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Multiple founder events explain the genetic diversity and structure of the model allopolyploid grass Brachypodium hybridum in the Iberian Peninsula hotspot

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Background and aims: It is accepted that contemporary allopolyploid species have originated recurrently, but very few cases have been documented using multiple natural formations of the same species. To extend our knowledge, we have investigated the multiple origins, genetic variation, and structure of the allotetraploid grass Brachypodium hybridum with respect to its progenitor diploid species B. distachyon (D genome) and B. stacei (S genome). For this, our primary focus is the Iberian Peninsula, an evolutionary hotspot for the genus Brachypodium. Methods: We analysed 342 B. hybridum individuals from 36 populations using 10 nuclear SSR loci and two plastid loci. The B. hybridum genetic profiles were compared with those previously reported for B. stacei and B. distachyon. In addition, phylogenetic analysis of the plastid data was performed for a reduced subset of individuals. Key results: The nuclear SSR genetic analysis detected medium to high genetic diversity, with a strong south-to-north genetic structure cline, and a high selfing rate in B. hybridum. Comparative genetic analysis showed a close relatedness of current B. hybridum D allelic profiles with those of B. distachyon, but a lack of similarity with those of B. stacei, suggesting another B. stacei source for the B. hybridum S alleles. Plastid analysis detected three different bidirectional allopolyploidization events: two involved distinct B. distachyon-like ancestors and one involved a B. stacei-like ancestor. The Southeastern (SE) Iberian Peninsula B. hybridum populations were more genetically diverse and could have originated from at least two hybridization events whereas Northeaster-Northwestern (NE-NW) Iberian Peninsula B. hybridum populations were less diverse and may have derived from at least one hybridization event. Conclusions: The genetic and evolutionary evidence support the plausible in situ origin of the SE and northern Iberian Peninsula B. hybridum allopolyploids from their respective local B. distachyon and unknown B. stacei ancestors. The untapped multiple origins and genetic variation detected in these B. hybridum populations opens the way to future evolutionary analysis of allopolyploid formation and genomic dominance and expression in the B. hybridum - B. distachyon - B. stacei grass model complex.

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... Recent phylogenetic studies have suggested that allopolyploidy has been a prevalent speciation mechanism in Brachypodium (Catalán et al. 2016;Díaz-Pérez et al. 2018) and, indeed, that most allopolyploid Brachypodium species likely resulted from crosses of dysploid progenitor species that had different basic chromosome numbers (Betekhtin et al. 2014;Díaz-Pérez et al. 2018). The best-known case is the annual allotetraploid B. hybridum (2n=30, x=10+5), which was derived from the cross and subsequent genome doubling of the diploid B. stacei-type (2n=20, x=10) and B. distachyon-type (2n=10, x=5) progenitors López-Álvarez et al. 2012;Catalán et al. 2014;Shiposha et al. 2019;Gordon et al. 2020). The re-creation of a stable synthetic allotetraploid that phenotypically resembles the natural B. hybridum corroborated the allopolyploid origin of this neopolyploid species (Dinh Thi et al. 2016). ...
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... Previous studies included single samples of this lineage, all originating from Sicily (Gordon et al., 2020;Tyler et al., 2016). We found this lineage to be present yet rare throughout Italy, in two instances growing on the very same meadow as plants belonging to lineage A. Recently a similar situation has been described for B. hybridum, where individuals with a common ancestor more than one million years ago coexist in the same place (Gordon et al., 2020;Shiposha et al., 2020). (Ossowski et al., 2010); it is at the fast end of the spectrum as it reflects the accumulation of mutations before purifying selection had a chance to remove them (Ho et al., 2011). ...
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The scientific presentations at the First International Brachypodium Conference (abstracts available at http://www.brachy2013.unimore.it) are evidence of the widespread adoption of Brachypodium distachyon as a model system. Furthermore, the wide range of topics presented (genome evolution, roots, abiotic and biotic stress, comparative genomics, natural diversity, and cell walls) demonstrates that the Brachypodium research community has achieved a critical mass of tools and has transitioned from resource development to addressing biological questions, particularly those unique to grasses.
