Biology subjects

Rensing, S. A.

Publications and source records attributed to Rensing, S. A..

At least 19 recordsLinked to original sources

bioRxiv2026

Prediction of plant organismal complexity based on transcription factor annotation: an AI approach

How morphological complexity evolves is still enigmatic. While there is evidence in algae and plants as well as animals that diversification of the repertoire of transcription factors (TF) is causative for evolution of organismal complexity, there are many examples from lineages that follow their own way of complexity evolution, for example by expansion of particular families. For land plants, correlation of the size of the TF complement with number of cell types (as a proxy for morphological complexity) has been shown, and several families were identified as candidates to drive complexity evolution. Here, we expand a previously available dataset of cell type numbers from 12 to 82 proteomes and introduce a four class body plan scheme. We find that the total TF complement correlates with the number of cell types of Archaeplastida (primary plastid bearing plants and algae). We used TabPFN (Tabular Prior-data Fitted Network) for binary (uni- vs. multicellularity) as well as for four class Bauplan classification. TabPFN is able to predict the morphological complexity with high accuracy. This approach allows to determine organismal complexity based on the gene space of an organism. Based on our results, we can confirm that plant morphological evolution is driven by gain and expansion of TF families.

evolutionary biology↗

bioRxiv2026

Old Yellow Enzyme from Brevibacillus nitrificans functions as 12-oxo-phytodienoic acid reductase in planta

Old Yellow Enzymes (OYEs) are a widely distributed family of ene-reductases that were first described in a Saccharomyces cerevisiae ferment. In plants, cis-12-oxo-phytodienoic acid (cis-OPDA) reductase (OPR) is the best studied OYE. In Arabidopsis thaliana, the peroxisomal AtOPR3 was characterized as the major OPDA reductase, which generates 3-oxo-2-(2-pentenyl)-cyclopentane-1-octanoic acid in the jasmonic acid (JA) biosynthesis. In Atopr3 lines, only small amounts of JA are detectable after wounding. Here, we describe an OPR-like enzyme (named BnOPR) from the gram-positive Brevibacillus nitrificans. The sequence was identified in an early version of the Physcomitrium patens genome and is assumed to be a contamination by a bacterium growing in association with P. patens. In complementation experiments with an Atopr3 line, we demonstrate that expression of BnOPR, fused with a peroxisomal targeting signal, rescues the male infertile phenotype and increases JA and JA-Ile levels. The catalytic parameters of BnOPR were determined for a set of substrates, including cis-OPDA and prednisone. Interestingly, B. nitrificans, B. brevis, and Paenibacillus physcomitrellae were shown to have a positive effect on P. patens growth. HighlightThe bacterial enzyme BnOPR rescues the male infertile phenotype of Atopr3 plants.

biochemistry↗

bioRxiv2025

SWI3 regulates male sex determination in Marchantia polymorpha

Land plants alternate between multicellular haploid and diploid phases, a life cycle requiring tight coordination between vegetative growth and sexual reproduction. Chromatin regulators such as SWI3, a core subunit of the SWI/SNF complex, are ancestral and highly diversified in angiosperms. As their functions outside of angiosperms remain unclear, we investigated SWI3 of the liverwort Marchantia polymorpha, a non-vascular dioecious land plant. A mutation in the promoter of MpSWI3 affected gametangiophore development and spermiogenesis in males, revealing its male-specific role in reproductive development. The MpSWI3 mutant line amplifies vegetative propagation in males under conditions that would normally induce reproductive growth. The phenotype was underpinned by transcriptomic changes, showing that MpSWI3 modulates key regulators of gametangiophore initiation (e.g. BONOBO, GLID), sperm development and motility (e.g. DUO1, PKAR), and asexual reproduction (e.g. KAI2). Together, this positions MpSWI3 as a chromatin-level regulator balancing vegetative and reproductive phases, highlighting an ancient epigenetic function that coordinates developmental phase transitions in land plants.

plant biology↗

bioRxiv2025

The Spirogyra genome: signatures of shared and divergent division and differentiation

