Reconstructing the evolution of Brachypodium genomes using comparative chromosome painting.

Brachypodium distachyon is a model for the temperate cereals and grasses and
has a biology, genomics infrastructure and cytogenetic platform fit for purpose. It is a member of a genus with fewer than 20 species, which have different genome sizes, basic chromosome numbers and ploidy levels. The phylogeny and
interspecific relationships of this group have not to date been resolved by sequence comparisons and karyotypical studies. The aims of this study are not only to reconstruct the evolution of Brachypodium karyotypes to resolve the phylogeny, but also to highlight the mechanisms that shape the evolution of grass genomes. This was achieved through the use of comparative chromosome painting (CCP) which hybridises fluorescent, chromosome-specific probes derived from B. distachyon to homoeologous meiotic chromosomes of its close relatives. The study included five diploids (B. distachyon 2n510, B. sylvaticum 2n518, B. pinnatum 2n516; 2n518, B. arbuscula 2n518 and B. stacei 2n520) three allotetraploids (B. pinnatum 2n528, B. phoenicoides 2n528 and B. hybridum 2n530), and two species of unknown ploidy (B. retusum 2n538 and B. mexicanum 2n540). On the basis of the patterns of hybridisation and incorporating published data, we propose twoalternative, but similar, models of karyotype evolution in the genus Brachypodium. According to the first model, the extant genome of B. distachyon derives from B. mexicanum or B. stacei by several rounds of descending dysploidy, and the other diploids evolve from B. distachyon via ascending dysploidy. The allotetraploids arise by interspecific hybridisation and chromosome doubling between B. distachyon and other diploids. The second model differs from the first insofar as it incorporates an intermediate 2n518 species between the B. mexicanum or B. stacei progenitors and the dysploidic B. distachyon.