The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences
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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 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.
KeywordBrachypodium BAC Genome Retrotransposons Phylogeny SSR
We thank R. Naderi and C.X. Wang for help in BAC DNA preparation and C.C. Crossman for technical assistance in BAC-end sequencing. This work was support in part by the United State Department of Agriculture, Agriculture Research Service CRIS 532502100-000, 532502100-011, and 532521000-13.
- Garvin DF, Gu YQ, Hasterok R, Hazen SP, Jenkins G, Mockler TC, Mur AL, Vogel JP (2007) Development of genetic research resources for Brachypodium distachyon, a new model system for grass crop research. The Plant Genome (In press)Google Scholar
- Hasterok R, Marasek A, Donnison IS, Armstead I, Thomas A, King IP, Wolny E, Idziak D, Draper J, Jenkins G (2006) Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization. Genetics 173:349–362PubMedCrossRefGoogle Scholar
- Lazo GR, Chao S, Hummel DD, Edwards H, Crossman CC, Lui N, Matthews DE, Carollo VL, Hane DL, You FM et al (2004) Development of an expressed sequence tag (EST) resource for wheat (Triticum aestivum L.): EST generation, unigene analysis, probe selection and bioinformatics for a 16,000-locus bin-delineated map. Genetics 168:585–593PubMedCrossRefGoogle Scholar