Zygnematophytes emerged as the unexpected closest algal relatives of land plants despite their simple body plans, raising questions about the morphogenetic toolkit present in the last common ancestor of land plants and algae. Genomic analyses have revealed that zygnematophytes are cellular giants, sharing homologous frameworks for several phytohormones, secondary metabolites, and key morphogenetic and transcriptional regulatory processes. Zygnematophytes fall into five orders, each of which has charted its own evolutionary path. Here, we have sequenced a contiguous genome of Spirogyra pratensis, the eponymous representative of Spirogyrales and a classical model system for evolutionary cell biology in the green lineage. Building on this genome, we transcriptionally profiled the tractable life cycle of Spirogyra and its responses to a bifactorial gradient of light and temperature. Our data highlight the activation of quiescence and homeostatic programs. Yet what stands out most in Spirogyra is its spiral chloroplast--undulating intracellularly and abscising during mixed phragmoplast formation and furrowing. Leveraging the genome in tandem with co-expression network analyses, we describe the molecular underpinnings of the unique cytokinetic processes that govern both cell and plastid division. We find that Spirogyra deploys a molecular program characteristic of Phragmoplastophyta, yet lacks the deeply conserved plastid division machinery found in other archaeplastid plastids.

plant biology↗

bioRxiv2025

How bibliometric analysis can help to specify and track interdisciplinary research areas: A term-based analysis approach

Inter- and transdisciplinary research is carried out with increasing frequency and intensity. Bibliometric analysis of disciplinary research is aided by i) classical topical categories that are used by databases cataloguing publications, and ii) via journals that either represent a topic, or attach appropriate disciplinary keywords to papers. In contrast, bibliometric analysis of interdisciplinary research is difficult to perform using disciplinary keywords. Here, we used unigram and bigram term analyses in order to analyse interdisciplinary research areas. These analyses are based on several training datasets representing different research areas at the same institution or with dispersed affiliations. Our results show that using modest investment in query determination, interdisciplinary research areas can be defined and tracked via term-based analysis of their publication output.

scientific communication and education↗

bioRxiv2024

Enhanced sensitivity of TAPscan v4 enables comprehensive analysis of streptophyte transcription factor evolution

Transcription associated proteins (TAPs) fulfill multiple functions in regulatory and developmental processes and display lineage-specific evolution. TAPscan is a comprehensive and highly reliable tool for genome-wide TAP annotation via domain profiles. Here, we present TAPscan v4, including an updated web interface (https://tapscan.plantcode.cup.uni-freiburg.de/), which enables an in-depth representation of the distribution of 138 TAP families across 678 species from diverse groups of organisms, with a focus on Archaeplastida (plants in the wide sense). With this release, we also make the underlying "Genome Zoo" available, a curated protein data set with scripts and metadata. 18 new TAP (sub)families were added as part of the update. Nine of those were gained in the most recent common ancestor of the Streptophyta (comprising streptophyte algae and land plants), or within the streptophyte algae. More than one-third of all detected TAP family gains were identified during the evolution of streptophyte algae, before the emergence of land plants, and are thus likely to have been significant for plant terrestrialization. The TAP complement of the Zygnematophyceae was identified to be the most similar to that of land plants, consistent with the finding that this lineage is sister to land plants. Overall, our data retrace the evolution of streptophyte TAPs, allowing us to pinpoint the regulatory repertoire of the earliest land plants.

bioinformatics↗

bioRxiv2024

Time-resolved oxidative signal convergence across the algae-embryophyte divide

The earliest land plants faced a significant challenge in adapting to environmental stressors. Stress on land is unique in its dynamics, entailing swift and drastic changes in light and temperature. While we know that land plants share with their closest streptophyte algal relatives key components of the genetic makeup for dynamic stress responses, their concerted action is little understood. Here, we combined time-course stress profiling using photophysiology, transcriptomics on 2.7 Tbp of data, and metabolite profiling analyses on more than 270 distinct samples, to study stress kinetics across three 600-million-year-divergent streptophytes. Through co-expression analysis and Granger causal inference we predict a gene regulatory network that retraces a web of ancient signal convergence at ethylene signaling components, osmosensors, and chains of major kinases. These kinase hubs already integrated diverse environmental inputs since before the dawn of plants on land.

