The study investigates the gene regulatory network (GRN) controlling flowering time in the allotetraploid crop Brassica napus by comparing its transcriptome to that of Arabidopsis thaliana. While most orthologous gene pairs show conserved expression dynamics, several flowering‑time genes display regulatory divergence, especially under cold conditions, indicating subfunctionalisation among paralogues. Despite these differences, the overall GRN topology remains similar to Arabidopsis, likely due to retention of multiple paralogues.

The study used comparative transcriptomics of dorsal and ventral petals across development, alongside expression profiling in floral symmetry mutants, to identify genes linked to dorsal (AmCYC-dependent) and ventral (AmDIV-dependent) identities in Antirrhinum majus. In situ hybridisation validated axis‑specific and boundary‑localized expression patterns, revealing that a conserved NGATHA‑LIKE1‑BRASSINAZOLE‑RESISTANT1‑miR164 module has been co‑opted to regulate AmDIV targets and shape the corolla. These findings delineate regulatory modules coordinating dorsoventral and proximal‑distal patterning in zygomorphic flowers.

The study sequenced genomes of ericoid mycorrhiza‑forming liverworts and experimentally reconstituted the symbiosis, revealing a nutrient‑regulated state that supports intracellular colonization. Comparative transcriptomics identified an ancestral gene module governing intracellular symbiosis, and functional validation in Marchantia paleacea through genetic manipulation, phylogenetics, and transactivation assays confirmed its essential role. The findings suggest plants have retained and independently recruited this ancestral module for diverse intracellular symbioses.

The study benchmarked several sampling approaches for simultaneous profiling of root exudates and rhizosphere microbiota in soil-grown barley, revealing consistent exudate chemistry across methods but variation in root morphology and nitrogen exudation. High‑throughput amplicon sequencing and quantitative PCR showed protocol‑specific impacts on microbial composition, yet most rhizosphere-enriched microbes were captured by all approaches. The authors conclude that different protocols provide comparable integrated data, though methodological differences must be aligned with experimental objectives.

The study used comparative transcriptomics across Erysimum species to identify two 2‑oxoglutarate‑dependent dioxygenases, CARD5 and CARD6, responsible for the 14β‑ and 21‑hydroxylation steps in cardenolide biosynthesis in Erysimum cheiranthoides. Knockout mutants lacking these genes accumulated pathway intermediates, and transient expression in Nicotiana benthamiana confirmed their enzymatic functions, while structural modeling pinpointed residues linked to neofunctionalization.

The study used comparative and de‑novo transcriptomic analyses in poplar to uncover plant and fungal gene regulons that govern ectomycorrhizal (ECM) compatibility, distinguishing general fungal‑sensing responses from ECM‑specific pathways. Key findings include modulation of jasmonic acid‑related defenses, coordinated regulation of secretory and cell‑wall remodeling genes, and dynamic expression of the Common Symbiosis Pathway during early and mature symbiosis stages.

The study compared early protective, repair, and stress responses to chronic gamma irradiation in the radiosensitive conifer Norway spruce (Picea abies) and the radiotolerant Arabidopsis thaliana. Norway spruce exhibited growth inhibition, mitochondrial damage, and higher DNA damage at low dose rates, while Arabidopsis maintained growth, showed minimal organelle damage, and activated DNA repair and antioxidant genes even at the lowest dose rates. Transcriptomic analysis revealed that the tolerant species mounts a robust transcriptional response at low doses, whereas the sensitive species only responds at much higher doses.

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 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 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.