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 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

From Single Cell to Plants: Mesophyll Protoplasts as a Versatile System for Investigating Plant Cell Reprogramming

Plants are sessile organisms that have a remarkable developmental plasticity, which ensures their optimal adaptation to environmental stresses. Plant cell totipotency is an extreme example of such plasticity, whereby somatic cells have the potential to form plants via direct shoot organogenesis or somatic embryogenesis in response to various exogenous and/or endogenous signals. Protoplasts provide one of the most suitable systems for investigating molecular mechanisms of totipotency, because they are e ectively single cell populations. In this review, we consider the current state of knowledge of the mechanisms that induce cell proliferation from individual, di erentiated somatic plant cells. We highlight initial explant metabolic status, ploidy level and isolation procedure as determinants of successful cell reprogramming. We also discuss the importance of auxin signalling and its interaction with stress-regulated pathways in governing cell cycle induction and further stages of plant cell totipotency

Plant cell and organism development

"Plants represent a unique and fascinating group of living organisms. By utilising photosynthesis, they are primary producers, which in one way or another are indispensable to the existence of heterotrophs, including humans. They also absorb carbon dioxide and release oxygen into the atmosphere, which is crucial to sustain not only the Earth’s biosphere but also the geosphere. As sessile organisms, plants had to develop unique strategies to deal with environmental stresses. These involve, inter alia, the presence of the cell wall, plant cell totipotency and a predisposition of plants to panorganismal polyploidisation, including interspecific or even intergeneric hybridisation followed by a stable restoration of sexual reproduction via allopolyploidisation." (fragm.

Plant cell and organism development 2.0

"In the editorial summarising the first edition of the Special Issue on “Plant Cell and Organism Development”, we listed the key features that make plants a unique and fascinating group of living organisms [1]. However, current climate changes are affecting plants in their natural environments and those that are under cultivation. Global warming will likely redefine many plant habitats regarding temperature, water availability, soil erosion, salinity and other abiotic and biotic parameters. The ever-growing human population and increasing food demand require more extensive or more efficient agriculture, all within the limited capacity of our planet. For those and many other reasons, comprehensive research on plants has become more vital than ever." [...] (fragm.

Ribosomal DNA loci derived from Brachypodium stacei are switched off for major parts of the life cycle of Brachypodium hybridum

Nucleolar dominance (ND) is an epigenetic phenomenon that occurs in some plant and animal allopolyploids and hybrids, whereby only one ancestral set of 35S rRNA genes retains the ability to form the nucleolus, whilst the rDNA loci derived from the other progenitor are transcriptionally silenced. Since there is substantial evidence that ND is regulated developmentally, this study focusses upon the establishment and/or maintenance of ND during different stages of development in the model grass allotetraploid, Brachypodium hybridum. Fluorescence in situ hybridisation with a 25S rDNA probe to 3-D cells shows that ND is present not only in root meristematic and differentiated cells of this species, but is also present in male meiocytes at prophase I, tetrads of microspores and different embryonic tissues. The inactive state of B. stacei-originated rDNA loci is confirmed by silver staining method. We show that only B. distachyon-derived 35S rDNA loci form a nucleolus/nucleoli in the aforementioned tissues, whereas B. stacei-like loci remain highly condensed and thus transcriptionally suppressed. The establishment of ND during earlier stages of B. hybridum embryo development cannot be ruled out. However, our proposal of gradual pseudogenisation of B. stacei-like loci in the evolution of the allotetraploid seems to be more likely

Defining the Genetic Basis of Plant-Endophytic Bacteria Interactions

Endophytic bacteria, which interact closely with their host, are an essential part of the plant microbiome. These interactions enhance plant tolerance to environmental changes as well as promote plant growth, thus they have become attractive targets for increasing crop production. Numerous studies have aimed to characterise how endophytic bacteria infect and colonise their hosts as well as conferring important traits to the plant. In this review, we summarise the current knowledge regarding endophytic colonisation and focus on the insights that have been obtained from the mutants of bacteria and plants as well as ‘omic analyses. These show how endophytic bacteria produce various molecules and have a range of activities related to chemotaxis, motility, adhesion, bacterial cell wall properties, secretion, regulating transcription and utilising a substrate in order to establish a successful interaction. Colonisation is mediated by plant receptors and is regulated by the signalling that is connected with phytohormones such as auxin and jasmonic (JA) and salicylic acids (SA). We also highlight changes in the expression of small RNAs and modifications of the cell wall properties. Moreover, in order to exploit the beneficial plant-endophytic bacteria interactions in agriculture successfully, we show that the key aspects that govern successful interactions remain to be defined

