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Functional & Integrative Genomics

, Volume 8, Issue 2, pp 135–147 | Cite as

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

  • 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
Original Paper

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.

Keyword

Brachypodium BAC Genome Retrotransposons Phylogeny SSR 

Notes

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.

Supplementary material

10142_2007_62_MOESM1_ESM.xls (64 kb)
Supplement 1 Analysis of unique Brachypodium repetitive element sequences (XLS 64.5 kb)
10142_2007_62_MOESM2_ESM.xls (92 kb)
Supplement 2 Sequence accessions used in each aligned sequences for phylogenetic analysis (XLS 92.5 kb)
10142_2007_62_MOESM3_ESM.ppt (292 kb)
Supplement 3 Characterizations of UBRES-4 in Brachypodium genome (PPT 292 kb)

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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Naxin Huo
    • 1
  • Gerard R. Lazo
    • 1
  • John P. Vogel
    • 1
  • Frank M. You
    • 2
  • Yaqin Ma
    • 2
  • Daniel M. Hayden
    • 1
  • Devin Coleman-Derr
    • 1
  • Theresa A. Hill
    • 1
  • Jan Dvorak
    • 2
  • Olin D. Anderson
    • 1
  • Ming-Cheng Luo
    • 2
  • Yong Q. Gu
    • 1
  1. 1.Genomics and Gene Discovery Research UnitUSDA-ARS Western Regional Research CenterAlbanyUSA
  2. 2.Department of Plant SciencesUniversity of CaliforniaDavisUSA

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