evolutionary biology↗

bioRxiv2024

Long days induce adaptive secondary dormancy in seed of the Mediterranean plant Aethionema arabicum

Secondary dormancy is an adaptive trait that increases reproductive success by aligning seed germination with permissive conditions for seedling establishment. Aethionema arabicum is an annual plant and member of the Brassicaceae that grows in environments characterized by hot and dry summers. Aethionema arabicum seeds may germinate in early spring when seedling establishment is permissible. We demonstrate that long-day light regimes induce secondary dormancy in seed of Aethionema arabicum (CYP accession) repressing germination in summer when seedling establishment is riskier. Characterization of mutants screened for defective secondary dormancy demonstrated that RGL2 mediates repression of genes involved in GA signalling. Exposure to high temperature alleviates secondary dormancy, restoring germination potential. These data are consistent with the hypothesis that long-day-induced secondary dormancy and its alleviation by high temperatures, may be part of an adaptive response limiting germination to conditions permissive for seedling establishment in spring and autumn.

plant biology↗

bioRxiv2023

The dimorphic diaspore model Aethionema arabicum (Brassicaceae): Distinct molecular and morphological control of responses to parental and germination temperatures

Plants in habitats with unpredictable conditions are often characterized by diversifying their bet-hedging strategies that ensure fitness over a wider range of variable environmental factors. A striking example is the diaspore (seed and fruit) heteromorphism that evolved to maximize species survival in Aethionema arabicum (Brassicaceae) in which external and endogenous triggers allow the production of two distinct diaspores on the same plant. Using this dimorphic diaspore model, we identified contrasting molecular, biophysical, and ecophysiological mechanisms in the germination responses to different temperatures of the mucilaginous seeds (M+ seed morphs), the dispersed indehiscent fruits (IND fruit morphs), and the bare non-mucilaginous M- seeds obtained by pericarp (fruit coat) removal from IND fruits. Large-scale comparative transcriptome and hormone analyses of M+ seeds, IND fruits, and M- seeds provided comprehensive datasets for their distinct thermal responses. Morph-specific differences in co-expressed gene modules in seeds, as well as seed and pericarp hormone contents identified a role of the IND pericarp in imposing coat dormancy by generating hypoxia affecting ABA sensitivity. This involved expression of morph-specific transcription factors, hypoxia response and cell wall-remodeling genes, as well as altered abscisic acid (ABA) metabolism, transport, and signaling. Parental temperature affected ABA contents and ABA-related gene expression and altered IND pericarp biomechanical properties. Elucidating the molecular framework underlying the diaspore heteromorphism can provide insight into developmental responses to globally changing temperatures. IN A NUTSHELL BackgroundHeteromorphic diaspores (fruits and seeds) are an adaptive bet-hedging strategy to ensure survival in spatiotemporally variable environments. The stone cress Aethionema arabicum, an annual plant native to semi-arid habitats in Anatolia (Turkey), one of the worlds hotspots of biodiversity. It is a close relative of Arabidopsis, rapeseed, cabbage and other Brassica crops, but in contrast to these Ae. arabicum disperses two distinct diaspores from the same plant. These dimorphic diaspores are the mucilaginous seeds (dispersed by pod shatter) and indehiscent fruits (dispersed by abscission). The wing-like pericarp (fruit coat) of the single-seeded indehiscent fruit allows wind dispersal over large distances. The amounts and ratios of the dimorphic diaspores are variable and depend on the environmental conditions. The dimorphic diaspores differ in morphology, dormancy and germination properties and thereby make Ae. arabicum an excellent model for the comparative investigation of the underpinning molecular mechanisms. QuestionWe asked how temperature during fruit and seed formation and during seed germination affect dormancy release and germination speed, and how the morphology, hormonal regulation, and the expression of genes differ between the dimorphic diaspores. FindingsLarge-scale comparative transcriptome and hormone analyses of the mucilaginous seeds and the indehiscent fruits, as well as the seeds artificially extracted from indehiscent fruits by pericarp (fruit coat) removal, provided comprehensive datasets for their distinct thermal responses. Material obtained from plants grown at different temperatures during reproduction was imbibed at different temperatures for germination. This altered the abscisic acid (ABA) metabolism and the pericarp biomechanical properties. Diaspore-specific differences in response to distinct imbibition temperatures identified distinct gene expression patterns in seeds, distinct seed and pericarp hormone contents, and a role of the pericarp in generating hypoxia inside the fruit and imposing coat dormancy. This revealed distinct combinations of specific transcription factors, hypoxia responses and cell wall-remodeling genes, as well as altered signaling pathway genes. Next stepsOur large-scale comparative transcriptome datasets are easily and publicly accessible via the Aethionema arabicum web portal (https://plantcode.cup.uni-freiburg.de/aetar_db/index.php). We plan to expand this by future work on seedlings derived from the dimorphic diaspores, by comparing different Ae. arabicum genotypes, and by studying responses to specific stresses. Understanding the molecular basis of this fascinating example of developmental diversity and plasticity and its regulation by temperature is expected to add insight how plants respond to changing environmental conditions.

