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.

The study investigates how cytosine methylation influences flowering time under drought stress in Arabidopsis thaliana, using the drm1 drm2 cmt3 triple mutant (ddc). Drought delayed flowering by one day in wild type but two days in ddc, coinciding with overexpression of BBX16/COL7 and BBX17/COL8 and down‑regulation of NF‑YA2, suggesting a trans‑acting methylation‑dependent regulatory network affecting FT induction.

The study generated a temporal physiological and metabolomic map of leaf senescence in diverse maize inbred lines differing in stay‑green phenotype, identifying 84 metabolites associated with senescence and distinct metabolic signatures between stay‑green and non‑stay‑green lines. Integration of metabolite data with genomic information uncovered 56 candidate genes, and reverse‑genetic validation in maize and Arabidopsis demonstrated conserved roles for phenylpropanoids such as naringenin chalcone and eriodictyol in regulating senescence.

The study generated a high-quality genome assembly for Victoria cruziana and used comparative transcriptomics to identify anthocyanin biosynthesis genes and their transcriptional regulators that are differentially expressed between white and light pinkish flower stages. Differential expression of structural genes (VcrF3H, VcrF35H, VcrDFR, VcrANS, VcrarGST) and transcription factors (VcrMYB123, VcrMYB-SG6_a, VcrMYB-SG6_b, VcrTT8, VcrTTG1) correlates with the observed flower color change.

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 demonstrates that RNA extracted from herbarium specimens can be used to generate high‑quality transcriptomes, comparable to those from fresh or silica‑dried samples. By assembling and comparing transcriptomes across specimen types, the authors validated a plant immune receptor synthesized from a 1956 collection, proving archival RNA’s utility for functional genomics. These findings challenge the prevailing view that herbarium RNA is unsuitable for transcriptomic analyses.