TCP transcription factors play a key role in regulating various developmental processes, particularly in shoot branching, flower development, and leaf development, and these factors are exclusively found in plants. However, comprehensive studies investigating TCP transcription factors in pepper (Capsicum annuum L.) are lacking. In this study, we identified 27 CaTCP members in the pepper genome, which were classified into Class I and Class II through phylogenetic analysis. The motif analysis revealed that CaTCPs in the same class exhibit similar numbers and distributions of motifs. We predicted that 37 previously reported miRNAs target 19 CaTCPs. The expression levels of CaTCPs varied in various tissues and growth stages. Specifically, CaTCP16, a member of Class II (CIN), exhibited significantly high expression in flowers. Class I CaTCPs exhibited high expression levels in leaves, while Class II CaTCPs showed high expression in lateral branches, especially in the CYC/TB1 subclass. The expression profile suggests that CaTCPs play specific roles in the developmental processes of pepper. We provide a theoretical basis that will assist in further functional validation of the CaTCPs.

Transposable elements (TEs) serve as important drivers mediating polyploidization events and phenotypic diversification in plant genomes. However, the dynamic changes in various TE subclasses post-polyploidization and their mechanisms of influencing phenotypic variation require further investigation. The allopolyploid Gossypium species, originating from two diploid progenitors, provide an ideal model for studying TE dynamics following polyploidization. This study investigated TE dynamics post-polyploidization based on 21 diploid and 7 polyploid cotton genomes. The Tekay subclass of the Gypsy serves as a major driver of Gossypium genome evolution, as it underwent two burst events in the At-subgenome and its progenitor, exhibiting the highest abundance, longest length, and largest proportion among all TE subclasses. In contrast, the Gopia superfamily Tork subclass has lower abundance but greater genic association, facilitating environmental adaptation and phenotypic variation. Additionally, a pan-TE-related structural variation, the pan-TRV map, was constructed by integrating resequencing data from 256 accessions. Genome-wide analysis of 28 cotton genomes identified 142,802 TRVs, among which 72,116 showed polymorphisms in the 256 G. hirsutum accessions. The Gypsy superfamily, particularly the Tekay subclass, has been identified as a major source of TRVs, while Copia-type elements demonstrate significantly greater enrichment in gene-proximal genomic regions. A total of 334 TRVs exhibiting statistically significant associations with 10 key phenotypic traits, including 164 TRVs affecting yield components and 170 TRVs determining fiber quality. This investigation delineates the evolutionary significance of transposable elements in Gossypium genome diversification while simultaneously providing novel functional markers and potential editing targets for genetic dissection and molecular breeding of key agronomic traits in cotton.

Vanillin, the principal aromatic compound in vanilla, is primarily derived from mature pods of vanilla (Vanilla planifolia Andrews). Although the biosynthetic pathway of vanillin has been progressively elucidated, the specific key enzymes and transcription factors (TFs) governing vanillin biosynthesis require further comprehensive investigation via combining transcriptomic and metabolomic analysis. For this study, V. planifolia (higher vanillin producer) and V. imperialis (lower vanillin producer) were selected. Time-series metabolomics analysis revealed 160–220 days after pollination (DAPs) as the critical phase for vanillin biosynthesis. Combined time-series transcriptome analysis revealed 984 upregulated differentially expressed genes (DEGs) in key periods, 2058 genes with temporal expression, and 4326 module genes through weighted gene co-expression network analysis (WGCNA), revealing six major classes of TFs: No Apical Meristem (NAC), Myb, WRKY, FLOWERING PROMOTING FACTOR 1-like (FPFL), DOF, and PLATZ. These TFs display strong regulatory relationships with the expression of key enzymatic genes, including P450s, COMT, and 4CL. The NAC TF family emerged as central regulators in this network, with NAC-2 (HPP92_014056) and NAC-3 (HPP92_012558) identified as key hub genes within the vanillin biosynthetic gene co-expression network. The findings of this study provide a theoretical foundation and potential target genes for enhancing vanillin production through genetic and metabolic engineering approaches, offering new opportunities for sustainable development in the vanilla industry and related applications.