Biology subjects

Grones, C.

Publications and source records attributed to Grones, C..

6 recordsLinked to original sources

bioRxiv2026

Local and distal signals drive cell-type-specific leaf responses during shade avoidance

Plants reposition and grow their leaves towards optimal light conditions in a canopy. To achieve both horizontal and vertical displacement, plants need to simultaneously elongate their cells unidirectionally and maintain an elongation rate differential between the abaxial and adaxial side of the organ to bend. Exposure to Far-Red (FR) light enrichment can induce both responses, depending on where FR is sensed. Here we studied how plants maintain both growth responses simultaneously within the same organ. To deduce the regulatory mechanisms governing the simultaneous regulation of differential and unidirectional elongation, we performed both organ specific and single cell RNA sequencing experiments on plants exposed to local or whole plant FR enrichment. Single cell transcriptomics resolved that FR light signalling occurs through all cell types, but core components of the shade avoidance pathway are expressed cell type-specifically and require signalling across tissues to control growth plasticity. The upstream photoreceptor targets, including auxin biosynthesis-associated genes, in the leaf lamina are expressed in the epidermis, whilst auxin response gene expression in the petiole occurs also in the deeper tissues layers. We thus identified the remotely triggered differential growth transcriptome acting in the abaxial cortex and show that this is complemented by locally induced second transcriptome signature that is associated with unidirectional petiole elongation. The latter is induced across all cell types. We propose that this spatial distinction of transcriptional regulation of gene clusters could represent how differential and unidirectional growth can occur simultaneously in the same organ under FR light enrichment.

plant biology↗

bioRxiv2026

A Myb-dominated gene regulatory network universally controls sexual cell fate transitions in diatoms

Diatoms are the foundation of aquatic food webs and contribute about 40% of the total marine primary productivity. Yet, the regulation of their complex size-dependent life cycles remains obscure. Here, we leveraged single-cell transcriptomics and transgenic reporter lines to uncover the molecular mechanisms behind partner recognition, nuclear fusion, and the remarkable 15-fold size expansion of auxospores. Gene regulatory network inference revealed that the irreversible commitment to differentiate into gametes is controlled by Myb transcription factors, whose specific activity in the global ocean underscores their significance for ploidy transitions across diatom clades. These findings reinforce microalgae as powerful models to study cell fate transitions and provide a mechanistic framework for the life cycle dynamics that underpin the functioning of aquatic systems worldwide. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=67 SRC="FIGDIR/small/714157v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@162f523org.highwire.dtl.DTLVardef@1cbe836org.highwire.dtl.DTLVardef@1fa6c9eorg.highwire.dtl.DTLVardef@1f12217_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Conserved transcriptional reprogramming in nematode infected root cells

Plant-parasitic nematodes are responsible for important annual losses in crop productivity worldwide1,2. Although the formation of feeding organs within the roots is essential for successful sedentary parasitism3, the molecular mechanisms underlying their development are poorly understood. This is partly because these organs originate from a limited number of root cells4-7, making difficult to capture the transcriptional reprogramming that occurs during the early stages of the infection. Here, we first developed a comparative host-pathogen framework to study the nematode infection process in Arabidopsis and rice. Using a cross-species single-cell transcriptomics approach, we identified a unique molecular signature in infected root cells and show that the cellular reprogramming during these early stages is highly conserved across both host-pathogen interactions. This transcriptional cell reprogramming is associated with stemness acquisition related to de novo organogenesis process. By cell-type specific gene regulatory network analysis, we identified AtATHB2/OsHOX28 as an evolutionary conserved and key regulator of the nematode infection process. Loss-of-function of this regulator in both species results in nematode resistance without affecting root growth. This discovery opens up new avenues for the development of sustainable nematode control strategies that could be translated across crop species.

plant biology↗

bioRxiv2025

Gene regulatory network analysis of somatic embryogenesis identifies morphogenic genes that increase maize transformation frequency

Somatic embryogenesis allows a somatic plant cell to develop into an embryo, and potentially into a fertile plant. Transcription factors such as BABY BOOM can induce somatic embryogenesis when ectopically expressed and are widely used for aiding regeneration in tissue culture for transformation and gene editing of crops. Nevertheless, regeneration remains a bottleneck and alternative morphogenic genes are highly desired. Here, we co-expressed BABY BOOM and WUSCHEL2 in zygotic maize (Zea mays L.) embryos and studied gene regulatory networks in induced somatic embryos at the single-cell level. By inferring cell-type-specific regulons, we prioritized candidate regulators and confirmed functionality of four transcription factors, bHLH48, EREB152, GRF4, and HB77, for enhanced maize transformation frequency, leading to fertile, transgenic plants. Interestingly, the basic helix-loop-helix and homeodomain-leucine zipper families had previously not been associated with induced somatic embryogenesis. Our work will contribute to more efficient transformation, much needed to deliver on the promise of gene editing for agriculture.

plant biology↗

bioRxiv2024

Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single-cell transcriptomics

Drought stress imposes severe challenges on agriculture by impacting crop performance. Understanding drought responses in plants at a cellular level is a crucial first step towards engineering improved drought resilience. However, the molecular responses to drought are complex as they depend on multiple factors including the severity of drought, the profiled organ, its developmental stage or even the cell types therein. Thus, deciphering the transcriptional responses to drought is specially challenging. Here, we investigated tissue-specific responses to mild drought in young Arabidopsis thaliana (Arabidopsis) leaves using single-cell RNA sequencing (scRNA-seq). To preserve transcriptional integrity during cell isolation, we inhibited RNA synthesis using the transcription inhibitor actinomycin D, demonstrating the benefits of transcriptome fixation for studying mild stress responses at single-cell level. We present a curated and validated single-cell atlas comprising 50,797 high-quality cells from almost all known cell types present in the leaf. We show that the mesophyll contains two spatially separated cell populations with distinct responses to drought: one enriched in canonical abscisic acid-related drought-responsive genes, and another one depicting iron starvation responses. Our study thus reveals a dual adaptive mechanism of the leaf mesophyll in response to mild drought and provides a valuable resource for future research on stress responses.

plant biology↗

bioRxiv2024

Scywalker: scalable end-to-end data analysis workflow for nanopore single-cell transcriptome sequencing

We introduce scywalker, an innovative and scalable package developed to comprehensively analyze long-read nanopore sequencing data of full-length single-cell or single-nuclei cDNA. Existing nanopore single-cell data analysis tools showed severe limitations in handling current data sizes. We developed novel scalable methods for cell barcode demultiplexing and single-cell isoform calling and quantification and incorporated these in an easily deployable package. Scywalker streamlines the entire analysis process, from sequenced fragments in FASTQ format to demultiplexed pseudobulk isoform counts, into a single command suitable for execution on either server or cluster. Scywalker includes data quality control, cell type identification, and an interactive report. Assessment of datasets from the human brain, Arabidopsis leaves, and previously benchmarked data from mixed cell lines, demonstrate excellent correlation with short-read analyses at both the cell-barcoding and gene quantification levels. At the isoform level, we show that scywalker facilitates the direct identification of cell-type-specific expression of novel isoforms.

bioinformatics↗