Abstract
Background and AimsThe Brachypodium genus represents a useful model system to study grass genome organization. Palaeogenomic analyses (e.g. Murat F, Armero A, Pont C, Klopp C, Salse J. 2017. Reconstructing the genome of the most recent common ancestor of flowering plants. Nature Genetics49: 490–496) have identified polyploidization and dysploidy as the prime mechanisms driving the diversity of plant karyotypes and nested chromosome fusions (NCFs) crucial for shaping grass chromosomes. This study compares the karyotype structure and evolution in B. distachyon (genome Bd), B. stacei (genome Bs) and in their putative allotetraploid B. hybridum (genomes BdBs).Methods Brachypodium chromosomes were measured and identified using multicolour fluorescence in situ hybridization (mcFISH). For higher resolution, comparative chromosome barcoding was developed using sets of low-repeat, physically mapped B. distachyon-derived bacterial artificial chromosome (BAC) clones.Key ResultsAll species had rather small chromosomes, and essentially all in the Bs genome were morphometrically indistinguishable. Seven BACs combined with two rDNA-based probes provided unambiguous and reproducible chromosome discrimination. Comparative chromosome barcoding revealed NCFs that contributed to the reduction in the x = 12 chromosome number that has been suggested for the intermediate ancestral grass karyotype. Chromosome Bd3 derives from two NCFs of three ancestral chromosomes (Os2, Os8, Os10). Chromosome Bs6 shows an ancient Os8/Os10 NCF, whilst Bs4 represents Os2 only. Chromosome Bd4 originated from a descending dysploidy that involves two NCFs of Os12, Os9 and Os11. The specific distribution of BACs along Bs9 and Bs5, in both B. stacei and B. hybridum, suggests a Bs genome-specific Robertsonian rearrangement.ConclusionsmcFISH-based karyotyping identifies all chromosomes in Brachypodium annuals. Comparative chromosome barcoding reveals rearrangements responsible for the diverse organization of Bd and Bs genomes and provides new data regarding karyotype evolution since the split of the two diploids. The fact that no chromosome rearrangements were observed in B. hybridum compared with the karyotypes of its phylogenetic ancestors suggests prolonged genome stasis after the formation of the allotetraploid.
Highlights
Brachypodium is a small genus of temperate grasses that belongs to the Brachypodieae tribe within the Pooideae subfamily
Comparative chromosome barcoding revealed nested chromosome fusions (NCFs) that contributed to the reduction in the x = 12 chromosome number that has been suggested for the intermediate ancestral grass karyotype
Lusinska et al — Karyotype structure and evolution in Brachypodium annuals rapidly promoted its use in diverse research programmes and ensured a continuous growth of various experimental tools and resources, such as large germplasm collections, sequenced (IBI, 2010) and resequenced (Gordon et al, 2014) genomes, cDNA libraries (Gordon et al, 2014), high-coverage genomic DNA libraries of ordered bacterial artificial chromosome (BAC) clones (Febrer et al, 2010) and efficient mutagenesis and transformation protocols (Vogel and Hill, 2008)
Summary
Brachypodium is a small genus of temperate grasses that belongs to the Brachypodieae tribe within the Pooideae subfamily. The close relationship of B. distachyon with economically important temperate cereals and forage grasses combined with many other favourable attributes, such as its very small nuclear genome, simple growth requirements, small stature and rapid annual life cycle, prompted Draper et al (2001) to propose it as a model organism. This species was initially used to facilitate functional genomics analyses in grasses, other useful features by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Lusinska et al — Karyotype structure and evolution in Brachypodium annuals rapidly promoted its use in diverse research programmes and ensured a continuous growth of various experimental tools and resources, such as large germplasm collections, sequenced (IBI, 2010) and resequenced (Gordon et al, 2014) genomes, cDNA libraries (Gordon et al, 2014), high-coverage genomic DNA libraries of ordered bacterial artificial chromosome (BAC) clones (Febrer et al, 2010) and efficient mutagenesis and transformation protocols (Vogel and Hill, 2008)
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