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

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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 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.

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Acknowledgement

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.

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Correspondence to Ming-Cheng Luo or Yong Q. Gu.

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N. Huo and G.R. Lazo contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplement 1

Analysis of unique Brachypodium repetitive element sequences (XLS 64.5 kb)

Supplement 2

Sequence accessions used in each aligned sequences for phylogenetic analysis (XLS 92.5 kb)

Supplement 3

Characterizations of UBRES-4 in Brachypodium genome (PPT 292 kb)

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Huo, N., Lazo, G.R., Vogel, J.P. et al. The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Funct Integr Genomics 8, 135–147 (2008). https://doi.org/10.1007/s10142-007-0062-7

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  • DOI: https://doi.org/10.1007/s10142-007-0062-7

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