The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes.
The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes.
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DOI：
10.1186/1756-0500-1-61
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发表时间：
2008-07-31
影响因子：
1.8
通讯作者：
Gu YQ
中科院分区：
文献类型：
--
作者：
Bortiri E;Coleman-Derr D;Lazo GR;Anderson OD;Gu YQ
小麦、大麦和黑麦是世界上最重要的作物之一，但它们对基因组学辅助作物改良提出了许多挑战。这些谷物的近亲短尾草（Brachypodium distachyon）最近作为草的功能基因组学模型出现。短柄藓的细胞核和细胞器基因组测序是使该物种成为对谷物生物学感兴趣的研究人员可利用的工具的第一步。利用含有整个叶绿体基因组的短尾草（Brachypodium diachyon）的BAC端和shotgun序列，对短尾草（Brachypodium diachyon）的叶绿体基因组进行了组合测序。比较分析表明，与其他谷物相比，其叶绿体基因组在基因数量和组织结构上具有保守性。然而，短柄草的一些基因进化速度比其他禾本科植物快。序列分析表明，水稻和小麦的质体基因组缺失约2.1 kb，这种缺失一定是独立发生的。我们证明BAC文库可以用于质体和其他细胞器基因组的测序。正如预期的那样，短柄草的叶绿体基因组与其他测序的禾本科植物非常相似。系统发育分析和叶绿体基因组的插入和缺失模式证实了短柄藓属是小麦科的近亲。然而，我们发现一些大的索引可以出现多次，并可能混淆系统发育重建。
Wheat, barley, and rye, of tribe Triticeae in the Poaceae, are among the most important crops worldwide but they present many challenges to genomics-aided crop improvement. Brachypodium distachyon, a close relative of those cereals has recently emerged as a model for grass functional genomics. Sequencing of the nuclear and organelle genomes of Brachypodium is one of the first steps towards making this species available as a tool for researchers interested in cereals biology. The chloroplast genome of Brachypodium distachyon was sequenced by a combinational approach using BAC end and shotgun sequences derived from a selected BAC containing the entire chloroplast genome. Comparative analysis indicated that the chloroplast genome is conserved in gene number and organization with respect to those of other cereals. However, several Brachypodium genes evolve at a faster rate than those in other grasses. Sequence analysis reveals that rice and wheat have a ~2.1 kb deletion in their plastid genomes and this deletion must have occurred independently in both species. We demonstrate that BAC libraries can be used to sequence plastid, and likely other organellar, genomes. As expected, the Brachypodium chloroplast genome is very similar to those of other sequenced grasses. The phylogenetic analyses and the pattern of insertions and deletions in the chloroplast genome confirmed that Brachypodium is a close relative of the tribe Triticeae. Nevertheless, we show that some large indels can arise multiple times and may confound phylogenetic reconstruction.