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Greiner, S.

Publications and source records attributed to Greiner, S..

10 recordsLinked to original sources

Insights into plant-part specific N2O production in roots and shoots of chicory (C. intybus) using stable isotope labelling

O_LINitrous oxide (N2O) substantially contributes to climate change and stratospheric ozone degradation, yet large uncertainties in its global budget indicate unknown or overlooked sources. Increasing evidence suggests that plants may also produce N2O, though the underlying mechanisms and pathways remain poorly constrained. C_LIO_LITo examine whether plants can form N2O under sterile conditions and to assess the contribution of different plant parts, we applied a novel 15N stable isotope labelling approach using sterile Cichorium intybus root and shoot cultures incubated separately under light and dark conditions. C_LIO_LIAll root/shoot cultures showed N2O formation under dark conditions, whereas shoots under light showed reduced or even uptake of N2O, indicating photosynthetically driven suppression of formation pathways or simultaneous internal degradation of N2O. C_LIO_LIIsotopic analyses revealed distinct formation pathways: roots supplemented with 15NO3- showed position-specific 15N enrichment consistent with N2O formation via nitric oxide as an intermediate, linking root-derived N2O to NO3- reduction. In contrast, root/shoot incubations with 15N-NH4+ supplementation and shoots in darkness emitted N O without clear 15N enrichment suggesting alternative formation pathways independent of these compounds. Our isotopic labelling approach powerfully disentangled N2O formation mechanisms yet highlights necessary further exploration of plant N2O cycling to improve global budgets and enable potential mitigation strategies. C_LI

biochemistry↗

Whole-Genome Sequencing of the Wild Barley Diversity Collection: A Resource for Identifying and Exploiting Genetic Variation for Cultivated Barley Improvement

To exploit allelic variation in Hordeum vulgare subsp. spontaneum, the Wild Barley Diversity Collection was evaluated for several agronomic traits and subjected to paired-end Illumina sequencing at [~]9X depth, generating 109.5 million single nucleotide polymorphisms after alignment to the Morex V3 assembly. A genome-wide association study of lemma color identified one marker-trait association (MTA) on chromosome 1HL close to HvBlp, the cloned gene controlling black lemma. Four MTAs were identified for stem rust resistance: one co-locating to the complex RMRL1-RMRL2 locus on 5HL, and three novel loci on 1HS, 1HL, and 5HL. Six MTAs for days to heading (DTH) on vernalized plants were identified on all chromosomes except 1H and 6H. Two MTAs for DTH on non-vernalized plants were identified on chromosomes 1HL and 2HS. All MTAs for DTH were novel. The whole genome sequence data described herein will facilitate the identification and utilization of new alleles for barley improvement.

genomics↗

Correction of frameshift mutations in the atpB gene by translational recoding in chloroplasts of Oenothera and tobacco.

Translational recoding, also known as ribosomal frameshifting, is a process that causes ribosome slippage along the messenger RNA, thereby changing the amino acid sequence of the synthesized protein. Whether the chloroplast employs recoding, is unknown. I-iota, a plastome mutant of Oenothera (evening primrose), carries a single adenine insertion in an oligoA stretch of atpB (encoding a {beta}-subunit of the ATP synthase). The mutation is expected to cause synthesis of a truncated, non-functional protein. We report that a full-length AtpB protein is detectable in I-iota leaves, suggesting operation of a recoding mechanism. To characterize the phenomenon, transplastomic tobacco lines were generated, in which the atpB reading frame was altered by insertions or deletions in the oligoA motif. We found that insertion of two adenines was more efficiently compensated than insertion of a single adenine, or deletion of one or two adenines. We further show that homopolymeric composition of the oligoA stretch is essential for recoding. Plants carrying a disrupted oligoA stretch have an albino-phenotype, indicating absence of indel correction. Our work provides evidence for the operation of translational recoding in chloroplasts. Recoding enables correction of frameshift mutations and can restore photoautotrophic growth in mutants that otherwise would be lethal.

plant biology↗

A photosynthesis operon in the chloroplast genome drives speciation in evening primroses

Incompatibility between the cytoplasm and the nucleus is considered as major factor in species formation, but mechanistic understanding is poor. In evening primroses, a model plant for organelle genetics and population biology, hybrid offspring regularly displays chloroplast-nuclear incompatibility. These incompatibilities affect photosynthesis, a trait under selection in changing environments. Here we show that light-dependent misregulation of the plastid psbB operon (encoding core subunits of photosystem II and the cytochrome b6f complex), can lead to hybrid incompatibility, thus ultimately driving speciation. This misregulation results in an impaired light acclimation response in incompatible plants. Moreover, as a result of their different chloroplast genotypes, the parental lines differ in their photosynthesis performance upon exposure to different light conditions. Significantly, the incompatible chloroplast genome is naturally found in xeric habitats with high light intensities, whereas the compatible one is limited to mesic habitats. Consequently, our data raise the possibility that the hybridization barrier evolved as a result of adaptation to specific climatic conditions.