plant biology↗

bioRxiv2023

Evolutionary conserved and divergent responses to copper zinc superoxide dismutase inhibition in plants

Life evolved in the presence of reactive oxygen species (ROS) and was further challenged by two consecutive great oxidation events. Therefore, ROS are deeply intertwined into the physological, morphological and transcriptional responses of organisms. Copper zinc superoxide dismutases (CuZnSODs) evolved around the first great oxidation event and have next to their classical role in ROS detoxification also important roles in signaling and transcriptional regulation. Here we addressed the role of CuZnSODs in early land plant evolution. We show, that pharmaceutical inhibition of CuZnSODs with Lung Cancer Screen 1 (LCS-1) in different plant species, including Marchantia polymorpha and Physcomitrium patens, representing the evolutionary early stages of land plants, and Arabidopsis thaliana as a modern vascular plant, lead to impairment of development and growth. Interestingly, Marchantia only possesses the cytosolic CuZnSOD isoform, whereas Physcomitrium additionally contains a plastidial isoform and Arabidopsis contains next to that a third peroxisomal isoform. An RNA-seq analysis revealed that the inhibition of CuZnSODs provoked a similar core response in all plant species analyzed, while those that contain more isoforms showed an extended response. In addition, an untargeted metabolomics approach revealed a specific metabolic signature for each plant species. Through the above approach the oxidative stress provoked by LCS-1 in plants can be specified and we argue that CuZnSOD functions are evolutionary conserved and might be important for plant terrestrialization.

plant biology↗

bioRxiv2023

Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution

The filamentous and unicellular algae of the class Zygnematophyceae are the closest algal relatives of land plants. Inferring the properties of the last common ancestor shared by these algae and land plants allows us to identify decisive traits that enabled the conquest of land by plants. We sequenced four genomes of filamentous Zygnematophyceae (three strains of Zygnema circumcarinatum and one strain of Z. cylindricum) and generated chromosome-scale assemblies for all strains of the emerging model system Z. circumcarinatum. Comparative genomic analyses reveal expanded genes for signaling cascades, environmental response, and intracellular trafficking that we associate with multicellularity. Gene family analyses suggest that Zygnematophyceae share all the major enzymes with land plants for cell wall polysaccharide synthesis, degradation, and modifications; most of the enzymes for cell wall innovations, especially for polysaccharide backbone synthesis, were gained more than 700 million years ago. In Zygnematophyceae, these enzyme families expanded, forming co-expressed modules. Transcriptomic profiling of over 19 growth conditions combined with co-expression network analyses uncover cohorts of genes that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution. HIGHLIGHTSO_LIGenomes of four filamentous algae (Zygnema) sisters to land plants C_LIO_LIZygnema are rich in genes for multicellular growth and environmental acclimation: signaling, lipid modification, and transport C_LIO_LICell wall innovations: diversification of hexameric rosette cellulose synthase in Zygnematophyceae C_LIO_LICo-expression networks reveal conserved modules for balancing growth and acclimation C_LI

evolutionary biology↗

bioRxiv2022

DELLA proteins regulate spore germination and reproductive development in Physcomitrium patens.

