The authors conducted a comprehensive phylogenetic and sequence analysis of the conserved YUCCA (YUC) gene family across representative plant lineages, classifying the family into six major classes and 41 subclasses. They linked YUC diversification to protein sequence conservation and spatial/temporal gene expression patterns, providing a framework for future functional investigations of auxin biosynthesis.

The study shows that heatwaves impair the ability of apple (Malus domestica) to mount ASM‑induced immunity against fire blight and apple scab, leading to a loss of protective gene expression. Transcriptomic analysis revealed a broad suppression of ASM‑regulated defense and other biological processes under high temperature, identifying thermo‑sensitive resistance and susceptibility marker genes. The findings highlight that elevated temperature both weakens plant defenses and creates a more favorable environment for pathogens.

The study analyzes ancient maize genomes from a 500–600 BP Bolivian offering and compares them with 16 archaeological samples spanning 5,000 years and 226 modern Zea mays lines, revealing close genetic affinity to ancient Peruvian maize and increased diversity during Inca‑local interactions. Phylogenetic and phenotypic analyses of ovule development indicate targeted breeding for seed quality and yield, suggesting culturally driven selection was already established by the 15th century CE.

The study identified a major QTL (qDTH3) on chromosome 3 responsible for a 7‑10‑day earlier heading phenotype in the rice line SM93, using QTL‑seq, KASP genotyping, association mapping, and transcriptomic analysis to fine‑map the locus to a 2.53 Mb region and pinpoint candidate genes. SNP markers linked to these genes were proposed as tools for breeding early‑maturing, climate‑resilient rice varieties.

The study compares transcriptional, proteomic, and metabolomic responses of wild‑type Arabidopsis and a cyp71A27 mutant to a plant‑growth‑promoting Pseudomonas fluorescens strain and a pathogenic Burkholderia glumeae strain, revealing distinct reprogramming and an unexpected signaling role for the non‑canonical P450 CYP71A27. Mutant analysis showed that loss of CYP71A27 alters gene and protein regulation, especially during interaction with the PGP bacterium, while having limited impact on root metabolites and exudates.

Using a barley pangenome of 76 genotypes and a pan‑transcriptome subset of 20, the study characterizes the diversity and evolutionary dynamics of CCT motif genes, uncovering novel frameshift variants and clade‑specific domain expansions. Phylogenetic and tissue‑specific expression analyses reveal functional divergence among paralogs, and the unexpected retention of the VRN2 repressor in spring barley suggests additional regulatory mechanisms beyond vernalization.

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.

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 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.

The study characterizes all seven malic enzyme genes in tomato, analyzing their tissue-specific expression, temperature and ethylene responsiveness, and linking specific isoforms to metabolic processes such as starch and lipid biosynthesis during fruit development. Phylogenetic, synteny, recombinant protein biochemical assays, and promoter analyses were used to compare tomato enzymes with Arabidopsis counterparts, revealing complex evolutionary dynamics that decouple phylogeny from functional orthology.