Study of excess manganese stress response highlights the central role of manganese exporter Mnx for holding manganese homeostasis in the cyanobacterium sp. PCC 6803.

Cellular levels of the essential micronutrient manganese (Mn) need to be carefully balanced within narrow borders. In cyanobacteria, a sufficient Mn supply is critical for ensuring the function of the oxygen-evolving complex as the central part of the photosynthetic machinery. However, Mn accumulation is fatal for the cells.

Transcriptome dynamics in developing leaves from C and C Flaveria species.

C species have evolved more than 60 times independently from C ancestors. This multiple and parallel evolution of the complex C trait suggests common underlying evolutionary mechanisms, which could be identified by comparative analysis of closely related C and C species. Efficient C function depends on a distinctive leaf anatomy that is characterised by enlarged, chloroplast-rich bundle sheath cells and narrow vein spacing.

Circularly assembled genome sequences of sp. strain MM231 and MM232, isolated from a pond at Bielefeld University campus.

Photosynthetic organisms often interact with heterotrophic microbes. We here report the complete genome sequences of the bacterial strains sp. MM231 and MM232.

Complete genome sequences of sp. strain MM2321 and sp. strain MM2322, isolated from a sand sample in Harsewinkel, Germany.

We cultivated bacteria contained in a sandy soil sample, isolated DNA from a single bacterial colony, and assembled from genomic reads the full genome sequence of and strains, termed MM2321 and MM2322. Besides the genome sequences, the phylogenetic classifications of both strains are reported.

How does plant chemodiversity evolve? Testing five hypotheses in one population genetic model.

Plant chemodiversity, the diversity of plant-specialized metabolites, is an important dimension of biodiversity. However, there are so far few mathematical models to test verbal hypotheses on how chemodiversity evolved. Here, we develop such a model to test predictions of five hypotheses: the 'fluctuating selection hypothesis', the 'dominance reversal hypothesis', the interaction diversity hypothesis, the synergy hypothesis, and the screening hypothesis.

Leaf transcriptomes from C3, C3-C4 intermediate, and C4Neurachne species give insights into C4 photosynthesis evolution.

The C4 photosynthetic pathway is hypothesized to have evolved from the ancestral C3 pathway through progressive changes in leaf anatomy and biochemistry with extant C3-C4 photosynthetic intermediate species representing phenotypes between species demonstrating full C3 and full C4 states. The Australian endemic genus Neurachne is the only known grass group that contains distinct, closely related species that carry out C3, C3-C4 intermediate, or C4 photosynthesis. To explore and understand the molecular mechanisms underlying C4 photosynthesis evolution in this genus, leaf transcriptomes were generated from two C3, three photosynthetic intermediate (proto-Kranz, C2-like, and C2), and two C4Neurachne species.

Using Publicly Available RNA-seq Data for Expression Analysis of Genes of Interest.

RNA-seq data in publicly available repositories enable the efficient reanalysis of transcript abundances in existing experiments. Graphical user interfaces usually only allow the visual inspection of a single gene and of predefined experiments. Here, we describe how experiments are selected from the Sequence Read Archive or the European Nucleotide Archive, how data is efficiently mapped onto a reference transcriptome, and how global transcript abundances and patterns are inspected.

The crane fly glycosylated triketide δ-lactone cornicinine elicits akinete differentiation of the cyanobiont in aquatic Azolla fern symbioses.

The restriction of plant-symbiont dinitrogen fixation by an insect semiochemical had not been previously described. Here we report on a glycosylated triketide δ-lactone from Nephrotoma cornicina crane flies, cornicinine, that causes chlorosis in the floating-fern symbioses from the genus Azolla. Only the glycosylated trans-A form of chemically synthesized cornicinine was active: 500 nM cornicinine in the growth medium turned all cyanobacterial filaments from Nostoc azollae inside the host leaf-cavities into akinetes typically secreting CTB-bacteriocins.

The Brassica napus boron deficient inflorescence transcriptome resembles a wounding and infection response.

Oilseed rape and other crops of Brassica napus have a high demand for boron (B). Boron deficiencies result in the inhibition of root growth, and eventually premature flower abortion. Understanding the genetic mechanisms underlying flower abortion in B-limiting conditions could provide the basis to enhance B-efficiency and prevent B-deficiency-related yield losses.

Whole-Genome Sequence of Paenibacillus marchantiae Isolated from the Liverwort Marchantia polymorpha subsp. Ecotype BoGa.

The bacterium Paenibacillus marchantiae was isolated from male plants of the liverwort Marchantia polymorpha subsp. ecotype BoGa. Here, we report on the complete genome sequence generated from long Nanopore reads.

Whole-Genome Sequence of sp. , Isolated from Riccia fluitans.

Here, we present the Nanopore-only genome sequence of sp. . It was isolated from Riccia fluitans ecotype BoGa-3 and its source was Botanical Garden Osnabrück (Germany).

The Gynandropsis gynandra genome provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae.

Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C4 photosynthesis due to its evolutionary proximity to C3 Arabidopsis (Arabidopsis thaliana). Here, we present the genome sequence of G. gynandra, anchored onto 17 main pseudomolecules with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models.

