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.

The study combined long‑read whole‑genome assembly, multi‑omics profiling (DNA methylation, mRNA, ribosome‑associated transcripts, tRNA abundance, and protein levels) in two Arabidopsis thaliana accessions to evaluate how genomic information propagates through the Central Dogma. Codon usage in gene sequences emerged as the strongest predictor of both mRNA and protein abundance, while methylation, tRNA levels, and ribosome‑associated transcripts contributed little additional information under stable conditions.

The study performed a comprehensive computational analysis of the Arabidopsis thaliana proteome, classifying 48,359 proteins by melting temperature (Tm) and melting temperature index (TI) and linking thermal stability to amino acid composition, molecular mass, and codon usage. Machine‑learning and evolutionary analyses revealed that higher molecular mass and specific codon pairs correlate with higher Tm, and that gene duplication has driven the evolution of high‑Tm proteins, suggesting a genomic basis for stress resilience.