Genetius

A genome-wide association study of 166 Iberian Arabidopsis accessions identified loci, including ABA3 and GA2ox2, that modulate the inhibitory effect of the auxin precursor indole-3-acetamide (IAM) on primary root elongation. Integrating sequence analysis, transcriptomics, 3D protein modeling, and mutant physiology revealed that IAM promotes ABA biosynthesis and signaling, uncovering a novel node of hormone crosstalk.

The study identifies GyrB3 as a novel nuclear factor that interacts with histone deacetylases to regulate transposable element silencing in plants, acting as a suppressor of IBM1 deficiency–induced epigenetic defects. Loss of GyrB3 reduces DNA methylation and increases H3 acetylation at TEs, demonstrating the importance of histone deacetylation for genome stability.

The study identifies the serine/threonine protein kinase CIPK14/SNRK3.15 as a regulator of sulfate‑deficiency responses in Arabidopsis thaliana seedlings, with mutants showing diminished early adaptive and later salvage responses under sulfur starvation. While snrk3.15 mutants exhibit no obvious phenotype under sufficient sulfur, the work provides a novel proteomic dataset comparing wild‑type and mutant seedlings under sulfur limitation.

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 surveyed vegetative water use and life‑history traits across Arabidopsis thaliana ecotypes in both controlled and outdoor environments to assess how climatic history shapes water‑use strategies. Trait‑climate correlations and genome‑wide association analyses uncovered that ecotypes from warmer regions exhibit higher water use, and identified MYB59 as a key gene whose temperature‑linked alleles affect water consumption, a finding validated using myb59 mutants. These results indicate that temperature‑driven adaptive differentiation partly explains intraspecific water‑use variation.

The study reveals that a set of REPRODUCTIVE MERISTEM (REM) transcription factors, termed RIMs, are essential for directing RNA‑directed DNA methylation (RdDM) to CLSY3 targets in a sex‑specific manner in Arabidopsis reproductive tissues. Disruption of RIM DNA‑binding domains or their target motifs abolishes RdDM at these loci, demonstrating that genetic cues can guide de novo methylation patterns.

The study identifies four Arabidopsis REM transcription factors (VDD, VAL, REM12, REM13) that bind specific DNA sequences and, together with GDE1, recruit RNA polymerase IV to produce 24‑nt siRNAs that direct DNA methylation at designated loci. Loss of GDE1 causes Pol IV complexes to relocalize to sites bound by REM8, indicating that REM proteins provide sequence‑specific cues for epigenetic patterning.

The study profiled the Arabidopsis apoplastic proteome during pattern‑triggered immunity induced by the flg22 peptide, using apoplastic washing fluid with minimal cytoplasmic contamination followed by LC‑MS/MS. Results showed consistent PTI‑specific enrichment and depletion of peptides, a bias toward ectodomain peptides of receptor‑like kinases, and increased abundance of the exosome marker tetraspanin 8, indicating heightened exosome levels during PTI.