Schlueter Jessica A, Dixon Phillip, Granger Cheryl, Grant David, Clark Lynn, Doyle Jeff J, Shoemaker Randy C
Interdepartmental Genetics, Department of Genetics Developmental and Cellular Biology, Iowa State University, Ames, IA 50011, USA.
Genome. 2004 Oct;47(5):868-76. doi: 10.1139/g04-047.
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.
利用植物EST文库，我们在8种植物中获得了1392个潜在的基因重复序列，这8种植物分别是：玉米、水稻、高粱、大麦、马铃薯、番茄、蒺藜苜蓿和大豆。我们估算了每对基因之间的同义距离和非同义距离，并确定了对应于每个物种中一到三轮基因组重复的两到三种正态分布混合情况。在禾本科植物中，我们发现在所有四个物种中都存在一个大约发生在5000万至6000万年前（Mya）的保守重复事件；该事件可能发生在禾本科植物主要辐射分化之前。在茄科植物中，我们发现了一个大约在5000万至5200万年前发生的保守重复事件的证据。大豆中的一次重复事件大约发生在4400万年前，而苜蓿中的一次重复事件约在5800万年前。比较同义距离和非同义距离使我们能够确定，大多数重复基因对处于纯化的负选择之下。我们计算了皮尔逊相关系数，以衡量重复基因对之间基因表达模式的变化程度，并在不同进化距离上进行比较。该分析表明，一些重复基因对似乎保留了成对之间的表达模式，而另一些则表现出不相关的表达。
