Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution
Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution
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DOI：
10.1105/tpc.107.056309
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发表时间：
2008-01-01
期刊：
影响因子：
11.6
通讯作者：
Feuillet, Catherine
中科院分区：
文献类型：
--
作者：
Salse, Jerome;Bolot, Stephanie;Feuillet, Catherine
禾本科包括最重要的谷类作物，是一个很好的研究系统，比较基因组学，进化机制，物种形成和驯化。在这里，我们确定和特点的共享重复在水稻（水稻）和小麦（小麦）基因组的进化比较42,654水稻基因序列与6426映射小麦EST使用改进的序列比对标准和统计分析。种内比较鉴定了29个染色体间重复，覆盖72%的水稻基因组和10个重复块，覆盖67.5%的小麦基因组。使用相同的方法，我们评估了两个基因组之间的直交关系，并检测到13块共线性，分别代表83.1%和90.4%的水稻和小麦基因组。整合种内重复数据与共线性关系揭示了7个重复的片段保守在orthopathic位置。详细分析的长度，组成，和分歧的时间，这些重复和比较高粱（高粱双色）和玉米（玉米）表明不同的基因组之间的共同和谱系特异性模式的保护。这使我们能够提出一个模型，在该模型中，草基因组通过一系列全基因组和片段复制、染色体融合和易位，从一个基本数量为5条染色体的共同祖先进化而来。
The grass family comprises the most important cereal crops and is a good system for studying, with comparative genomics, mechanisms of evolution, speciation, and domestication. Here, we identified and characterized the evolution of shared duplications in the rice (Oryza sativa) and wheat (Triticum aestivum) genomes by comparing 42,654 rice gene sequences with 6426 mapped wheat ESTs using improved sequence alignment criteria and statistical analysis. Intraspecific comparisons identified 29 interchromosomal duplications covering 72% of the rice genome and 10 duplication blocks covering 67.5% of the wheat genome. Using the same methodology, we assessed orthologous relationships between the two genomes and detected 13 blocks of colinearity that represent 83.1 and 90.4% of the rice and wheat genomes, respectively. Integration of the intraspecific duplications data with colinearity relationships revealed seven duplicated segments conserved at orthologous positions. A detailed analysis of the length, composition, and divergence time of these duplications and comparisons with sorghum(Sorghum bicolor) and maize (Zea mays) indicated common and lineage-specific patterns of conservation between the different genomes. This allowed us to propose a model in which the grass genomes have evolved from a common ancestor with a basic number of five chromosomes through a series of whole genome and segmental duplications, chromosome fusions, and translocations.