Salse Jérôme, Bolot Stéphanie, Throude Michaël, Jouffe Vincent, Piegu Benoît, Quraishi Umar Masood, Calcagno Thomas, Cooke Richard, Delseny Michel, Feuillet Catherine
Institut National de la Recherche Agronomique/Université Blaise Pascal Unité Mixte de Recherche 1095, Amélioration et Santé des Plantes, 63100 Clermont-Ferrand, France.
Plant Cell. 2008 Jan;20(1):11-24. doi: 10.1105/tpc.107.056309. Epub 2008 Jan 4.
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.
禾本科包含了最重要的谷类作物，是通过比较基因组学研究进化、物种形成和驯化机制的良好体系。在此，我们通过使用改进的序列比对标准和统计分析，将42,654条水稻基因序列与6426条定位的小麦EST进行比较，鉴定并描述了水稻（Oryza sativa）和小麦（Triticum aestivum）基因组中共享重复序列的进化情况。种内比较确定了29个染色体间重复，覆盖了72%的水稻基因组，以及10个重复块，覆盖了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系同源关系，检测到13个共线性块，分别占水稻和小麦基因组的83.1%和90.4%。将种内重复数据与共线性关系整合，揭示了在直系同源位置保守的7个重复片段。对这些重复的长度、组成和分歧时间进行详细分析，并与高粱（Sorghum bicolor）和玉米（Zea mays）进行比较，表明不同基因组之间存在共同和谱系特异性保守模式。这使我们能够提出一个模型，即禾本科基因组从具有五条基本染色体的共同祖先通过一系列全基因组和片段重复、染色体融合及易位进化而来。
