Genome-Wide Identification, Quantification, and Validation of Differentially Expressed miRNAs in Eggplant (Solanum melongena L.) Based on Their Response to Ralstonia solanacearum Infection

Decoding drought resilience: a comprehensive exploration of the cotton Eceriferum (CER) gene family and its role in stress adaptation

BACKGROUND

The cuticular wax serves as a primary barrier that protects plants from environmental stresses. The Eceriferum (CER) gene family is associated with wax production and stress resistance.

RESULTS

In a genome-wide identification study, a total of 52 members of the CER family were discovered in four Gossypium species: G. arboreum, G. barbadense, G. raimondii, and G. hirsutum. There were variations in the physicochemical characteristics of the Gossypium CER (GCER) proteins. Evolutionary analysis classified the identified GCERs into five groups, with purifying selection emerging as the primary evolutionary force. Gene structure analysis revealed that the number of conserved motifs ranged from 1 to 15, and the number of exons varied from 3 to 13. Closely related GCERs exhibited similar conserved motifs and gene structures. Analyses of chromosomal positions, selection pressure, and collinearity revealed numerous fragment duplications in the GCER genes. Additionally, nine putative ghr-miRNAs targeting seven G. hirsutum CER (GhCER) genes were identified. Among them, three miRNAs, including ghr-miR394, ghr-miR414d, and ghr-miR414f, targeted GhCER09A, representing the most targeted gene. The prediction of transcription factors (TFs) and the visualization of the regulatory TF network revealed interactions with GhCER genes involving ERF, MYB, Dof, bHLH, and bZIP. Analysis of cis-regulatory elements suggests potential associations between the CER gene family of cotton and responses to abiotic stress, light, and other biological processes. Enrichment analysis demonstrated a robust correlation between GhCER genes and pathways associated with cutin biosynthesis, fatty acid biosynthesis, wax production, and stress response. Localization analysis showed that most GCER proteins are localized in the plasma membrane. Transcriptome and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) expression assessments demonstrated that several GhCER genes, including GhCER15D, GhCER04A, GhCER06A, and GhCER12D, exhibited elevated expression levels in response to water deficiency stress compared to control conditions. The functional identification through virus-induced gene silencing (VIGS) highlighted the pivotal role of the GhCER04A gene in enhancing drought resistance by promoting increased tissue water retention.

CONCLUSIONS

This investigation not only provides valuable evidence but also offers novel insights that contribute to a deeper understanding of the roles of GhCER genes in cotton, their role in adaptation to drought and other abiotic stress and their potential applications for cotton improvement.

Genome-Wide Identification and Expression Analysis of Respiratory Burst Oxidase Homolog (RBOH) Gene Family in Eggplant (Solanum melongena L.) under Abiotic and Biotic Stress

Respiratory burst oxidase homologs (RBOHs) are important proteins that catalyze the production of reactive oxygen species (ROS), which play important roles in growth and stress response. For a comprehensive analysis of SmRBOH genes, we conducted genome-wide identification of the SmRBOH gene family in eggplant (Solanum melongena L.) and analyzed the expression of SmRBOHs under abiotic (salt, high-temperature, and low-temperature) and biotic stress (Verticillium dahliae inoculation) by quantitative real-time PCR (qRT-PCR). The result showed that a total of eight SmRBOH members were identified from the genome database of eggplant, and they were relatively evenly distributed across seven chromosomes. The analysis of Motif and the conserved domain showed that SmRBOHs have high similarity in protein sequences and functions. Based on phylogenetics, SmRBOHs were classified into three distinct clades. Furthermore, the promoter regions of SmRBOHs were found to contain different cis-elements. Additionally, the results of the qRT-PCR demonstrated differential expression patterns of SmRBOHs in different tissues (the roots, stems, and leaves) and stress conditions. SmRBOHB, SmRBOHD, SmRBOHH1, and SmRBOHH2 showed significant upregulation (>20-fold) under at least one stress condition. Subcellular localization analysis of the above four members further confirmed that they localized on the plasma membrane. This study provides a theoretical foundation for understanding the functions of SmRBOHs in eggplant.

Comprehensive analysis of NAC transcription factors in Scutellaria baicalensis and their response to exogenous ABA and GA3

The NAC is a plant-specific family of transcription factor that plays important roles in various biological processes. Scutellaria baicalensis Georgi, belongs to the Lamiaceae family and has been widely used as a traditional herb with a wide range of pharmacological activities, including antitumor, heat-clearing, and detoxifying functions. However, no study on the NAC family in S. baicalensis has been conducted to date. In the present study, we identified 56 SbNAC genes using genomic and transcriptome analyses. These 56 SbNACs were unevenly distributed across nine chromosomes and were phylogenetically divided into six clusters. Cis-element analysis identified plant growth and development-, phytohormone-, light-, and stress-responsive elements were present in SbNAC genes promoter regions. Protein-protein interaction analysis was performed using Arabidopsis homologous proteins. Potential transcription factors, including bHLH, ERF, MYB, WRKY, and bZIP, were identified and constructed a regulatory network with SbNAC genes. The expression of 12 flavonoid biosynthetic genes was significantly upregulated with abscisic acid (ABA) and gibberellin (GA₃) treatments. Eight SbNAC genes (SbNAC9/32/33/40/42/43/48/50) also exhibited notable variation with two phytohormone treatments, among which SbNAC9 and SbNAC43 showed the most significant variation and deserved further study. Additionally, SbNAC44 displayed a positive correlation with C4H3, PAL5, OMT3, and OMT6, while SbNAC25 had negatively correlated with OMT2, CHI, F6H2, and FNSII-2. This study constitutes the first analysis of SbNAC genes and lays the basis foundation for further functional studies of SbNAC genes family members, while it may also facilitate the genetic improvement of plants and breeding of elite S. baicalensis varieties.