Orthology between genomes of Brachypodium, wheat and rice.
Orthology between genomes of Brachypodium, wheat and rice.
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DOI：
10.1186/1756-0500-2-93
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发表时间：
2009-05-27
影响因子：
1.8
通讯作者：
Gupta PK
中科院分区：
文献类型：
--
作者：
Kumar S;Mohan A;Balyan HS;Gupta PK
过去，水稻基因组是研究禾本科植物比较基因组学的一个很好的模型。然而，最近，短柄短柱草基因组已经成为包括小麦在内的温带谷物基因组的更好的模式系统。在本研究中，利用Brachypodium EST重叠群来解决Brachypodium、小麦和水稻基因组之间的同源关系。对3,818个Brachypodium EST(Best)重叠群和3,792个小麦EST(West)物理定位重叠群的比较序列分析表明，多达449个最佳重叠群与1,154个West基因座是直源的，这些位点被定位在所有21条小麦染色体上。同样，743个最佳重叠群与分布在所有12条水稻染色体上的特定水稻基因组序列同源。多达183个最好的重叠群同时与小麦和水稻基因组序列同源，这些基因组序列包含多达17个SSR，这些SSR在这三个物种中保守。为这17个保守的SSR中的12个开发的引物用于湿法实验室实验，解决了青冈属、小麦和水稻基因组之间相对较高的保守性。本研究证实，对于小麦和大麦等温带谷类作物的基因组分析，短穗麦是一个比水稻更好的模式。在不久的将来，短柄蕨属植物的全基因组序列将进一步便利涉及谷物比较基因组学的研究。
In the past, rice genome served as a good model for studies involving comparative genomics of grass species. More recently, however, Brachypodium distachyon genome has emerged as a better model system for genomes of temperate cereals including wheat. During the present study, Brachypodium EST contigs were utilized to resolve orthologous relationships among the genomes of Brachypodium, wheat and rice. Comparative sequence analysis of 3,818 Brachypodium EST (bEST) contigs and 3,792 physically mapped wheat EST (wEST) contigs revealed that as many as 449 bEST contigs were orthologous to 1,154 wEST loci that were bin-mapped on all the 21 wheat chromosomes. Similarly 743 bEST contigs were orthologous to specific rice genome sequences distributed on all the 12 rice chromosomes. As many as 183 bEST contigs were orthologous to both wheat and rice genome sequences, which harbored as many as 17 SSRs conserved across the three species. Primers developed for 12 of these 17 conserved SSRs were used for a wet-lab experiment, which resolved relatively high level of conservation among the genomes of Brachypodium, wheat and rice. The present study confirmed that Brachypodium is a better model than rice for analysis of the genomes of temperate cereals like wheat and barley. The whole genome sequence of Brachypodium, which should become available in the near future, will further facilitate greatly the studies involving comparative genomics of cereals.