The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences |
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Authors: | Naxin Huo Gerard R Lazo John P Vogel Frank M You Yaqin Ma Daniel M Hayden Devin Coleman-Derr Theresa A Hill Jan Dvorak Olin D Anderson Ming-Cheng Luo Yong Q Gu |
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Institution: | (1) Genomics and Gene Discovery Research Unit, USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA;(2) Department of Plant Sciences, University of California, Davis, CA 95616, USA |
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Abstract: | Due in part to its small genome (~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 . 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.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
N. Huo and G.R. Lazo contributed equally to this work. |
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Keywords: | Brachypodium BAC Genome Retrotransposons Phylogeny SSR |
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