Transcriptional responses of Solanum lycopersicum to three distinct parasites reveal host hubs and networks underlying parasitic successes
Authors: Truch, J., Jaouannet, M., Da Rocha, M., Kulhanek-Fontanille, E., Van Ghelder, C., Rancurel, C., Migliore, O., Pere, A., Jaubert, S., Coustau, C., Galiana, E., Favery, B.
The study used transcriptomic profiling to compare tomato (Solanum lycopersicum) responses to three evolutionarily distant pathogens—nematodes, aphids, and oomycetes—during compatible interactions, identifying differentially expressed genes and key host hubs. Integrating public datasets and performing co‑expression and GO enrichment analyses, the authors mapped shared dysregulation clusters and employed Arabidopsis interactome data to place tomato candidates within broader networks, highlighting potential targets for multi‑pathogen resistance.
Phylogenomic challenges in polyploid-rich lineages: Insights from paralog processing and reticulation methods using the complex genus Packera (Asteraceae: Senecioneae)
Authors: Moore-Pollard, E. R., Ellestad, P., Mandel, J.
The study examined how polyploidy, hybridization, and incomplete lineage sorting affect phylogenetic reconstructions in the genus Packera, evaluating several published paralog‑processing pipelines. Results showed that the choice of orthology and paralog handling methods markedly altered tree topology, time‑calibrated phylogenies, biogeographic histories, and detection of ancient reticulation, underscoring the need for careful methodological selection alongside comprehensive taxon sampling.
Integrative comparative transcriptomics using cultivated and wild rice reveals key regulators of developmental and photosynthetic progression along the rice leaf developmental gradient
Authors: Jathar, V., Vivek, A., Panda, M. K., Daware, A. V., Dwivedi, A., Rani, R., Kumar, S., Ranjan, A.
The study performed comparative gene expression profiling across four rice accessions—from shoot apical meristem to primordia stage P5—to delineate developmental and photosynthetic transitions in leaf development. By integrating differential expression and gene regulatory network analyses, the authors identified stage-specific regulatory events and key transcription factors, such as RDD1, ARID2, and ERF3, especially in the wild rice Oryza australiensis, offering a comprehensive framework for optimizing leaf function.
The study functionally characterizes three tomato CNR/FWL proteins (SlFWL2, SlFWL4, SlFWL5) and demonstrates that SlFWL5 localizes to plasmodesmata, where it regulates leaf size and morphology by promoting cell expansion likely through cell‑to‑cell communication. Gain‑ and loss‑of‑function transgenic tomato lines reveal that SlFWL5 is a key regulator of organ growth via modulation of plasmodesmatal signaling.
The study constructs a ~1‑million‑cell single‑nuclei transcriptome atlas of Arabidopsis leaves to reveal that drought stress accelerates transcriptional programs associated with maturation and aging, thereby limiting leaf growth in proportion to stress intensity. Targeted upregulation of FERRIC REDUCTION OXIDASE 6 in mesophyll cells partially rescues leaf growth under drought, demonstrating the functional relevance of these transcriptional changes.