It has been confirmed that the plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) gene family plays a pivotal role during plant growth and development. M. candidum is a native ornamental species and has a wide range of pharmacodynamic effects. However, there is still a lack of research on TCP’s role in controlling M. candidum’s development, abiotic stress responses and hormone metabolism. A comprehensive description of the TCP gene family in M. candidum is urgently needed. In this study, we used the HMMER search method in conjunction with the BLASTp method to identify the members of the TCP gene family, and a total of 35 TCP genes were identified. A domain analysis further confirmed that all 35 TCPs contained a TCP superfamily, a characteristic involved in dimerization and DNA binding that can be found in most genes from this gene family, suggesting that our identification was effective. As a result of the domain conservation analysis, the 35 TCP genes could be classified into two classes, TCP-P and TCP-C, based on the conservative regions of 55 and 59 amino acids, respectively. Gene-duplication analysis revealed that most TCP genes were present in duplication events that eventually led to TCP gene expansion in M. candidum. All the detected gene pairs had a Ka/Ks value of less than one, suggesting that purification selection is the most important factor that influences the evolution of TCP genes. Phylogenetic analysis of three species displayed the evolutionary relationship of TCP genes across different species and further confirmed our results. The real-time quantitative PCR (qRT-PCR) results showed that McTCP2a, McTCP7a, McTCP10, McTCP11, McTCP12a, McTCP13, McTCP16, McTCP17, McTCP18, McTCP20 and McTCP21 may be involved in leaf development; McTCP4a, McTCP1, McTCP14, McTCP17, McTCP18, McTCP20, McTCP22 and McTCP24 may be involved in flower development; and McTCP2a, McTCP3, McTCP5a, McTCP6, McTCP7a, McTCP9, McTCP11, McTCP14 and McTCP16 may be involved in seed development. Our results dissect the TCP gene family across the genome of M. candidum and provide valuable information for exploring TCP genes to promote molecular breeding and property improvement of M. candidum in the future.

The MYB gene family is significant in plants, playing a role in numerous plant development processes, including metabolism, hormone signal transduction, cell identity, and biotic and abiotic stresses. Due to the recent availability of the Melastoma candidum genome, this is the first time that the MYB gene family has been identified in this species. This study identified 421 MYB gene members in the M. candidum genome using the HMMER search and BLASTp method. These MYBs were further divided into 10 sub-types, including R2R3, R-R, CPC-like, CCA1-like, TBP-like, R1R2R3, I-box, atypical MYB, MYB-CC, and MYB-like. Domain and conservation analyses revealed that each type of MYB was characterized by a different number and combination of SANTs/myb DNA-binding domains. Collinearity analysis revealed several gene duplication events within the MYB gene family. The Ka to Ks ratio suggested that most of the MYB genes underwent purifying selection during the evolution process. Phylogenetic analysis among three species confirmed our findings and displayed the evolutionary relationship of MYB genes in different species. RNA-seq of three developmental stages of flowers and WGCNA analysis identified McMYB113h, McMYB21b, and McGLK1c as playing a pivotal role during flower development in M. candidum. Finally, we conducted qRT-PCR experiments for 20 flower-development-related MYBs across 9 tissues to illustrate their expression patterns in M. candidum. This study establishes a foundation for exploring MYB gene resources and their potential applications in related industries of M. candidum.

The NAC transcription factor family represents a large group of plant-specific genes involved in various biological processes, including secondary metabolite biosynthesis, responses to biotic and abiotic stresses, and hormone signaling. Taxus yunnanensis, a well-known medicinal plant, is the natural source of the anticancer diterpene paclitaxel. Despite the biological importance of NAC transcription factors, no comprehensive genome-wide study of the NAC gene family has been conducted in T. yunnanensis. In this study, 44 NAC genes were identified from the T. yunnanensis genome. Gene structure analysis revealed that the number of exons ranged from 1 to 7, with most genes containing 2 to 3 exons. Chromosomal mapping showed an uneven distribution of TyuNACs across the 11 chromosomes. Duplication type analysis indicated that dispersed duplication is the primary mechanism driving the expansion of the TyuNACs, accounting for the largest proportion (24 genes), followed by tandem (12 genes) and proximal duplications (8 genes); no whole-genome or segmental duplication events were detected. Cis-regulatory element analysis suggested that TyuNACs are involved in key biological processes such as development, light response, stress adaptation, and hormone signaling. Expression profiling revealed diverse tissue-specific expression patterns, with most TyuNACs highly expressed in bark. Moreover, qRT-PCR analysis demonstrated that several TyuNACs respond to methyl jasmonate (MeJA) treatment. Yeast one-hybrid and related assays revealed that TyuNAC30 functions as a negative regulator of TyuDBTNBT, a key enzyme gene in the paclitaxel biosynthetic pathway. This study presents the comprehensive genome-wide characterization of the NAC transcription factor family in T. yunnanensis. The findings underscore the predominant role of dispersed duplication in the expansion of the TyuNAC family, with additional contributions from tandem and proximal duplications. Importantly, TyuNAC30 was identified as a negative regulator of TyuDBTNBT, suggesting a key role in the transcriptional regulation of paclitaxel biosynthesis. These findings offer valuable insights for further exploration of the functional roles of NAC genes, particularly their involvement in the regulatory mechanisms underlying paclitaxel biosynthesis.

Robinia pseudoacacia (black locust) is a widely introduced and extensively cultivated species notably for its specialized thorn-like structure, known as the stipular spine. Here, combining Oxford Nanopore high-accuracy long-read sequencing and high-throughput chromatin conformation capture (Hi-C) scaffolding, a de novo, chromosome-level assembly of the R. pseudoacacia genome is presented, with a total size of 681.6 Mb and an N50 of 1.1 Mb. Observations showed that fiber cells beneath the epidermis of stipular spines undergo extensive lignification. The total lignin content is significantly higher in stipular spines (48.57%−63.71%) than in stem xylem (24.57%−27.99%), with syringyl (S-type) lignin being the predominant form in both, accounting for 69.79%−73.27% of the total lignin. By leveraging this genome, the transcriptomic and time-ordered gene co-expression network (TO-GCN) analyses uncovered core regulatory networks underlying stipular spine lignification, in which NAC transcription factors RopNST1/2 regulate secondary cell wall thickening and lignin biosynthesis during stipular spine hardening and the monolignol biosynthetic pathway enzyme genes RopCCoAOMT3, RopHCT13b/79/48/14b/20/86/9a, and RopCCR3b/16/24/5a act downstream during lignin biosynthesis. Collectively, these results provide cytological and molecular insights into the hardness of black locust stipular spines, and the high-quality reference genome offers a valuable resource for genomic and evolutionary studies in this species.