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The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences
- Source :
- Functionalintegrative genomics. 8(2)
- Publication Year :
- 2007
-
Abstract
- Due in part to its small genome (approximately 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.
- Subjects :
- Chromosomes, Artificial, Bacterial
DNA, Plant
Retroelements
Molecular Sequence Data
Retrotransposon
Genomics
Poaceae
Genome
Genetics
Repeated sequence
Triticeae
Phylogeny
Repetitive Sequences, Nucleic Acid
Cell Nucleus
Expressed Sequence Tags
Bacterial artificial chromosome
biology
Base Sequence
Terminal Repeat Sequences
food and beverages
General Medicine
biology.organism_classification
Brachypodium
Brachypodium distachyon
Genome, Plant
Microsatellite Repeats
Subjects
Details
- ISSN :
- 1438793X
- Volume :
- 8
- Issue :
- 2
- Database :
- OpenAIRE
- Journal :
- Functionalintegrative genomics
- Accession number :
- edsair.doi.dedup.....fcdd3b6b0d9ed2e9b8a80a5a7b0e6210