O_LIProteins of the DELLA family integrate environmental signals to regulate growth and development throughout the plant kingdom. Plants expressing non-degradable DELLA proteins underpinned the development of high-yielding Green Revolution dwarf crop varieties in the 1960s. In vascular plants, DELLAs are regulated by gibberellins, diterpenoid plant hormones. How DELLA protein function has changed during land plant evolution is not fully understood. C_LIO_LIWe have examined the function and interactions of DELLA proteins in the moss Physcomitrium (Physcomitrella) patens, in the sister group of vascular plants (Bryophytes). C_LIO_LIPpDELLAs do not undergo the same regulation as flowering plant DELLAs. PpDELLAs are not degraded by diterpenes, do not interact with GID1 gibberellin receptor proteins and do not participate in responses to abiotic stress. PpDELLAs do share a function with vascular plant DELLAs during reproductive development. PpDELLAs also regulate spore germination. PpDELLAs interact with moss-specific photoreceptors although a function for PpDELLAs in light responses was not detected. PpDELLAs likely act as hubs for transcriptional regulation similarly to their homologues across the plant kingdom. C_LIO_LITaken together, these data demonstrate that PpDELLA proteins share some biological functions with DELLAs in flowering plants, but other DELLA functions and regulation evolved independently in both plant lineages. C_LI

plant biology↗

bioRxiv2022

Genome dynamics in mosses: Extensive synteny coexists with a highly dynamic gene space

BackgroundWhile genome evolutionary processes of seed plants are intensively investigated, very little is known about seed-free plants in this respect. Here, we use one of the largest groups of seed-free plants, the mosses, and newly generated chromosome-scale genome assemblies to investigate three poorly known aspects of genome dynamics and their underlying processes in seed-free plants: (i) genome size variation, (ii) genomic collinearity/synteny, and (iii) gene set differentiation. ResultsComparative genomic analyses on the model moss Physcomitrium (Physcomitrella) patens and two genomes of Funaria hygrometrica reveal that, like in seed plants, genome size change (approx. 140 Mbp) is primarily due to transposable element expansion/contraction. Despite 60 million years of divergence, the genomes of P. patens and F. hygrometrica show remarkable chromosomal stability with the majority of homologous genes located in conserved collinear blocks. In addition, both genomes contain a relatively large set of lineage-specific genes with no detectible homologs in the other species genome, suggesting a highly dynamic gene space fueled by the process of de novo gene birth and loss rather than by gene family diversification/duplication. ConclusionsThese, combined with previous observations suggest that genome dynamics in mosses involves the coexistence of a collinear homologous and a highly dynamic species-specific gene sets. Besides its significance for understanding genome evolution, the presented chromosome-scale genome assemblies will provide a foundation for comparative genomic and functional studies in the Funariaceae, a family holding historical and contemporary model taxa in the evolutionary biology of mosses.

genomics↗

bioRxiv2022

Neanderthals did not likely consume Physcomitrium patens - a model moss species

This manuscript is discussing the method of Weyrich et al., 2017, "Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus". When studying the dietary profile of a Neanderthal specimen from El Sidron cave (Spain) by sequencing ancient DNA present in calcified dental plaque (calculus) the authors identified a wide-range of potential food sources, including woolly rhinoceros, mushrooms, pine nuts, and moss - namely the less-than-abundant model species Physcomitrium patens. We doubted that Neanderthals were actually eating P. patens. By analyzing the ancient DNA reads using different mapping methods, we show likely a misinterpretation based on the previously used methods. The probability of Neanderthals eating P. patens is the same as eating rice or tomato. However, neither crop was grown in Europe at the time Neanderthals thrived.

evolutionary biology↗

bioRxiv2021

Comparative transcriptomics identifies the transcription factors BRANCHED1 and TCP4, as well as the microRNA miR166 as candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae)

