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Poaceae also called Grasses are an important botanical family consisting in nearly 12,000 species in over 700 genres including cereals. This family is of major economic interest because it comprises cereals that are among the most important crops for human and animal nutrition. This family has been extensively studied in comparative genomics since the 1990s and showed a high degree of gene conservation among species since they diverged from a common ancestor.

With the sequencing of Brachypodium distachyon in 2009, we performed an analysis of its genome by the identification of twelve synteny blocks with the sequenced genomes of rice, sorghum and maize and seven duplications blocks shared with these last grass species. These data allowed us to suggest the five chromosomes of Brachypodium are from the common ancestor composed of twelve chromosomes and having undergone seven fusions during the evolution. This work allowed us to confirm a possible grass ancestor with five chromosomes carrying almost 10,000 genes with a size of 35Mb.

Then, based on these comparative genomics results, we studied more particularly the evolution of different families of microRNAs (miRNAs). The comparison of non-coding RNA from rice, sorghum, maize and Brachypodium showed conservation into this family for the grass species with 50% of orthologs and 20% of paralogs. Based on the paleogenomics results, we proposed an evolutionary scenario of miRNA genes, which supports the hypothesis of an ancient origin of this gene silencing mechanism in plants.

Beyond the fundamental knowledge generated on the evolution of grass genomes during this PhD, these results have potential applications in breeding, for example with the possibility to identify COS (Conserved Orthologous Set) molecular markers. Such COS markers have been used for the study of agronomic traits in species not completely sequenced as wheat.