evolutionary biology↗

The effects of losing sex on the molecular evolution of plant defense

It is hypothesized that the loss of sexual reproduction and reduced recombination rates decrease the ability for hosts to evolve in response to selection by parasites. Using transcriptomes from 32 species, we test whether repeated losses of sex in the plant genus Oenothera has resulted in changes to the evolution of defense genes against herbivores and pathogens. To achieve this, the function of 2,431 Oenothera orthologous genes was determined based on GO annotations from Arabidopsis thaliana. Phylogenetic Analysis by Maximum Likelihood (PAML) was then used to examine how the patterns of molecular evolution in 721 defense and 1,710 non-defense genes differ between sexual (16 spp.) and asexual (16 spp.) taxa. We test whether the relative rates of nonsynonymous to synonymous substitutions ({omega} = dN/dS) in proteins with defensive function were higher in lineages with sexual reproduction ({omega}sexual> {omega}a-sexual), and we asked if such patterns were exclusive for defense genes or not. We detected variability in the rate of amino acid replacements of proteins in >50% of genes and positive selection on 3% of the genes examined. Nevertheless, our results clearly show that on average, signatures of positive and purifying selection on defense and non-defense genes are similar and only a small number of specific genes related to plant immune function may be affected by a loss of sex.

evolutionary biology↗

Chloroplast nucleoids are highly dynamic in ploidy, number, and structure during angiosperm leaf development

Chloroplast nucleoids are large, compact nucleoprotein structures containing multiple copies of the plastid genome. Studies on structural and quantitative changes of plastid DNA (ptDNA) during leaf development are scarce and have produced controversial data. We have systematically investigated nucleoid dynamics and ptDNA quantities in mesophyll of Arabidopsis, tobacco, sugar beet, and maize from the early post-meristematic stage until necrosis. DNA of individual nucleoids was quantified by DAPI-based supersensitive epifluorescence microscopy. Nucleoids occurred in scattered, stacked or ring-shaped arrangements and in recurring patterns during leaf development remarkably similar between the species studied. Nucleoids per organelle varied from few in meristematic plastids to >30 in mature chloroplasts (corresponding to about 20-750 nucleoids per cell). Nucleoid ploidies ranged from haploid to >20-fold even within individual organelles, with average values between 2.6- and 6.7-fold and little changes during leaf development. DNA quantities per organelle increased gradually from about a dozen plastome copies in tiny plastids of apex cells to 70-130 copies in chloroplasts of about 7 m diameter in mature mesophyll tissue, and from about 80 plastome copies in meristematic cells to 2,600-3,300 copies in mature diploid mesophyll cells without conspicuous decline during leaf development. Pulsed-field electrophoresis, restriction of high-molecular weight DNA from chloroplasts and gerontoplasts, and CsCl equilibrium centrifugation of single- and double-stranded ptDNA revealed no noticeable fragmentation of the organelle DNA during leaf development, implying that plastid genomes in mesophyll tissues are remarkably stable until senescence. Significance StatementPlastid DNA is organized in nucleoids that are highly dynamic in organization, structure and amount during leaf development. The present investigation fully resolves now this dynamic and is a precise cytogenetic characterization of nucleoids DNA spanning the entire life cycle of the leaf.

plant biology↗

OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes

Key points O_LIOGDRAW has become the standard tool for displaying maps of organellar genomes C_LIO_LIit converts GenBank entries into graphical maps C_LIO_LIa new version with improved functionality has been released C_LI AbstractOrganellar (plastid and mitochondrial) genomes play an important role in resolving phylogenetic relationships, and next-generation sequencing technologies have led to a burst in their availability. The ongoing massive sequencing efforts require software tools for routine assembly and annotation of organellar genomes as well as their display as physical maps. OrganellarGenomeDRAW (OGDRAW) has become the standard tool to draw graphical maps of plastid and mitochondrial genomes. Here were present a new version of OGDRAW equipped with a new front end. Besides several new features, OGDRAW has now access to a local copy of the organelle genome database of the NCBI RefSeq project. Together with batch processing of (multi-)GenBank files, this enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades. The new OGDRAW server can be accessed at https://chlorobox.mpimp-golm.mpg.de/OGDraw.html.