BackgroundFruits are the seed-bearing structures of flowering plants and are highly diverse in terms of morphology, texture and maturation. Dehiscent fruits split open upon maturation to discharge their seeds while indehiscent fruits are dispersed as a whole. Indehiscent fruits evolved from dehiscent fruits several times independently in the crucifer family (Brassicaceae). The fruits of Lepidium appelianum, for example, are indehiscent while the fruits of the closely related L. campestre are dehiscent. Here, we investigate the molecular and genetic mechanisms underlying the evolutionary transition from dehiscent to indehiscent fruits using these two Lepidium species as model system. ResultsWe have sequenced the transcriptomes and small RNAs of floral buds, flowers and fruits of L. appelianum and L. campestre and analyzed differentially expressed genes (DEGs) and differently differentially expressed genes (DDEGs). DEGs are genes that show significantly different transcript levels in the same structures (buds, flowers and fruits) in different species, or in different structures in the same species. DDEGs are genes for which the change in expression level between two structures is significantly different in one species than in the other. Comparing the two species, the highest number of DEGs was found in flowers, followed by fruits and floral buds while the highest number of DDEGs was found in fruits versus flowers followed by flowers versus floral buds. Several gene ontology terms related to cell wall synthesis and degradation were overrepresented in different sets of DEGs highlighting the importance of these processes for fruit opening. Furthermore, the fruit valve identity genes FRUITFUL and YABBY3 were among the DEGs identified. Finally, the microRNA miR166 as well as the TCP transcription factors BRANCHED1 (BRC1) and TCP FAMILY TRANSCRIPTION FACTOR 4 (TCP4) were found to be DDEGs. ConclusionsOur study reveals differences in gene expression between dehiscent and indehiscent fruits and uncovers miR166, BRC1 and TCP4 as possible causes for the evolutionary transition from dehiscent to indehiscent fruits in Lepidium.

evolutionary biology↗

bioRxiv2021

Construction of multicellular yeast networks using the communication toolkit with variable specificity and attenuation

The key next step in synthetic biology is to extend cellular network engineering to the multicellular level by utilizing cell-cell communication for information processing. To facilitate the implementation of multicellular networks in the most commonly used eukaryotic chassis, Saccharomyces cerevisiae, we developed the yeast communication toolkit (YCTK). This toolkit is based on the fungal mating pathway and contains five pheromone-inducible promoters (response parts), eleven pheromones (-factors; sender parts), eleven pheromone receptors (Ste2; receiver parts), as well as five Bar1 proteases (suppressor parts). All YCTK parts were thoroughly characterized and are compatible with the commonly used yeast Golden Gate cloning standard. We demonstrated the application of the YCTK by implementing several different logic gate-like population networks. Furthermore, we used this toolkit to investigate the pheromone-receptor promiscuity patterns among different yeast species. This toolkit extends currently available resources for construction of complex multicellular eukaryotic networks with varying degrees of promiscuity and attenuation.

synthetic biology↗

bioRxiv2020

Chromosome fusions shape an ancient UV sex chromosome system

Non-recombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration1,2. The correlation between suppressed recombination and degeneration is clear in animal XY systems1,2, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions3,4. Here we test for degeneration in the bryophyte UV sex chromosome system through genomic comparisons with new female and male chromosome-scale reference genomes of the moss Ceratodon purpureus. We show that the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes show signs of weaker purifying selection than autosomes, we find suppressed recombination alone is insufficient to drive gene loss on sex-specific chromosomes. Instead, the U and V sex chromosomes harbor thousands of broadly-expressed genes, including numerous key regulators of sexual development across land plants.

evolutionary biology↗

bioRxiv2020

A target enrichment probe set for resolving the flagellate plant tree of life

Premise of the studyNew sequencing technologies enable the possibility of generating large-scale molecular datasets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate plants, comprising hornworts, liverworts, mosses, lycophytes, ferns, and gymnosperms. Methods and ResultsWe leveraged existing transcriptome and genome sequence data to design a set of 56,989 probes for target enrichment sequencing of 451 nuclear exons and non-coding flanking regions across flagellate plant lineages. We describe the performance of target enrichment using the probe set across flagellate plants and demonstrate the potential of the data to resolve relationships among both ancient and closely related taxa. ConclusionsA target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate plants.

evolutionary biology↗