Stability and instability processes in the calli of Fagopyrum tataricum that have different morphogenic potentials

The morphogenic callus (MC) of Fagopyrum tataricum contains a large amount of flavonoids, especially rutin, and exhibits a high level of antioxidant activity. A non-morphogenic callus (NC) may appear on the surface of the MC after two to three years of cultivation and is then subjected to a consistently high level of oxidative stress. The elucidation of the molecular background of this instability is essential for gaining a better understanding of the somaclonal variation mechanisms in tissue cultures that have different morphogenic potentials. Thus, in this study we show that continuous oxidative stress in a NC might be connected with a rapid senescence process and as a result, in the upregulation of the genes that are connected with the telomere complexity, ethylene biosynthesis and the expression of DNA methyltransferases. Moreover, we analysed the presence of the hydroxyproline-rich glycoproteins in the calli and demonstrated the differences between the MC and NC. The LM2 antibody can be useful as a marker of the cells in the MC that are embryogenically determined, while the MAC207 antibody seems to be a positive marker of a MC as its signal was absent in the NC. This study also provides the first report on the effect of trichostatin A on the DNA methyltransferases and demethylases in a MC

Chromosome identification and reconstruction of evolutionary rearrangements in Brachypodium distachyon, B. stacei and B. hybridum

Background and Aims The 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 Genetics 49: 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 Results All 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. • Conclusions mcFISH-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

Hydroxyproline-Rich Glycoproteins as Markers of Temperature Stress in the Leaves of Brachypodium distachyon

Plants frequently encounter diverse abiotic stresses, one of which is environmental thermal stress. To cope with these stresses, plants have developed a range of mechanisms, including altering the cell wall architecture, which is facilitated by the arabinogalactan proteins (AGP) and extensins (EXT). In order to characterise the localisation of the epitopes of the AGP and EXT, which are induced by the stress connected with a low (4 C) or a high (40 C) temperature, in the leaves of Brachypodium distachyon, we performed immunohistochemical analyses using the antibodies that bind to selected AGP (JIM8, JIM13, JIM16, LM2 and MAC207), pectin/AGP (LM6) as well as EXT (JIM11, JIM12 and JIM20). The analyses of the epitopes of the AGP indicated their presence in the phloem and in the inner bundle sheath (JIM8, JIM13, JIM16 and LM2). The JIM16 epitope was less abundant in the leaves from the low or high temperature compared to the control leaves. The LM2 epitope was more abundant in the leaves that had been subjected to the high temperatures. In the case of JIM13 and MAC207, no changes were observed at the di erent temperatures. The epitopes of the EXT were primarily observed in the mesophyll and xylem cells of the major vascular bundle (JIM11, JIM12 and JIM20) and no correlation was observed between the presence of the epitopes and the temperature stress. We also analysed changes in the level of transcript accumulation of some of the genes encoding EXT, EXT-like receptor kinases and AGP in the response to the temperature stress. In both cases, although we observed the upregulation of the genes encoding AGP in stressed plants, the changes were more pronounced at the high temperature. Similar changes were observed in the expression profiles of the EXT and EXT-like receptor kinase genes. Our findings may be relevant for genetic engineering of plants with increased resistance to the temperature stress

Organ and tissue-specific localisation of selected cell wall epitopes in the zygotic embryo of Brachypodium distachyon

The plant cell wall shows a great diversity regarding its chemical composition, which may vary significantly even during different developmental stages. In this study, we analysed the distribution of several cell wall epitopes in embryos of Brachypodium distachyon (Brachypodium). We also described the variations in the nucleus shape and the number of nucleoli that occurred in some embryo cells. The use of transmission electron microscopy, and histological and immunolocalisation techniques permitted the distribution of selected arabinogalactan proteins, extensins, pectins, and hemicelluloses on the embryo surface, internal cell compartments, and in the context of the cell wall ultrastructure to be demonstrated. We revealed that the majority of arabinogalactan proteins and extensins were distributed on the cell surface and that pectins were the main component of the seed coat and other parts, such as the mesocotyl cell walls and the radicula. Hemicelluloses were localised in the cell wall and outside of the radicula protodermis, respectively. The specific arrangement of those components may indicate their significance during embryo development and seed germination, thus suggesting the importance of their protective functions. Despite the differences in the cell wall composition, we found that some of the antibodies can be used as markers to identify specific cells and the parts of the developing Brachypodium embryo