Mining EST databases to resolve evolutionary events in major crop species
Mining EST databases to resolve evolutionary events in major crop species
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DOI：
10.1139/g04-047
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发表时间：
2004-10-01
期刊：
影响因子：
3.1
通讯作者：
Shoemaker, RC
中科院分区：
文献类型：
--
作者：
Schlueter, JA;Dixon, P;Shoemaker, RC
利用植物EST收集，我们在8种植物中获得了1392个潜在基因重复序列：玉米、水稻、双色高粱、普通Hordeum vulgare、龙葵、番茄、苜蓿和甘氨酸。我们估计了每个基因对之间的同义和非同义距离，并确定了两到三个正态分布的混合物，对应于每个物种的一到三轮基因组复制。在Poaceae中，我们发现所有四个物种之间都发生了大约5000万至6000万年前（Mya）的保守复制事件；这一事件可能发生在草的主要辐射之前。在茄科中，我们发现了大约50-52亿年前的保守复制事件的证据。大豆的重复发生在大约44万年前，苜蓿的重复发生在大约58万年前。比较同义和非同义的距离使我们能够确定大多数重复的基因对处于纯化的负选择状态。我们计算了皮尔逊相关系数，为我们提供了基因表达模式在重复对之间如何变化的衡量标准，并将其与进化距离进行了比较。该分析表明，一些重复似乎保留了对之间的表达模式，而另一些则表现出不相关的表达。
Using plant EST collections, we obtained 1392 potential gene duplicates across 8 plant species: Zea mays, Oryza sativa, Sorghum bicolor, Hordeum vulgare, Solanum tuberosum, Lycopersicon esculentum, Medicago truncatula, and Glycine max. We estimated the synonymous and nonsynonymous distances between each gene pair and identified two to three mixtures of normal distributions corresponding to one to three rounds of genome duplication in each species. Within the Poaceae, we found a conserved duplication event among all four species that occurred approximately 50-60 million years ago (Mya); an event that probably occurred before the major radiation of the grasses. In the Solanaceae, we found evidence for a conserved duplication event approximately 50-52 Mya. A duplication in soybean occurred approximately 44 Mya and a duplication in Medicago about 58 Mya. Comparing synonymous and nonsynonymous distances allowed us to determine that most duplicate gene pairs are under purifying, negative selection. We calculated Pearson's correlation coefficients to provide us with a measure of how gene expression patterns have changed between duplicate pairs, and compared this across evolutionary distances. This analysis showed that some duplicates seemed to retain expression patterns between pairs, whereas others showed uncorrelated expression.