The study generated a high-quality, phased diploid reference genome for the grapevine cultivar Pinot noir and combined it with Oxford Nanopore sequencing of 23 clones to map genome-wide genetic and epigenetic variation. While somatic SNPs and structural variants are rare and depleted from coding regions, extensive CG methylation differences were found within gene bodies and accurately recapitulated clonal phylogenies, indicating stable, mitotically inherited epialleles that record propagation history.

The study generated chromosome‑scale de novo assemblies for two wild tomato relatives, Solanum pennellii and Solanum cheesmaniae, using PacBio HiFi, Oxford Nanopore ultra‑long reads, and Hi‑C scaffolding, achieving >99% completeness. Comparative analysis with nine Lycopersicon clade genomes revealed species‑specific structural variants and independent Tekay retrotransposon expansions, while recombination mapping in 709 backcross hybrids demonstrated higher female crossover rates and identified gender‑biased recombination regions and coldspots associated with large structural differences.

The study reveals that red pigmentation in quinoa (Chenopodium quinoa) epidermal bladder cells is due to a ~4‑kb genomic insertion that restores the full-length CYP76AD gene, which is the rate‑limiting enzyme for betacyanin synthesis. Cell‑type‑specific RNA‑sequencing showed that this restored CYP76AD is highly upregulated in red bladder cells, and subgenome analysis indicated B‑subgenome dominance for this gene in pigmented tissues.

The authors used a bottom‑up thermodynamic modelling framework to investigate how plants decode calcium signals, starting from Ca2+ binding to EF‑hand proteins and extending to higher‑order decoding modules. They identified six universal Ca2+-decoding modules that can explain variations in calcium sensitivity among kinases and provide a theoretical basis for interpreting calcium signal amplitude and frequency in plant cells.

Chromosome-level, 100% complete genomes of the Australian mango cultivar Kensington Pride and the wild relative M. laurina were assembled using high-coverage PacBio HiFi sequencing. Comparative analyses uncovered extensive structural variation, identified key genes in carotenoid, anthocyanin, and terpenoid pathways, and pinpointed a SNP in the β-1,3-glucanase 2 gene associated with anthracnose resistance. Whole-genome duplication and collinearity analyses revealed two polyploidization events and conserved gene blocks across mango genomes.

The study used Arabidopsis thaliana mutants with low (vtc2, vtc4) and high (vtc2/OE-VTC2) ascorbate levels to examine how ascorbate concentration affects gene expression and cellular homeostasis. Transcriptomic analysis revealed that altered ascorbate levels modulate defense and stress pathways, and that TAA1/TAR2‑mediated auxin biosynthesis is required for coping with elevated ascorbate in a light‑dependent manner.

The authors present a straightforward protocol that uses brief exposure to the topoisomerase II inhibitor etoposide to generate heritable structural variants in plants, demonstrated in Arabidopsis thaliana with high frequency. Long-read sequencing and genetic analyses revealed deletions and inversions responsible for semi‑dominant and recessive phenotypes, offering a low‑resource alternative to irradiation for inducing large‑effect genomic changes.