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- Publisher
- Springer Journals
- Copyright
- Copyright © 2007 by Springer-Verlag
- Subject
- Life Sciences; Animal Genetics and Genomics; Bioinformatics; Biochemistry, general; Microbial Genetics and Genomics; Plant Genetics & Genomics; Cell Biology
- ISSN
- 1438-793X
- eISSN
- 1438-7948
- DOI
- 10.1007/s10142-007-0062-7
- pmid
- 17985162
- Publisher site
- See Article on Publisher Site
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.
Journal
Functional & Integrative Genomics – Springer Journals
Published: Nov 6, 2007