INRA/Université Blaise Pascal UMR 1095, Génétique, Diversité et Ecophysiologie des Céréales, Domaine de Crouelle, 234 avenue du Brézet, 63100 Clermont-Ferrand, France.
Brief Bioinform. 2009 Nov;10(6):619-30. doi: 10.1093/bib/bbp037. Epub 2009 Aug 31.
In the past decade, a number of bioinformatics tools have been developed to perform comparative genomics studies in plants and animals. However, most of the publicly available and user friendly tools lack common standards for the identification of robust orthologous relationships between genomes leading non-specialists to often over interpret the results of large scale comparative sequence analyses. Recently, we have established a number of improved parameters and tools to define significant relationships between genomes as a basis to develop paleogenomics studies in grasses. Here, we describe our approaches and propose the development of community-based standards that can be used in comparative genomic studies to (i) identify robust sets of orthologous gene pairs, (ii) derive complete sets of chromosome to chromosome relationships within and between genomes and (iii) model common paleo-ancestor genome structures. The rice and sorghum genome sequences are used to exemplify step-by-step a methodology that should allow users to perform accurate comparative genome analyses in their favourite species. Finally, we describe two applications for accurate gene annotation and synteny-based cloning of agronomically important traits.
在过去的十年中，已经开发了许多生物信息学工具来进行动植物的比较基因组学研究。然而，大多数可用的和用户友好的工具缺乏识别基因组之间稳健的直系同源关系的通用标准，这导致非专业人员经常过度解释大规模比较序列分析的结果。最近，我们已经建立了许多改进的参数和工具，以确定基因组之间的显著关系，作为在禾本科植物中开展古基因组学研究的基础。在这里，我们描述了我们的方法，并提出了开发基于社区的标准的建议，这些标准可用于比较基因组学研究，以(i) 确定稳健的直系同源基因对集，(ii) 推导出基因组内和基因组之间完整的染色体对染色体关系，以及 (iii) 构建常见的古祖先基因组结构。利用水稻和高粱基因组序列逐步举例说明了一种方法，该方法应允许用户在他们喜欢的物种中进行准确的比较基因组分析。最后，我们描述了两种应用，用于准确的基因注释和基于共线性的农艺重要性状克隆。
