The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes

<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Wheat, barley, and rye, of tribe Triticeae in the Poaceae, are among the most important crops worldwide but they present many challenges to genomics-aided crop improvement.<jats:italic>Brachypodium distachyon</jats:italic>, a close relative of those cereals has recently emerged as a model for grass functional genomics. Sequencing of the nuclear and organelle genomes of<jats:italic>Brachypodium</jats:italic>is one of the first steps towards making this species available as a tool for researchers interested in cereals biology.</jats:p></jats:sec><jats:sec><jats:title>Findings</jats:title><jats:p>The chloroplast genome of<jats:italic>Brachypodium distachyon</jats:italic>was sequenced by a combinational approach using BAC end and shotgun sequences derived from a selected BAC containing the entire chloroplast genome. Comparative analysis indicated that the chloroplast genome is conserved in gene number and organization with respect to those of other cereals. However, several<jats:italic>Brachypodium</jats:italic>genes evolve at a faster rate than those in other grasses. Sequence analysis reveals that rice and wheat have a ~2.1 kb deletion in their plastid genomes and this deletion must have occurred independently in both species.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>We demonstrate that BAC libraries can be used to sequence plastid, and likely other organellar, genomes. As expected, the<jats:italic>Brachypodium</jats:italic>chloroplast genome is very similar to those of other sequenced grasses. The phylogenetic analyses and the pattern of insertions and deletions in the chloroplast genome confirmed that<jats:italic>Brachypodium</jats:italic>is a close relative of the tribe Triticeae. Nevertheless, we show that some large indels can arise multiple times and may confound phylogenetic reconstruction.</jats:p></jats:sec>