Xinlong Gao

Plant SABATH methyltransferases contribute to volatile formation, hormone homeostasis and stress responses, but their family-wide organization in sunflower remains poorly characterized. Using the HanXRQr2.0-SUNRISE reference genome, we identified 33 high-confidence HaSABATH genes and integrated phylogenetic, duplication, synteny, promoter and protein-structure analyses with expression profiles from 200 public RNA sequencing (RNA-seq) libraries representing 87 distinct conditions. Twelve genes belonged to the salicylic acid/jasmonic acid methyltransferase-related Clade I, 19 to the benzoic acid/salicylic acid methyltransferase-related Clade II, and two to other lineages. Tandem, proximal, dispersed and whole-genome/segmental duplication contributed to the family, with overlapping tandem and segmental evidence for HaSABATH4 and HaSABATH15. Eleven reliable nonsynonymous-to-synonymous substitution ratios were below one. Most predicted proteins showed high model confidence. Across the sampled conditions, Clade I members generally showed higher expression levels and broader expression, while many Clade II members were weakly expressed or condition-biased. HaSABATH4 and HaSABATH6 were prioritized for follow-up under combined saline–alkali stress. This integrated analysis links evolutionary context to expression divergence and provides candidates for targeted biochemical and genetic studies.

In this study, we performed the first genome-wide identification and characterization of the cinnamoyl-CoA reductase (CCR) gene family in upland cotton (Gossypium hirsutum), focusing on its potential association with stem strength. We identified 76 GhCCR genes and classified them into four subfamilies. We then analyzed their evolutionary relationships, conserved domains, synteny, promoter cis-elements, and expression patterns. All GhCCR proteins possess the NADB_Rossmann superfamily domain, and family expansion appears to have been driven mainly by segmental and tandem duplications. A small number of GhCCR genes showed relatively high expression in leaf, pistil, and torus tissues, while genes such as GhCCR3/9/10 exhibited elevated transcript levels under abiotic stress conditions. RT-qPCR results indicated that three candidate GhCCR genes (GhCCR25, GhCCR52 and GhCCR64) were significantly more highly expressed in multiple tissues of the stiff-stem line JY-25 than in the soft-stem line JR-15. Together, these findings suggest that GhCCR genes may contribute to the regulation of growth, development, and stress adaptation in G. hirsutum. However, direct biochemical or genetic validation is required to confirm their functional roles in lignin biosynthesis and stem rigidity.

RNA editing in various organisms commonly restores RNA sequences to their ancestral state, but its adaptive advantages are debated. In fungi, restorative editing corrects premature stop codons in pseudogenes specifically during sexual reproduction. We characterized 71 pseudogenes and their restorative editing in Fusarium graminearum , demonstrating that restorative editing of 16 pseudogenes is crucial for germ tissue development in fruiting bodies. Our results also revealed that the emergence of premature stop codons is facilitated by restorative editing and that premature stop codons corrected by restorative editing are selectively favored over ancestral amino acid codons. Furthermore, we found that ancestral versions of pseudogenes have antagonistic effects on reproduction and survival. Restorative editing eliminates the survival costs of reproduction caused by antagonistic pleiotropy and provides a selective advantage in fungi. Our findings highlight the importance of restorative editing in the evolution of fungal complex multicellularity and provide empirical evidence that restorative editing serves as an adaptive mechanism enabling the resolution of genetic trade-offs.