biostudies-arrayexpressAmey RedkarMarchantia polymorpha subsp. polymorphahttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-1509121 DPI Marchantia polymorpha Tak-1 thalli were infected with Fol WT and erc3 knock out alongside mock(water) control and axenically grown Fol WT culture. At 3 days post infection, thalli were harvested and RNA was extracted. After polyA enrichment, and library preparation, sequencing was carried on NovaSeq6000 platform using SP flowcell with 2 x 100 bp read length.biostudies-arrayexpressNucleic Acid Extraction - After crushing the tissue in liquid nitrogen, RNA was extracted using Qiagen RNeasy Kit using 100 mg tissue and 500 μL of lysis buffer (washing and elution were done as per the manufacturer’s guidelines). RNA was eluted in 40 μL nuclease water.Library Construction - The extracted RNA was eluted in 40 μL nuclease-free water and quantified using Qubit and quality assessment was performed on Agilent TapeStation. From the total RNA, mRNA was enriched using NEBNext Poly(A) mRNA magnetic isolation Module. The library was prepared using NEBNext Ultra™ II Directional RNA Library Prep with sample purification beads.Growth Protocol - Gemmae from the Mp Tak-1 were plated on Gamborg B5 media without sucrose, solidified with 1.5% agar, and maintained at 22°C under a 20:4-hour day-night photoperiod. For infection, 21-day-old thalli (≥ nine thalli per treatment) were dipped in microconidial suspension for 20 mins. Dipping in water was performed as a mock/control treatment. After air drying for 15 minutes, the infected thalli were incubated at 28°C with a 20:4-hour day-night cycle and samples were harvested at the defined time points. Fo isolates were grown in Potato Dextrose Broth (PDB) for 72 hours at 28°C and 140 rpm. Microconidia were harvested by filtering fungal cultures through the cheese cloth. The spores were pelleted by centrifugation and resuspended in sterile water.Spore suspension for infection was created by diluting the spore suspension to a final concentration of 10^5 spores/mL.Sequencing - Sequencing was performed on the NovaSeq 6000 platform, using SP flowcell with 2x100bp sequencing read length.Sample Collection - Infected thalli were collected and snap-frozen in liquid nitrogen.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000<h4>ABSTRACT</h4> The Fusarium oxysporum (Fo) species complex encompasses a diverse range of filamentous plant pathogens, some of which provoke systemic infections in angiosperms, leading to vascular wilt disease. Current understanding of the Fo pathogenicity mechanisms is primarily centered on vascular plants, where individual isolates of Fo exhibit contrasting lifestyles across the endophyte-pathogen continuum on different host species. Although, Fo isolates were recently shown to cause disease on the non-vascular liverwort Marchantia polymorpha (Mp), the transcriptional control of Fo effectors during infection of this bryophytic host is largely unknown. Here, we took a comparative transcriptomic approach to ask how different Fo isolates with contrasting interaction outcomes on angiosperms (pathogenic versus endophytic) adapt to a distantly related plant lineage lacking xylem. We found that the core effector complement encoded on genomic regions shared across all Fo isolates are actively transcribed in Mp, whereas effectors encoded on lineage-specific (LS) genomic regions that contribute towards host-specific pathogenicity in angiosperms are not. Moreover, we observed enhanced transcriptional activation of effector clusters located on the three highly syntenic fast core chromosomes during growth on Mp, as well as divergent lineages and lifestyles, suggesting a conserved role in plant associations. Loss of a compatibility-associated effector encoded in a core effector cluster led to misregulation of other effectors in core clusters. Our findings reveal an unexpected role of fast core chromosomes in determining compatibility of Fo across a broad spectrum of plant lineages and establishes evolutionarily conserved gene networks essential for fungus-plant associations.RNA-seq of coding RNAMarchantia polymorpha subsp. polymorphaTranscriptional plasticity of fast core chromosomes governs establishment of a fungal pathogen on evolutionarily distant plant lineagesVidha Srivastava, Siddharth Kaushik L S, Naga Jyothi Pullagurla, Bernd Zechmann, Antonio Di Pietro, Debabrata Laha, Amey RedkarAmey RedkarfalseRNA sequencing to assess the transcriptional dynamics of infection when Fusarium oxysporum f. sp. lycopersici (Fol) WT and erc3 (Early Root Colonisation 3) knock out strain infect Marchantia polymorpha Tak-1 thalli21 DPI Marchantia polymorpha Tak-1 thalli were infected with Fol WT and erc3 knock out alongside mock(water) control and axenically grown Fol WT culture. At 3 days post infection, thalli were harvested and RNA was extracted. After polyA enrichment, and library preparation, sequencing was carried on NovaSeq6000 platform using SP flowcell with 2 x 100 bp read length.2026-05-04T00:00:00Z2026-05-04T01:03:01.702Z2025-04-25T10:46:01.993ZE-MTAB-15091ERP171968EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003738EFO_000418410.1101/2025.03.27.645276