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Contents Summary334I.Introduction335II.A challenge for the Brachypodium Tool Box: the legacy of cereal domestication335III.Opening the Brachypodium Tool Box: what is Brachypodium?336IV.The Brachypodium Tool Box: where are we now?337V.Targets for the Brachypodium Tool Box: key traits342VI.Whence for the Brachypodium Tool box? Primus inter pares?344 Acknowledgements345 References345SummaryIt is now a decade since Brachypodium distachyon (Brachypodium) was suggested as a model species for temperate grasses and cereals. Since then transformation protocols, large expressed sequence tag (EST) databases, tools for forward and reverse genetic screens, highly refined cytogenetic probes, germplasm collections and, recently, a complete genome sequence have been generated. In this review, we will describe the current status of the Brachypodium Tool Box and how it is beginning to be applied to study a range of biological traits. Further, as genomic analysis of larger cereals and forage grasses genomes are becoming easier, we will re-evaluate Brachypodium as a model species. We suggest that there remains an urgent need to employ reverse genetic and functional genomic approaches to identify the functionality of key genetic elements, which could be employed subsequently in plant breeding programmes; and a requirement for a Pooideae reference genome to aid assembling large pooid genomes. Brachypodium is an ideal system for functional genomic studies, because of its easy growth requirements, small physical stature, and rapid life cycle, coupled with the resources offered by the Brachypodium Tool Box.
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Mediterranean annual grasses have invaded California and have replaced vast areas of native grassland. One of these invasive grasses is Brachypodium distachyon, a new model species for the grasses with extensive genomic resources and a nearly completed genome sequence. This study shows that the level of genetic variation in invaded California grasslands is lower compared to the native range in Eurasia. The invaded regions are characterized by highly differentiated populations of B. distachyon isolated by distance, most likely as a result of founder effects and a dearth of outcrossing events. EXP6 and EXP10 encoding alpha-expansins responsible for rapid growth, and AGL11 and AGL13 encoding proteins involved in vegetative phase regulation, appear to be under purifying selection with no evidence for local adaptation. Our data show that B. distachyon has diverged only recently from related Brachypodium species and that tetraploidization might have been as recent as a few thousand years ago. Observed low genetic variation in EXP10 and AGL13 appears to have been present in Eurasia before tetraploidization, potentially as a result of strong selective pressures on advantageous mutations, which are most likely responsible for its fast growth and rapid completion of its life cycle.
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The geology and climate of the western Mediterranean area were strongly modified during the Late Tertiary and the Quaternary. These geological and climatic events are thought to have induced changes in the population histories of plants in the Iberian Peninsula. However, fine-scale genetic spatial architecture across western Mediterranean steppe plant refugia has rarely been investigated. A population genetic analysis of amplified fragment length polymorphism variation was conducted on present-day, relict populations of Ferula loscosii (Apiaceae). This species exhibits high individual/population numbers in the middle Ebro river valley and, according to the hypothesis of an abundant-centre distribution, these northern populations might represent a long-standing/ancestral distribution centre. However, our results suggest that the decimated southern and central Iberian populations are more variable and structured than the northeastern ones, representing the likely vestiges of an ancestral distribution centre of the species. Phylogeographical analysis suggests that F. loscosii likely originated in southern Spain and then migrated towards the central and northeastern ranges, further supporting a Late Miocene southern-bound Mediterranean migratory way for its oriental steppe ancestors. In addition, different glacial-induced conditions affected the southern and northern steppe Iberian refugia during the Quaternary. The contrasting genetic homogeneity of the Ebro valley range populations compared to the southern Iberian ones possibly reflects more severe bottlenecks and subsequent genetic drift experienced by populations of the northern Iberia refugium during the Pleistocene, followed by successful postglacial expansion from only a few founder plants.