The study shows that the membrane lipids PI4P, PI(4,5)P2, and phosphatidylserine have distinct spatial and temporal dynamics during lateral root primordium formation in Arabidopsis thaliana, with PI4P acting as a stable basal lipid, PI(4,5)P2 serving as a negative regulator of initiation, and phosphatidylserine increasing after founder cell activation. Using live-cell biosensors, genetic mutants, and an inducible PI(4,5)P2 depletion system, the authors demonstrate that reducing PI(4,5)P2 enhances lateral root initiation and development.

Using a controlled field experiment on clonal 35‑year‑old Norway spruce trees, the study examined molecular defense responses to Ips typographus attacks. A multi‑omics approach revealed rapid local increases in jasmonic acid and other phytohormones, leading to differential expression of up to 1,900 genes and corresponding proteomic and metabolomic changes that elevated deterrent compounds such as phenolic aglycones, diterpene resin acids, terpenes, and lignin.

The study investigates the evolutionary shift from archegonial to embryo‑sac reproduction by analyzing transcriptomes of Ginkgo reproductive organs and related species. It reveals that the angiosperm pollen‑tube guidance module MYB98‑CRP‑ECS is active in mature Ginkgo archegonia and that, while egg cell transcription is conserved, changes in the fate of other female gametophyte cells drove the transition, providing a molecular framework for this major reproductive evolution.

Using integrated metabolomics, fluxomics, and proteomics, the study shows that Bamboo mosaic virus infection in Nicotiana benthamiana redirects carbon flux toward glycolysis and the TCA cycle, enhancing mitochondrial metabolism. Silencing the mitochondrial NAD⁺-dependent malic enzyme 1 disrupts cytoplasmic NADH/NAD⁺ balance and alters defense gene expression, indicating that mitochondrial redox regulation is crucial for antiviral defense.

The study uses a high‑throughput comparative multi‑omics strategy to profile transcript, metabolite, and protein dynamics in Arabidopsis thaliana seedlings throughout the heat‑stress memory (HSM) phase following acquired thermotolerance. Early recovery stages show rapid transcriptional activation of memory‑related genes, while protein levels stay elevated longer, and distinct metabolite patterns emerge, highlighting temporal layers of the memory process.

The study engineers Type‑B response regulators to alter their transcriptional activity and cytokinin sensitivity, enabling precise modulation of cytokinin‑dependent traits. Using tissue‑specific promoters, the synthetic transcription factors were deployed in Arabidopsis thaliana to reliably increase or decrease lateral root numbers, demonstrating a modular platform for controlling developmental phenotypes.

The study profiled root transcriptomes of Arabidopsis wild type and etr1 gain-of-function (etr1-3) and loss-of-function (etr1-7) mutants under ethylene or ACC treatment, identifying 4,522 ethylene‑responsive transcripts, including 553 that depend on ETR1 activity. ETR1‑dependent genes encompassed ethylene biosynthesis enzymes (ACO2, ACO3) and transcription factors, whose expression was further examined in an ein3eil1 background, revealing that both ETR1 and EIN3/EIL1 pathways regulate parts of the network controlling root hair proliferation and lateral root formation.

A comparative physiological study of persimmon cultivars with flat (Hiratanenashi) and round (Koushimaru) fruit shapes revealed that differences in cell proliferation, cell shape, and size contribute to shape variation. Principal component analysis of elliptic Fourier descriptors tracked shape changes, while histology and transcriptome profiling identified candidate genes, including a WOX13 homeobox gene, potentially governing fruit shape development.

The study characterizes the tomato class B heat shock factor SlHSFB3a, revealing its age‑dependent expression in roots and its role in enhancing lateral root density by modulating auxin homeostasis. Overexpression of SlHSFB3a increases lateral root emergence, while CRISPR‑mediated knockouts produce the opposite phenotype, indicating that SlHSFB3a regulates auxin signaling through repression of auxin repressors and activation of the ARF7/LOB20 pathway.

The study employed a multi‑omics workflow (transcriptomics, ribosome profiling, and proteomics) to uncover small peptides encoded by long non‑coding RNAs (LSEPs) in rice, finding that over 40% of surveyed lncRNAs associate with ribosomes. An optimized small‑peptide extraction followed by LC‑MS/MS identified 403 LSEPs, confirming the peptide‑coding capacity of plant lncRNAs and providing a scalable pipeline for large‑scale screening.