Biology subjects

Grones, C.

Publications and source records attributed to Grones, C..

4 recordsLinked to original sources

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↗