Huo Naxin, Lazo Gerard R, Vogel John P, You Frank M, Ma Yaqin, Hayden Daniel M, Coleman-Derr Devin, Hill Theresa A, Dvorak Jan, Anderson Olin D, Luo Ming-Cheng, Gu Yong Q
Genomics and Gene Discovery Research Unit, USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA.
Funct Integr Genomics. 2008 May;8(2):135-47. doi: 10.1007/s10142-007-0062-7. Epub 2007 Nov 6.
Due in part to its small genome (approximately 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% of 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.
由于其基因组较小（约350兆碱基对），短柄草正逐渐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。我们基于64,696个细菌人工染色体（BAC）末端序列（BES）对短柄草基因组的10.9%进行了分析。对BES中重复DNA含量的分析表明，约11.0%的基因组由已知的重复DNA组成。短柄草的绝大多数重复元件是LTR反转录转座子。虽然Bare - 1反转录转座子在小麦和大麦中很常见，但与Bare - 1密切相关的短柄草重复元件序列 - 1（BRES - 1）在短柄草中也很丰富。此外，鉴定出的独特短柄草重复元件序列约占其基因组的7.4%。对BES中的简单序列重复进行了分析，用于SSR检测且可能对遗传作图有用的侧翼引物序列可在http://brachypodium.pw.usda.gov获取。BES的序列分析表明，约21.2%的短柄草基因组代表编码序列。此外，尽管水稻和玉米的EST文库规模相似，但短柄草BES与小麦EST的匹配度比与水稻或玉米EST的匹配度更高。基于七个禾本科物种共有的335个序列进行的系统发育分析进一步表明，短柄草与小麦族的关系比与水稻或玉米的关系更密切。
