The authors adapted OpenPlant kit CRISPR/Cas9 tools to enable multiplex gRNA expression from a single transcript using tRNA sequences in the liverwort Marchantia polymorpha, markedly enhancing editing efficiency and scalability. They coupled this vector system with a simplified, optimized thallus transformation protocol, providing a rapid and versatile platform for generating CRISPR/Cas9 mutants and advancing functional genomics in this model species.

The study characterizes MpACR3, an ACR3 transporter from the liverwort Marchantia polymorpha, demonstrating its role as a metalloid/proton antiporter that provides resistance to arsenic and moderate tolerance to antimony. The authors reveal an N‑terminal arsenic‑sensing domain that controls Golgi retention and plasma‑membrane trafficking via cysteine‑mediated conformational changes, and show that a conserved arginine motif influences both membrane accumulation and transport activity. These findings suggest a plant‑specific adaptation of ACR3 transporters to arsenic toxicity.

The study combined long‑read whole‑genome assembly, multi‑omics profiling (DNA methylation, mRNA, ribosome‑associated transcripts, tRNA abundance, and protein levels) in two Arabidopsis thaliana accessions to evaluate how genomic information propagates through the Central Dogma. Codon usage in gene sequences emerged as the strongest predictor of both mRNA and protein abundance, while methylation, tRNA levels, and ribosome‑associated transcripts contributed little additional information under stable conditions.

The study used comparative transcriptomics to examine how Fusarium oxysporum isolates with different lifestyles on angiosperms regulate effector genes during infection of the non‑vascular liverwort Marchantia polymorpha. Core effector genes on fast core chromosomes are actively expressed in the bryophyte host, while lineage‑specific effectors linked to angiosperm pathogenicity are silent, and disruption of a compatibility‑associated core effector alters the expression of other core effectors, highlighting conserved fungal gene networks across plant lineages.

Phylogenetic analysis reveals that non‑seed plants, exemplified by the liverwort Marchantia polymorpha, possess a streamlined repertoire of cyclin and CDK genes, with only three cyclins active in a phase‑specific manner during vegetative development. Single‑cell RNA‑seq and fluorescent reporter assays, combined with functional overexpression studies, demonstrate the distinct, non‑redundant roles of MpCYCD;1, MpCYCA, and MpCYCB;1 in G1 entry, S‑phase progression, and G2/M transition, respectively.

Chromatin accessibility profiling and transcriptomics of Marchantia polymorpha heat‑shock transcription factor (HSF) mutants reveal that HSFA1 governs the placement of cis‑regulatory elements for heat‑induced gene activation, a mechanism conserved across plants, mice, and humans. Integrated gene regulatory network modeling identifies MpWRKY10 and MpABI5B as indirect regulators linking phenylpropanoid and stress pathways, while abscisic acid influences gene expression downstream of HSFA1 without broadly reshaping chromatin. A cross‑species, cross‑condition machine‑learning framework successfully predicts chromatin accessibility and expression, underscoring a conserved regulatory logic in stress responses.

The study performed a comprehensive computational analysis of the Arabidopsis thaliana proteome, classifying 48,359 proteins by melting temperature (Tm) and melting temperature index (TI) and linking thermal stability to amino acid composition, molecular mass, and codon usage. Machine‑learning and evolutionary analyses revealed that higher molecular mass and specific codon pairs correlate with higher Tm, and that gene duplication has driven the evolution of high‑Tm proteins, suggesting a genomic basis for stress resilience.

The study mapped the subcellular localization of isoprenoid biosynthetic enzymes in Marchantia polymorpha, confirming most predictions and identifying oil body cells as primary sites of terpene synthesis. Overexpression and CRISPR knockout of the ABC transporter ABCG1 revealed its essential role in retaining sesquiterpenes within oil bodies, while attempts to boost heterologous diterpene and triterpene production in oil bodies did not increase yields.

The study examined transcriptomic responses of the tropical seagrass Halophila stipulacea from a pristine and an impacted site under single and combined thermal and excess nutrient stress in mesocosms. Combined stress caused greater gene reprogramming than individual stresses, with thermal effects dominating and the impacted population showing reduced plasticity but higher resilience. Core stress‑response genes were identified as potential early field indicators of environmental stress.