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

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 *1.0 Mb 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 (*9 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.

Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces

“…Gene islands reflect inhomogeneous expansion of the genome and are not found in compact genome species such as rice, Arabidopsis thaliana (Arabidopsis Genome Initiative, 2000), and Brachypodium (Huo et al, 2009). They are, however, common features of large and repetitive genomes, such as the 2.5 Gb maize genome.…”

Prolamin storage proteins and alloploidy in wild populations of the small grass Brachypodium distachyon (L.) P. Beauv.

“…Various molecular phylogenetic analyses have shown that Brachypodium diverged from the ancestral stock of Pooideae immediately prior to the radiation of the modern ''core pooids'' (Catalan et al 1997;Catalan and Olmstead 2000;Draper et al 2001). It is also ancestral, but equally related to, Avena and Triticum (Kellogg 2001;Huo et al 2009). …”

Brachypodium distachyon as a model plant in wheat rust research

“…In both plant species, larger rust infection sites were proven to be able to suppress callose production in weak or old cells, supporting the theory of the presence of mechanistic overlap between the Brachypodium response to cereal rust infection and the wheat basal defence response. The data also shows the absence of change in salicylic acid level in Brachypodium leaf upon artificial infection with Puccinia subtypes [16][17][18].…”