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United States Department of Agriculture

Agricultural Research Service

Title: The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences.

Authors
item Huo, Naxin - UC DAVIS
item Lazo, Gerard
item Vogel, John
item You, Frank - UC DAVIS
item Ma, Yaqin - UC DAVIS
item Hayden, Daniel
item Coleman-Derr, Devin - UC DAVIS
item Hill, Theresa
item Dvorak, Jan - UC DAVIS
item Anderson, Olin
item Luo, Ming-Cheng - UC DAVIS
item Gu, Yong

Submitted to: Functional and Integrative Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 6, 2007
Publication Date: November 6, 2007
Citation: Huo, N., Lazo, G.R., Vogel, J.P., You, F., Ma, Y., Hayden, D.M., Coleman-Derr, D., Hill, T., Dvorak, J., Anderson, O.D., Luo, M., Gu, Y.Q. 2007. Characterizing the nuclear genome structure of Brachypodium distachyon using BAC end sequences. Functional and Integrative Genomics. 8:135-147.

Interpretive Summary: The Brachypodium distachyon is emerging as a model system for temperate grasses, including important crops like wheat and barley. Analysis of 10.9% of the Brachypodium genome is presented in this study based on 64,696 BAC end sequences (BES). Analysis of repeat DNA content in BES revealed that approximately 11.0% of the genome consists of known repetitive DNA. Another 7.4% of the genome was identified as repetitive and unique in Brachypodium. Sequence data was analyzed for Simple Sequence Repeat (SSR) markers and flanking primer sequences for SSR detection potentially useful for genetic mapping were developed. Sequence analyses of BES indicated that approximately 21.2% of the Brachypodium genome represents coding sequence. Brachypodium BES have more significant matches to expressed sequence tags (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. Sequence analysis in this study provides a preview of the genome organization in preparation for the sequencing of the Brachypodium genome.

Technical 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 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, 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 repeat markers 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.

Last Modified: 12/22/2014