The study examined how DNA methylation influences cold stress priming in Arabidopsis thaliana, revealing that primed plants exhibit distinct gene expression and methylation patterns compared to non-primed plants. DNA methylation mutants, especially met1 lacking CG methylation, showed altered cold memory and misregulation of the CBF gene cluster, indicating that methylation ensures transcriptional precision during stress recall.

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.

The study generated the first high-quality avocado pangenome from seven genetically diverse accessions using PacBio HiFi long‑read sequencing and partially phased, near chromosome‑level assemblies. Comparative analyses revealed lineage‑specific expansions and extensive diversity of NLR immune genes, with accessory regions enriched for pathogen response and secondary metabolism, providing a graph‑based framework for resistance breeding.

The study generated a watermelon super‑pangenome from 138 high‑quality, near‑gapless assemblies covering all seven species, uncovering ~1 million structural variants (SVs) and enabling precise SV genotyping across ~900 accessions. Incorporating SVs into genome‑wide association studies pinpointed a dosage‑dependent copy‑number variant affecting flesh color, and the comprehensive variant map supported accurate genomic prediction for 18 agronomic traits, providing a framework for precision breeding in watermelon.

The study constructs a graph-based cucumber pangenome from 39 high-quality assemblies, identifying 171,892 high-confidence structural variants (SVs) and genotyping them across 443 diverse accessions. Analyses reveal that SVs are more strongly purged than mildly deleterious SNPs during domestication and expansion, with gene flow contributing to increased SV burden in African and European populations, and demonstrate that incorporating SV burden improves genomic prediction of key agronomic traits.

The study generated high‑quality genome assemblies for 12 indica and japonica rice accessions and demonstrated that structural variants (SVs) are abundant and strongly associated with heterosis across 17 agronomic traits. Correlation analyses revealed that SV count between parental lines predicts hybrid performance, and functional validation of SVs in S5‑ORF5 and OsBZR1 confirmed their contributions to seed setting rate and yield heterosis, supporting an overdominance model for inter‑subspecific hybrid vigor.