In response to biotic and abiotic stresses, the WRKY gene family plays a crucial role in plant growth and development. This study focused on Phoebe bournei and involved genome-wide identification of WRKY gene family members, clarification of their molecular evolutionary characteristics, and comprehensive mapping of their expression profiles under diverse abiotic stress conditions. A total of 60 WRKY gene family members were identified, and their phylogenetic classification revealed three distinct groups. A conserved motif analysis underscored the significant conservation of motif 1 and motif 2 among the majority of PbWRKY proteins, with proteins within the same class sharing analogous gene structures. Furthermore, an examination of cis-acting elements and protein interaction networks revealed several genes implicated in abiotic stress responses in P. bournei. Transcriptomic data were utilized to analyze the expression patterns of WRKY family members under drought and waterlogged conditions, with subsequent validation by quantitative real-time PCR (RT-qPCR) experiments. Notably, PbWRKY55 exhibited significant expression modulation under drought stress; PbWRKY36 responded prominently to waterlogging stress; and PbWRKY18, PbWRKY38, and PbWRKY57 demonstrated altered expression under both drought and waterlogging stresses. This study revealed the PbWRKY candidate genes that potentially play a pivotal role in enhancing abiotic stress resilience in P. bournei. The findings have provided valuable insights and knowledge that can guide further research aimed at understanding and addressing the impacts of abiotic stress within this species.

The MADS-box transcription factor gene family is essential for the differentiation and development of floral organs. Genome-wide and transcriptome data from Phoebe bournei provide the foundation for studying its floral development. In this study, phylogenetic relationships, protein characteristics, conserved domains, gene structures, and cis-acting elements in promoter regions of P. bournei MADS-box genes were systematically analyzed through bioinformatics methodologies. A total of 69 PbMADS genes were identified and classified into 15 subfamilies based on their phylogenetic relationships. The potential functions of these genes were inferred based on transcriptomic data and GO classification. In addition, we selected genes from the ABCDE model to analyze protein interactions and performed RT-qPCR to analyze their expression in each floral organ whorl (outer tepals, inner tepals, stamens, and carpel). Based on these analyses, we rationally constructed a model for the floral organ development in P. bournei. This study, thus, provides a theoretical reference for germplasm innovation in P. bournei and offers insights into the floral development in other Lauraceae species.

The Tripterospermum, comprising 34 species, is a genus of Gentianaceae. Members of Tripterospermum are mostly perennial, entwined herbs with high medicinal value and rich in iridoids, xanthones, flavonoids, and triterpenes. However, our inadequate understanding of the differences in the plastid genome sequences of Tripterospermum species has severely hindered the study of their evolution and phylogeny. Therefore, we first analyzed the 86 Gentianae plastid genomes to explore the phylogenetic relationships within the Gentianae subfamily where Tripterospermum is located. Then, we analyzed six plastid genomes of Tripterospermum, including two newly sequenced plastid genomes and four previously published plastid genomes, to explore the plastid genomes’ evolution and phylogenetic relationships in the genus Tripterospermum. The Tripterospermum plastomes have a quadripartite structure and are between 150,929 and 151,350 bp in size. The plastomes of Tripterospermum encoding 134 genes were detected, including 86 protein-coding genes (CDS), 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes, and three pseudogenes (infA, rps19, and ycf1). The result of the comparison shows that the Tripterospermum plastomes are very conserved, with the total plastome GC content ranging from 37.70% to 37.79%. In repeat sequence analysis, the number of single nucleotide repeats (A/T) varies among the six Tripterospermum species, and the identified main long repeat types are forward and palindromic repeats. The degree of conservation is higher at the SC/IR boundary. The regions with the highest divergence in the CDS and the intergenic region (IGS) are psaI and rrn4.5-rrn5, respectively. The average pi of the CDS and the IGS are only 0.071% and 0.232%, respectively, indicating that the Tripterospermum plastomes are highly conserved. Phylogenetic analysis indicated that Gentianinae is divided into two clades, with Tripterospermum as a sister to Sinogeniana. Phylogenetic trees based on CDS and CDS + IGS combined matrices have strong support in Tripterospermum. These findings contribute to the elucidation of the plastid genome evolution of Tripterospermum and provide a foundation for further exploration and resource utilization within this genus.

Dendrobium chrysotoxum, a perennial medicinal and horticulture plant in the genus Dendrobium within the orchid family (Orchidaceae), holds significant medicinal, ornamental, and scientific value, and thus it is recognized as an innovative horticultural crop. Despite its importance, the mitochondrial genome (mitogenome) of D. chrysotoxum, remains unexamined in the current scientific literature. In this study, we assembled an annotation of the complete mitogenome of D. chrysotoxum, which comprises 18 circular chromosomes with a total length of 582,418 bp. The mitogenome encodes a total of 63 genes including 37 protein-coding genes (PCGs), three rRNA genes, and 18 tRNA genes. Comparative analyses with other angiosperms revealed variations in gene content. Notably, our analysis revealed the retention of sdh4 in the D. chrysotoxum mitogenome, and it has contracted to 153 bp. Using RNA editing sites, we predicted a total of 605 editing sites across all PCGs, with the nad4 gene exhibiting the highest number of sites at 57. Our research further identified the extensive presence of mitochondrial plastid DNA sequences, with 87 fragments accounting for 12.75% of the mitogenome. Phylogenetic and synteny analyses further elucidated the evolutionary dynamics and rearrangement events in D. chrysotoxum as compared to other Dendrobium species. Additionally, we identified a 5,601 bp secondary horizontal gene transfer event involving fungal genes and tRNA genes. Our results provide valuable insights into the symbiotic relationships between orchids and fungi and aids in further research on its potential applications as a medicinal herb with ornamental value.

The ARF gene family is a representative transcription factor that plays a crucial role in the regulation of various growth and development processes in plants. Although the ARF gene family has been identified in five Orchidaceae species, limited research has been conducted on the ARF gene within Dendrobium. To explore ARF family genes in different Dendrobium species, we selected chromosome-level genomic data from D. nobile, D. chrysotoxum, and D. huoshanense for genome-wide identification, and to analyze expression patterns in the D. nobile flower. In this study, 13, 18, and 23 ARF genes were identified in the genomes of D. chrysotoxum, D. huoshanense, and D. nobile, respectively. These genes were then subsequently classified into four classes (Classes I, II, III, and IV) based on our phylogenetic analysis. Additional protein sequence analysis found that 30 ARF proteins with three classically conserved structural domains (BDB, MR, and RD) were present in the three Dendrobium species. Our gene structure comparative analysis also found the same evolutionary branch with similar intron-exon structural features. Specifically, Class I and Class III display longer introns that potentially constitute a distinctive characteristic of Dendrobium. Gene expression patterns analysis showed the potential involvement of DnoARF 5, 7, 10, 11, 12, 13, 16, 17, and 23 in initial differentiation and flower bud formation. Likewise, transcriptomic analysis and RT-qPCR expression profiles indicated flower-specific expression patterns for four ARF genes (DnoARF5, DnoARF6, DnoARF16, and DnoARF22), which suggest an important impact on flower development and regulation. Ultimately, this study provides comprehensive data to elucidate the potential functions of ARF genes in three Dendrobium species and suggests new insights for further exploration concerning the function and regulatory mechanisms in Dendrobium during flower development.