Abstract
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 2n = 10, B. sylvaticum 2n = 18, B. pinnatum 2n = 16; 2n = 18, B. arbuscula 2n = 18 and B. stacei 2n = 20) three allotetraploids (B. pinnatum 2n = 28, B. phoenicoides 2n = 28 and B. hybridum 2n = 30), and two species of unknown ploidy (B. retusum 2n = 38 and B. mexicanum 2n = 40). On the basis of the patterns of hybridisation and incorporating published data, we propose two alternative, 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 2n = 18 species between the B. mexicanum or B. stacei progenitors and the dysploidic B. distachyon.
Highlights
The Poaceae is one of the largest families of flowering plants, with over 10,000 species spread widely throughout the earth in different climatic zones, and is an important component of most land ecosystems
Pools of 142, 55, 96, 59 and 23 low-repeat BAC clones derived from B. distachyon chromosomes (Bd1–B. distachyon chromosome 5 (Bd5)) were used for comparative chromosome painting (CCP) of homoeologous chromosomes of both diploid and allotetraploid Brachypodium species, as well as B. mexicanum and B. retusum whose ploidy status is unclear
B. distachyon chromosomes B. distachyon chromosome 1 (Bd1), B. distachyon chromosome 3 (Bd3) and B. distachyon chromosome 4 (Bd4) were derived from two nested insertions of six entire ancestral chromosomes into the centromeric regions of, respectively, three chromosomes, whilst B. distachyon chromosome 2 (Bd2) was derived from one similar insertion of one entire ancestral chromosome into another one
Summary
The Poaceae is one of the largest families of flowering plants, with over 10,000 species spread widely throughout the earth in different climatic zones, and is an important component of most land ecosystems. In comparison with other groups of organisms, plant nuclear genomes show exceptional plasticity in terms of DNA contents, and number, size and shape of chromosomes. These features are subject to evolutionary changes, and may differ greatly even amongst closely related species [2]. Most of the information about the evolutionary forces which have shaped the structure of extant grass genomes comes from in silico archeogenomic studies of DNA sequences [4] Recent technological advances, such as high-throughput DNA sequencing, have enabled high-resolution comparative genomics and bioinformatic analyses. More than 15 plant genomes have currently been sequenced which offers the opportunity to compare the organisation of modern genomes and to infer their evolutionary history from in silico ‘reconstruction’ of their putative ancestors [4, 5]
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