The nuclear genome of Brachypodium distachyon:: analysis of BAC end sequences
The nuclear genome of Brachypodium distachyon:: analysis of BAC end sequences
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DOI：
10.1007/s10142-007-0062-7
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发表时间：
2008-05-01
影响因子：
2.9
通讯作者：
Gu, Yong Q.
中科院分区：
文献类型：
--
作者：
Huo, Naxin;Lazo, Gerard R.;Gu, Yong Q.
部分由于其小基因组（类似于350 Mb），二穗短柄草正在成为温带禾本科植物的模式系统，包括小麦和大麦等重要作物。我们提出了基于64，696个细菌人工染色体（BAC）末端序列（BES）的10.9%的短柄草基因组的分析。重复DNA含量的分析表明，大约11.0%的基因组由已知的重复DNA组成。绝大多数的短柄草属重复元件是LTR反转录转座子。虽然Bare-1逆转录转座子在小麦和大麦中很常见，但与Bare-1密切相关的Brachypodium重复元件序列-1（BRES-1）在Brachypodium中也很丰富。此外，鉴定的独特短柄草属重复元件序列占其基因组的约7.4%。对BES的简单重复序列进行了分析，可在http：//brachypodium.pw.usda.gov上获得可能用于遗传作图的SSR检测的侧翼引物序列。BES的序列分析表明，约21.2%的Brachypodium基因组代表编码序列。此外，短足草BES有更多的显着匹配的EST从小麦比水稻或玉米，虽然这些物种有相似的大小的EST集合。基于7种禾本科植物共有的335个序列的系统发育分析进一步揭示了短柄草属植物与小麦族的亲缘关系比短柄草属植物与水稻或玉米的亲缘关系更近。
Due in part to its small genome (similar to 350 Mb), Brachypodium distachyon is emerging as a model system for temperate grasses, including important crops like wheat and barley. We present the analysis of 10.9% of the Brachypodium genome based on 64,696 bacterial artificial chromosome (BAC) end sequences (BES). Analysis of repeat DNA content in BES revealed that approximately 11.0% or the genome consists of known repetitive DNA. The vast majority of the Brachypodium repetitive elements are LTR retrotransposons. While Bare-1 retrotransposons are common to wheat and barley, Brachypodium repetitive element sequence-1 (BRES-1), closely related to Bare-1, is also abundant in Brachypodium. Moreover, unique Brachypodium repetitive element sequences identified constitute approximately 7.4% of its genome. Simple sequence repeats from BES were analyzed, and flanking primer sequences for SSR detection potentially useful for genetic mapping are available at http:// brachypodium.pw.usda.gov. Sequence analyses of BES indicated that approximately 21.2% of the Brachypodium genome represents coding sequence. Furthermore, Brachypodium BES have more significant matches to ESTs from wheat than rice or maize, although these species have similar sizes of EST collections. A phylogenetic analysis based on 335 sequences shared among seven grass species further revealed a closer relationship between Brachypodium and Triticeae than Brachypodium and rice or maize.