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Title: Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat

Author
item HUO, NAXIN - University Of California
item Vogel, John
item Lazo, Gerard
item YOU, FRANK - University Of California
item MA, YAQIN - University Of California
item Patfield, Stephanie
item DVORAK, JAN - University Of California
item Anderson, Olin
item LUO, MING-CHENG - University Of California
item Gu, Yong

Submitted to: Plant Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/7/2009
Publication Date: 1/29/2009
Citation: Huo, N., Vogel, J.P., Lazo, G.R., You, F., Ma, Y., McMahon, S.A., Dvorak, J., Anderson, O.D., Luo, M., Gu, Y.Q. 2009. Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat. Plant Molecular Biology. 70: 47-61.

Interpretive Summary: Brachypodium becomes a new model system for plant research because of its compact genome and a range of biological features. To further evaluate the utility of Brachypodium for crop research, we compared large genomic segments of the Brachypodium genome with the corresponding regions in wheat and rice. It was found that Brachypodium and wheat are more closely related than either to rice, suggesting that Brachypodium will be useful in understanding the structure and evolution of wheat genome and aid in cloning of important wheat genes for crop improvement.

Technical Abstract: Brachypodium distachyon (Brachypodium) has been recently recognized as an emerging model system for both comparative and functional genomics in grass species. In this study, 55,221 repeat masked Brachypodium BAC end sequences (BES) were used for comparative analysis against the 12 rice pseudomolecules. The analysis revealed that ~ 26.4% of BES have significant matches with the rice genome and 82.4% of the matches were homologous to known genes. Further analysis of paired-end BES and ~1.0Mb sequences from nine selected BACs proved to be useful in revealing conserved regions and regions that have undergone considerable genomic changes. Differential gene amplification, insertions/deletions and inversions appeared to be the common evolutionary events that caused variations of microcolinearity at different orthologous genomic regions. It was found that ~17% of genes in the two genomes are not colinear in the orthologous regions. Analysis of BAC sequences also revealed higher gene density (~ 8 kb/gene) and lower repeat DNA content (~13.1%) in Brachypodium when compared to the orthologous rice regions, consistent with the smaller size of the Brachypodium genome. The 119 annotated Brachypodium genes were BLASTN compared against the wheat EST database and deletion bin mapped wheat ESTs. About 77% of the genes retrieved significant matches in the EST database, while 9.2% matched to the bin mapped ESTs. In some cases, genes in single Brachypodium BACs matched to multiple ESTs that were mapped to the same deletion bins, suggesting that the Brachypodium genome will be useful for ordering wheat ESTs within the deletion bins and developing specific markers at targeted regions in the wheat genome.