The study investigates the evolutionary shift from archegonial to embryo‑sac reproduction by analyzing transcriptomes of Ginkgo reproductive organs and related species. It reveals that the angiosperm pollen‑tube guidance module MYB98‑CRP‑ECS is active in mature Ginkgo archegonia and that, while egg cell transcription is conserved, changes in the fate of other female gametophyte cells drove the transition, providing a molecular framework for this major reproductive evolution.

The study profiled small interfering RNAs (siRNAs) in barley (Hordeum vulgare) seeds differing in viability after controlled long‑term storage, identifying 85,728 differentially expressed siRNAs associated with seed vigor. Trans‑acting siRNAs displayed distinct temporal patterns during imbibition, and functional analyses linked siRNA targets to key processes such as cytochrome activity, root development, and carbohydrate metabolism, suggesting a role in maintaining metabolic activity during germination.

The study integrates genome, transcriptome, and chromatin accessibility data from 380 soybean accessions to dissect the genetic and regulatory basis of symbiotic nitrogen fixation (SNF). Using GWAS, TWAS, eQTL mapping, and ATAC-seq, the authors identify key loci, co‑expression modules, and regulatory elements, and validate the circadian clock gene GmLHY1b as a negative regulator of nodulation via CRISPR and CUT&Tag. These resources illuminate SNF networks and provide a foundation for soybean improvement.

The study demonstrates that in barley (Hordeum vulgare) the MAPK pathway, specifically the MKK3 kinase, controls grain dormancy through a combination of haplotype variation, copy-number changes, and intrinsic kinase activity. Historical selection of particular MKK3 haplotypes correlates with climatic pressures, offering a genetic basis to balance short dormancy with resistance to pre‑harvest sprouting under climate change.

A comparative physiological study of persimmon cultivars with flat (Hiratanenashi) and round (Koushimaru) fruit shapes revealed that differences in cell proliferation, cell shape, and size contribute to shape variation. Principal component analysis of elliptic Fourier descriptors tracked shape changes, while histology and transcriptome profiling identified candidate genes, including a WOX13 homeobox gene, potentially governing fruit shape development.

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 performed transcriptome profiling of Cryptomeria japonica individuals from different geographic origins grown in three common gardens across Japan, assembling 77,212 transcripts guided by the species' genome. Using SNP-based genetic clustering and weighted gene co‑expression network analysis, they identified gene modules whose expression correlated with genetic differentiation, revealing that defense‑related genes are up‑regulated in Pacific‑side populations while terpenoid metabolism genes are higher in Sea‑of‑Japan populations, indicating local adaptation via regulatory changes.