The study used genome‑wide bioinformatics to uncover phased secondary small interfering RNA (phasiRNA) regulatory modules active during tomato fruit ripening, linking them to traits such as color, firmness, brightness, and nutritional content. These findings lay groundwork for exploiting phasiRNAs in molecular breeding to improve tomato fruit quality.

The study compared tomato genotypes under supplemental far‑red light (W+FR) and identified the Solanum pennellii introgression line IL2-2 as shade‑tolerant, displaying reduced seedling elongation and altered auxin‑gene expression relative to the parental M82 line. While W+FR enhanced fruit quality (°Brix, ascorbic acid, carotenoids) in M82, IL2-2 maintained stable quality and showed higher fruit yield under high‑density planting, suggesting its utility for dense or intercropped agricultural systems.

The study investigates the role of the Arabidopsis transcription factor AtMYB93 in sulfur (S) signaling and root development, revealing that AtMYB93 mutants exhibit altered expression of S transport and metabolism genes and increased shoot S levels, while tomato plants overexpressing SlMYB93 show reduced shoot S. Transcriptomic profiling, elemental analysis, and promoter activity assays indicate that AtMYB93 contributes to root responses to S deprivation, though functional redundancy masks clear phenotypic effects on lateral and adventitious root formation.

The study presents a chromosome-level reference genome for the invasive fern Lygodium microphyllum and compares the transcriptomic and epigenomic profiles of its haploid gametophyte and diploid sporophyte phases, revealing differential regulation of developmental genes and similar methylation patterns across tissues. Base‑pair resolution methylome data and freezing‑stress experiments show that each life phase employs distinct molecular pathways for stress response, emphasizing the importance of considering both phases in invasive‑species management.

The study investigates the Arabidopsis ribosomal protein RPS6A and its role in auxin‑related root growth, revealing that rps6a mutants display shortened primary roots, fewer lateral roots, and defective vasculature that are not rescued by exogenous auxin. Cell biological observations and global transcriptome profiling show weakened auxin signaling and reduced levels of PIN auxin transporters in the mutant, indicating a non‑canonical function of the ribosomal subunit in auxin pathways.

The study investigates how miR394 influences flowering time in Arabidopsis thaliana by combining transcriptomic profiling of mir394a mir394b double mutants with histological analysis of reporter lines. Bioinformatic analysis identified a novel lncRNA overlapping MIR394B (named MIRAST), and differential promoter activity of MIR394A and MIR394B suggests miR394 fine‑tunes flower development through transcription factor and chromatin remodeler regulation.