Complete Genome Sequences of Pseudomonas sp. Strains MM223 and MM227 and sp. Strain MM224, Isolated from a Pond Edge in Bielefeld, Germany.

Pseudomonas sp. strain MM223, Pseudomonas sp. strain MM227, and sp.

The Full Genome Sequences of Pseudomonas sp. Strain MM221 and sp. Strain MM222, Isolated from a Meadow in Bielefeld, Germany.

The bacterial strains Pseudomonas sp. strain MM221 and sp. strain MM222 were isolated from a sandy soil sample.

Evolutionary implications of C2 photosynthesis: how complex biochemical trade-offs may limit C4 evolution.

The C2 carbon-concentrating mechanism increases net CO2 assimilation by shuttling photorespiratory CO2 in the form of glycine from mesophyll to bundle sheath cells, where CO2 concentrates and can be re-assimilated. This glycine shuttle also releases NH3 and serine into the bundle sheath, and modelling studies suggest that this influx of NH3 may cause a nitrogen imbalance between the two cell types that selects for the C4 carbon-concentrating mechanism. Here we provide an alternative hypothesis outlining mechanisms by which bundle sheath NH3 and serine play vital roles to not only influence the status of C2 plants along the C3 to C4 evolutionary trajectory, but to also convey stress tolerance to these unique plants.

Local DNA shape is a general principle of transcription factor binding specificity in Arabidopsis thaliana.

Understanding gene expression will require understanding where regulatory factors bind genomic DNA. The frequently used sequence-based motifs of protein-DNA binding are not predictive, since a genome contains many more binding sites than are actually bound and transcription factors of the same family share similar DNA-binding motifs. Traditionally, these motifs only depict sequence but neglect DNA shape.

Engineering of Crassulacean Acid Metabolism.

Crassulacean acid metabolism (CAM) has evolved from a C ground state to increase water use efficiency of photosynthesis. During CAM evolution, selective pressures altered the abundance and expression patterns of C genes and their regulators to enable the trait. The circadian pattern of CO fixation and the stomatal opening pattern observed in CAM can be explained largely with a regulatory architecture already present in C plants.

Comparative Transcriptomics of Lowland Rice Varieties Uncovers Novel Candidate Genes for Adaptive Iron Excess Tolerance.

Iron (Fe) toxicity is a major challenge for plant cultivation in acidic waterlogged soil environments, where lowland rice is a major staple food crop. Only few studies have addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance. Out of 16 lowland rice varieties, we identified a pair of contrasting lines, Fe-tolerant Lachit and -susceptible Hacha.

The Arabidopsis condensin CAP-D subunits arrange interphase chromatin.

Condensins are best known for their role in shaping chromosomes. Other functions such as organizing interphase chromatin and transcriptional control have been reported in yeasts and animals, but little is known about their function in plants. To elucidate the specific composition of condensin complexes and the expression of CAP-D2 (condensin I) and CAP-D3 (condensin II), we performed biochemical analyses in Arabidopsis.

Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia.

Bacteria occupy all major ecosystems and maintain an intensive relationship to the eukaryotes, developing together into complex biomes (i.e., phycosphere and rhizosphere).

The transcription factor WRKY22 is required during cryo-stress acclimation in Arabidopsis shoot tips.

Storage of meristematic tissue at ultra-low temperatures offers a mean to maintain valuable genetic resources from vegetatively reproduced plants. To reveal the biology underlying cryo-stress, shoot tips of the model plant Arabidopsis thaliana were subjected to a standard preservation procedure. A transcriptomic approach was taken to describe the subsequent cellular events which occurred.

Molecular plant responses to combined abiotic stresses put a spotlight on unknown and abundant genes.

Environmental stresses such as drought, heat, and salinity limit plant development and agricultural productivity. While individual stresses have been studied extensively, much less is known about the molecular interaction of responses to multiple stresses. To address this problem, we investigated molecular responses of Arabidopsis to single, double, and triple combinations of salt, osmotic, and heat stresses.

Evolution of C4 photosynthesis predicted by constraint-based modelling.

Constraint-based modelling (CBM) is a powerful tool for the analysis of evolutionary trajectories. Evolution, especially evolution in the distant past, is not easily accessible to laboratory experimentation. Modelling can provide a window into evolutionary processes by allowing the examination of selective pressures which lead to particular optimal solutions in the model.

Functional evolution of nodulin 26-like intrinsic proteins: from bacterial arsenic detoxification to plant nutrient transport.

Nodulin 26-like intrinsic proteins (NIPs) play essential roles in transporting the nutrients silicon and boron in seed plants, but the evolutionary origin of this transport function and the co-permeability to toxic arsenic remains enigmatic. Horizontal gene transfer of a yet uncharacterised bacterial AqpN-aquaporin group was the starting-point for plant NIP evolution. We combined intense sequence, phylogenetic and genetic context analyses and a mutational approach with various transport assays in oocytes and plants to resolve the transorganismal and functional evolution of bacterial and algal and terrestrial plant NIPs and to reveal their molecular transport specificity features.