The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences.
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.
Huo
Naxin
N
Genomics and Gene Discovery Research Unit, USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA.
Lazo
Gerard R
GR
Vogel
John P
JP
You
Frank M
FM
Ma
Yaqin
Y
Hayden
Daniel M
DM
Coleman-Derr
Devin
D
Hill
Theresa A
TA
Dvorak
Jan
J
Anderson
Olin D
OD
Luo
Ming-Cheng
MC
Gu
Yong Q
YQ
D001483:Base Sequence; D002467:Cell Nucleus / Q000235:genetics; D022202:Chromosomes, Artificial, Bacterial; D018744:DNA, Plant / Q000737:chemistry*; D020224:Expressed Sequence Tags / Q000737:chemistry; D018745:Genome, Plant; D023281:Genomics; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D010802:Phylogeny; D006109:Poaceae / Q000145:classification / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid; D018626:Retroelements; D020079:Terminal Repeat Sequences
D018744:DNA, Plant; D018626:Retroelements