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

Author
item Bortiri, Esteban
item COLEMAN-DERR, DEVIN - UC DAVIS
item Lazo, Gerard
item Anderson, Olin
item Gu, Yong

Submitted to: BMC Research Notes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/18/2008
Publication Date: 7/31/2008
Citation: Bortiri, E., Coleman-Derr, D., Lazo, G.R., Anderson, O.D., Gu, Y.Q. 2008. The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes. BMC Research Notes. 1:61.

Interpretive Summary: Brachypodium has been emerged as a new model for functional genomics of cereals crop due to its close relationship with Triticeae crops, small genome size, and other desirable attributes. Chloroplasts are dynamic organelles of within the plant cells that house the photosynthetic apparatus. In addition to photosynthesis, other important metabolic activities take place within chloroplasts including the production of starch, certain amino acid and lipid, some of the colorful pigments in flowers, vitamins and several key aspects of sulfur and nitrogen metabolism. Chloroplasts possess their won genome and a full machinery to express their genetic information. Chloroplast bioengineering offers a number of advantages over nuclear transformation including high levels of transgene expression and gene containment. In this report, the entire chloroplast genome of Brachypodium was sequenced and analyzed by comparing other grass chloroplast genomes. The sequence information of the Brachypodium genome provides resources and facilitates chloroplast-related research for crop improvement.

Technical Abstract: 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. Brachypodium distachyon, a close relative of those cereals has recently emerged as a model for grass functional genomics. Sequencing of the nuclear and organelle genomes of Brachypodium is one of the first steps towards making this species available as a tool for researchers interested in cereals biology. The chloroplast genome of Brachypodium distachyon was sequenced by a combinational approach using BAC end sequences 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 Brachypodium 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. The phylogenetic analyses and the pattern of insertions and deletions in the chloroplast genome confirmed that Brachypodium is a close relative of the tribe Triticeae. With its small genome, short life cycle, and high efficiency of transformation, Brachypodium is poised to become an important model organism for temperate grasses including important cereal and bioenergy crops. Sequencing of the Brachypodium genome will enable researchers conduct studies on broad biological topics ranging from comparative genomics among grass species to cell wall composition and biomass accumulation.