Genome-Wide Analysis of the GRF-GIF Module in Coffea arabica L.: Insights into the Starlet-Flower Phenomenon

Genome-Wide Exploration of SUPPRESSOR OF MAX2 1-LIKE Genes in Peanut (Arachis hypogaea) Reveals Developmental and Stress-responsive Expression Patterns

Genome-Wide Identification of the CmTIFY Gene Family and Analysis of Its Expression Patterns under Cold Stress (Cucumis melo L.)

Genome-Wide Characterization of PEBP, FD, and GRF Families in Amomum villosum Lour. and Their Potential Roles in Flowering

A detailed understanding of the molecular mechanisms governing the flowering time of Amomum villosum Lour., a medicinal plant within the Zingiberaceae family, is currently lacking. In modern plants, the florigen activation complex (FAC), which includes PEBP, FD/bZIP, and GRF proteins, is known to regulate flowering. In this study, we identified 13 PEBP, 5 FD, and 19 GRF genes within the A. villosum genome and conducted phylogenetic, structural and promoter analysis. Notably, cross-species protein–protein interaction predictions and yeast two-hybrid assays uncovered an unexpected interaction pattern: an AREB3-like FD protein (AvFD5) and a GRF protein (AvGRF13) directly interact with specific PEBP members, whereas canonical FD-like proteins (AvFD1 and AvFD4) did not, which contrasts with the classical rice FAC model (Hd3a-14-3-3-OsFD1). These results imply that FAC assembly in A. villosum may involve alternative components or regulatory mechanisms, potentially indicating lineage-specific divergence within monocots. This research represents the first systematic characterization of FAC core gene families in A. villosum and Zingiberaceae, laying the groundwork for understanding flowering time regulation and facilitating future molecular breeding efforts in this economically significant plant.

Evolutionary Analysis and Expression Profiling of the TIFY Gene Family in Banana Under Multiple Stresses and Functional Characterization of MaTIFY20 in Drought Tolerance

A genome-wide identification and comprehensive analysis of the MaTIFY gene family in Musa acuminata provides novel insights into the evolutionary dynamics and stress-responsive functions of banana TIFY genes and identifies candidate targets for molecular breeding to improve abiotic and biotic stress resilience in banana.

The SlDUF789 Gene Family in Tomato: Genome-Wide Identification and Responsiveness to Hormonal and Abiotic Stress Signals

The DUF789 protein family comprises conserved domain proteins in plants, most of which remain functionally uncharacterized despite their involvement in growth, development, and stress responses. Moreover, systematic identification of the DUF789 family in tomato (Solanum lycopersicum L.) has not been reported. In this study, 11 SlDUF789 members were identified from the tomato genome, unevenly distributed across seven chromosomes, with members within the same subgroup sharing similar exon–intron structures and conserved motifs. Promoter analysis revealed the enrichment of cis-acting elements associated with light, hormone, and stress responses. Quantitative real-time PCR (qRT-PCR) analysis revealed diverse expression patterns across tissues: most SlDUF789 members exhibited relatively high expression levels in reproductive tissues, whereas SlDUF789-7 was broadly expressed across all tissues, with elevated expression in fully open flowers and red-ripe fruits. Under stress and hormone treatments, SlDUF789-7 exhibited the highest induction under ABA and salt stress; SlDUF789-8 under MeJA and PEG; and SlDUF789-11 under SA and low-light. Notably, SlDUF789-7 responded strongly across all treatments, whereas SlDUF789-11 showed sustained upregulation under low-light stress. This study provides the first systematic characterization of the SlDUF789 gene family in tomato and establishes a foundation for future research on their biological functions and potential roles in stress responses.

Genome-Wide Identification of the CmABF Gene Family in Melon (Cucumis melo L.) and Their Response to Ozone and ABA

Melon (Cucumis melo L.) is a globally significant horticultural crop whose fruit quality and postharvest shelf life are profoundly influenced by oxidative stress. Abscisic acid (ABA)-responsive element binding factors (ABFs), which represent the Group A subfamily of the basic leucine zipper (bZIP) transcription factor family, serve as pivotal components in the ABA signaling pathway. These factors play essential roles in regulating plant responses to abiotic stress as well as fruit development and maturation processes. In this study, a total of nine CmABF gene family members (CmABF1–CmABF9) were successfully identified within the melon genome using genome-wide identification techniques. Bioinformatic analysis indicated that all CmABF proteins contain a conserved bZIP domain. Physicochemical property analysis revealed that most of these proteins are unstable hydrophilic proteins and all are localized to the cell nucleus. Phylogenetic analysis categorized the CmABF family into three distinct evolutionary branches (Groups A, B, and C), exhibiting high conservation with homologous genes in Arabidopsis thaliana, Solanum tuberosum, and other species. Promoter analysis demonstrated that CmABF genes are rich in hormone-responsive elements (such as abscisic acid-responsive element (ABRE) and gibberellin-responsive element (GARE)) and stress-responsive elements (such as MYB binding sites (MBS) and anaerobic-response element (ARE)). To investigate their responses to oxidative stress and ABA signaling, we analyzed the expression patterns of these genes in melon fruit at 0, 7, 14, 21, 28, and 35 days of postharvest storage under ozone (O3, an oxidative stressor), exogenous abscisic acid (ABA), and the ABA synthesis inhibitor nordihydroguaiaretic acid (NDGA) using RNA-seq and qRT-PCR. The results showed that ozone treatment significantly induced the up-regulation of CmABF9 while inhibiting the early expression of CmABF2 and CmABF4. ABA treatment generally promoted the transcription of family members during the late stages of storage (35 d). NDGA treatment suppressed the expression of CmABF2 and CmABF4 during the early storage stage (7 d), while markedly increasing their expression levels at later storage stages (28 d and 35 d), suggesting a compensatory feedback response under endogenous ABA deficiency. Furthermore, protein–protein interaction predictions indicated potential close interactions between CmABF proteins and SnRK2 protein kinases. This study provides a theoretical basis for elucidating the molecular mechanisms of the CmABF family in regulating postharvest oxidative stress in melon and provides candidate gene resources for molecular breeding aimed at enhancing resistance and extending the shelf life of melon fruit.