bioinformatics↗

Thermal plasticity of the circadian clock is under nuclear and cytoplasmic control in wild barley

Temperature compensation, expressed as the ability to maintain clock characteristics (mainly period) in face of temperature changes, is considered a key feature of circadian clock systems. In this study, we explore the genetic basis for circadian clock plasticity under high temperatures by utilizing a new doubled haploid (DH) population derived from two reciprocal Hordeum vulgare sps. spontaneum hybrids genotypes (crosses between B1K-50-04 and B1K-09-07). Genotyping by sequencing of DH lines indicated a rich recombination landscape, with minor fixation (less than 8%), for one of the parental alleles, yet with prevalent and varied segregation distortion across seven barley chromosomes. Phenotyping was conducted with a high-throughput platform under optimal and high temperature environments. Genetic analysis, which included QxE and binary-threshold models, identified a significant influence of the maternal organelle genome (the plasmotype), as well as several nuclear quantitative trait loci (QTL), on clock phenotypes (free-running period and amplitude). Moreover, it showed the differential contribution of cytoplasmic genome clock rhythm buffering against high temperature. Resequencing of the parental chloroplast indicated the presence of several candidate genes underlying these significant effects. This first reported plasmotype-driven clock plasticity paves the way for identifying an hitherto unknown impact of nuclear and plasmotype variations on clock robustness and on plant adaptation to changing environments.\n\nHighlightCircadian clock robustness to high temperature is controlled by nuclear and plasmotype quantitative trait loci in a wild barley (Hordeum vulgare ssp. spontaneum) reciprocal doubled haploid population.

genetics↗

Biparental inheritance of chloroplasts is controlled by lipid biosynthesis

In most eukaryotes, organellar genomes are transmitted preferentially by the mother, but molecular mechanisms and evolutionary forces underlying this fundamental biological principle are far from understood. It is believed that biparental inheritance promotes competition between the cytoplasmic organelles and allows the spread of so-called selfish cytoplasmic elements. Those can be, for example, fast replicating or aggressive chloroplasts (plastids) that are incompatible with the hybrid nuclear genome and therefore maladaptive.\n\nHere we show that the ability of plastids to compete against each other is a metabolic phenotype determined by extremely rapidly evolving genes in the plastid genome of the evening primrose Oenothera. Repeats in the regulatory region of accD (the plastid-encoded subunit of the acetyl-CoA carboxylase, which catalyzes the first and rate limiting step of lipid biosynthesis), as well as in ycf2 (a giant reading frame of still unknown function), are responsible for the differences in competitive behavior of plastid genotypes. Polymorphisms in these genes influence lipid synthesis and most likely profiles of the plastid envelope membrane. These in turn determine plastid division and/or turn-over rates and hence competitiveness. This work uncovers cytoplasmic drive loci controlling the outcome of biparental chloroplast transmission. Here, they define the mode of chloroplast inheritance, since plastid competitiveness can result in uniparental inheritance (through elimination of the \"weak\" plastid) or biparental inheritance (when two similarly \"strong\" plastids are transmitted).\n\nSignificance statementPlastids and mitochondria are usually uniparentally inherited, typically maternally. When the DNA-containing organelles are transmitted to the progeny by both parents, evolutionary theory predicts that the maternal and paternal organelles will compete in the hybrid. As their genomes do not undergo sexual recombination, one organelle will \"try\" to outcompete the other, thus favoring the evolution and spread of aggressive cytoplasms. The investigations described here in the evening primrose, a model species for biparental plastid transmission, have discovered that chloroplast competition is a metabolic phenotype. It is conferred by rapidly evolving genes that are encoded on the chloroplast genome and control lipid biosynthesis. Due to their high mutation rate these loci can evolve and become fixed in a population very quickly.

genetics↗

GenBank 2 Sequin - a file converter preparing custom GenBank files for database submission

The typical wet lab user often annotates smaller sequences in the GenBank format, but resulting files are not accepted for database submission by NCBI. This makes submission of such annotations a cumbersome task. Here we present \"GenBank 2 Sequin\" an easy-to-use web application that converts custom annotations in the GenBank format into the NCBI direct submission format Sequin. Additionally, the program generates a \"five-column, tab-delimited feature table\" and a FASTA file required for submission through BankIt or for the update an existing GenBank entry. We specifically developed \"GenBank 2 Sequin\" for the regular wet lab researcher with strong focus on user-friendliness and flexibility. It is equipped with an intuitive graphical interface and a comprehensive documentation. The application can be employed to prepare any GenBank file for database submission. It is freely available online at https://chlorobox.mpimp-golm.mpg.de/GenBank2Sequin.html.

genomics↗