贝，从而形成了所有禾本科谷物，饲料和生物质作物的基因组。禾本科似乎已经作为独立的谱系进化了大约5000万年，或自复制事件以来三分之二的时间。染色体被预测为homoeologs从这个古老的重复事件的帐户不成比例的份额不一致的基因座的水稻序列的比较发现一个详细的高粱序列标记的位点为基础的遗传图谱。二倍体化过程中的差异基因丢失可能导致了许多这些不协调。这种预测的同源物也占不成比例的份额重复高粱位点，进一步支持的假设，多倍化事件是共同的高粱和水稻。比较基因顺序沿着古同源染色体片段提供了一种手段，使染色体结构重排，区分禾本科植物之间的系统发育推断。将主要重复事件的发生时间叠加在分类学关系上，可以提高对比较基因顺序的理解，增强植物学模型数据对作物改良和进一步探索基因组生物多样性的价值。在其他被子植物谱系中，可能还需要发现更多的古代复制事件。
Integration of structural genomic data from a largely assembled rice genome sequence, with phylogenetic analysis of sequence samples for many other taxa, suggests that a polyploidization event occurred approximate to70 million years ago, before the divergence of the major cereals from one another but after the divergence of the Poales from the Liliales and Zingiberales. Ancient polyploidization and subsequent "diploidization" (loss) of many duplicated gene copies has thus shaped the genomes of all Poaceae cereal, forage, and biomass crops. The Poaceae appear to have evolved as separate lineages for approximate to50 million years, or two-thirds of the time since the duplication event. Chromosomes that are predicted to be homoeologs resulting from this ancient duplication event account for a disproportionate share of incongruent loci found by comparison of the rice sequence to a detailed sorghum sequence-tagged site-based genetic map. Differential gene loss during diploidization may have contributed many of these incongruities. Such predicted homoeologs also account for a disproportionate share of duplicated sorghum loci, further supporting the hypothesis that the polyploidization event was common to sorghum and rice. Comparative gene orders along paleo-homoeologous chromosomal segments provide a means to make phylogenetic inferences about chromosome structural rearrangements that differentiate among the grasses. Superimposition of the timing of major duplication events on taxonomic relationships leads to improved understanding of comparative gene orders, enhancing the value of data from botanical models for crop improvement and for further exploration of genomic biodiversity. Additional ancient duplication events probably remain to be discovered in other angiosperm lineages.