Epidendrum, one of the three largest genera of Orchidaceae, exhibits significant horticultural and ornamental value and serves as an important research model in conservation, ecology, and evolutionary biology. Given the ambiguous identification of germplasm and complex evolutionary relationships within the genus, the complete plastome of this genus (including five species) were firstly sequenced and assembled to explore their characterizations. The plastomes exhibited a typical quadripartite structure. The lengths of the plastomes ranged from 147,902 bp to 150,986 bp, with a GC content of 37.16% to 37.33%. Gene annotation revealed the presence of 78–82 protein-coding genes, 38 tRNAs, and 8 rRNAs. A total of 25–38 long repeats and 130–149 SSRs were detected. Analysis of relative synonymous codon usage (RSCU) indicated that leucine (Leu) was the most and cysteine (Cys) was the least. The consistent and robust phylogenetic relationships of Epidendrum and its closely related taxa were established using a total of 43 plastid genomes from the tribe Epidendreae. The genus Epidendrum was supported as a monophyletic group and as a sister to Cattleya. Meanwhile, four mutational hotspots (trnC^GCA–petN, trnD^GUC–trnY^GUA, trnS^GCU–trnG^UCC, and rpl32–trnL^UAG) were identified for further phylogenetic studies. Our analysis demonstrates the promising utility of plastomes in inferring the phylogenetic relationships of Epidendrum.

Background: The Orchid family is the largest families of the monocotyledons and an economically important ornamental plant worldwide. Given the pivotal role of this plant to humans, botanical researchers and breeding communities should have access to valuable genomic and transcriptomic information of this plant. Previously, we established OrchidBase, which contains expressed sequence tags (ESTs) from different tissues and developmental stages ofPhalaenopsisas well as biotic and abiotic stress-treatedPhalaenopsis. The database includes floral transcriptomic sequences from 10 orchid species across all the five subfamilies of Orchidaceae.Description: Recently, the whole-genome sequences ofApostasia shenzhenica,Dendrobium catenatum, andPhalaenopsis equestriswere de novo assembled and analyzed. These datasets were used to develop OrchidBase 4.0, including genomic and transcriptomic data for these three orchid species. OrchidBase 4.0 offers information for gene annotation, gene expression with fragments per kilobase of transcript per millions mapped reads (FPKM), KEGG pathways and BLAST search. In addition, assembled genome sequences and location of genes and miRNAs could be visualized by the genome browser. The online resources in OrchidBase 4.0 can be accessed by browsing or using BLAST. Users can also download the assembled scaffold sequences and the predicted gene and protein sequences of these three orchid species.Conclusions: OrchidBase 4.0 is the first database that contain the whole-genome sequences and annotations of multiple orchid species. OrchidBase 4.0 is available athttp://orchidbase.itps.ncku.edu.tw/

It is beneficial for breeding and boosting the flower value of ornamental plants such as orchids, which can take several years of growth before blooming. Over the past few years, in vitro flowering of Cymbidium nanulum Y. S. Wu et S. C. Chen has been successfully induced; nevertheless, the production of many abnormal flowers has considerably limited the efficiency of this technique. We carried out transcriptomic analysis between normal and abnormal in vitro flowers, each with four organs, to investigate key genes and differentially expressed genes (DEGs) and to gain a comprehensive perspective on the formation of abnormal flowers. Thirty-six DEGs significantly enriched in plant hormone signal transduction, and photosynthesis-antenna proteins pathways were identified as key genes. Their broad upregulation and several altered transcription factors (TFs), including 11 MADS-box genes, may contribute to the deformity of in vitro flowers. By the use of weighted geneco−expression network analysis (WGCNA), three hub genes, including one unknown gene, mitochondrial calcium uniporter (MCU) and harpin-induced gene 1/nonrace-specific disease resistance gene 1 (NDR1/HIN1-Like) were identified that might play important roles in floral organ formation. The data presented in our study may serve as a comprehensive resource for understanding the regulatory mechanisms underlying flower and floral organ formation of C. nanulum Y. S. Wu et S. C. Chen in vitro.

Background: Tissue culture is one of the most important methods for propagating orchids. Notably, many orchid seedlings exhibit autonomous flowering during the cultivation process. To explore the underlying mechanism, Anoectochilus roxburghii (Wall.) Lindl., an orchid that spontaneously forms in vitro flowers, was analyzed in this study. Methods: Bud samples at the early, middle, and fully open stages were collected for transcriptome sequencing, followed by differential expression, trend, enrichment and protein–protein interaction (PPI) network analyses. Results: Differential gene expression analysis identified 2364, 4137, and 6522 differentially expressed genes (DEGs) in the early vs. middle, middle vs. open, and early vs. open comparisons, respectively. These DEGs were significantly enriched in various metabolic and biosynthetic pathways, particularly in ko01100 (metabolic pathways). PPI network analysis further identified hub genes, including MCM3, MCM4, and MCM7, which are associated with DNA replication, and CURL3, which is linked to plant hormone signal transduction pathways. Conclusion: Our findings provide novel insights into the molecular mechanisms driving in vitro flowering in A. roxburghii, highlighting the importance of metabolic and biosynthetic process signaling in this unique developmental transition. These results provide valuable resources for future studies on orchid propagation and floral development.

Taeniophyllum is a distinct taxon of epiphytic leafless plants in the subtribe Aeridinae of Orchidaceae. The differences in chloroplast genomes between extremely degraded epiphytic leafless orchids and other leafy orchids, as well as their origins and evolution, raise intriguing questions. Therefore, we report the chloroplast genome sequence of Taeniophyllum complanatum, including an extensive comparative analysis with other types of leafless orchids. The chloroplast genome of T. complanatum exhibited a typical quadripartite structure, and its overall structure and gene content were relatively conserved. The entire chloroplast genome was 141,174 bp in length, making it the smallest known chloroplast genome of leafless epiphytic orchids. It encoded a total of 120 genes, including repetitive genes, comprising 74 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A phylogenetic analysis was conducted on the chloroplast genomes of 43 species belonging to five subfamilies of Orchidaceae. The results showed that the five subfamilies were monophyly, with nearly all segments having a 100% bootstrap value. T. complanatum and Chiloschista were clustered together as a sister group to Phalaenopsis and occupied the highest position in the Epidendroideae. Phylogenetic analysis suggested that T. complanatum and other leafless orchids within the Orchidaceae evolved independently. This study may provide the foundation for research on phylogenetic and structural diversity in leafless epiphytic orchids, thereby enhancing the resources available for chloroplast genome studies in Orchidaceae.

A new orchid species, Dendrobium yongjiaense, from Zhejiang, China, is described and illustrated here. Detailed morphological study indicates that D. yongjiaense is similar to D. monticola and D. strongylanthum, but it differs in the shape and size of leaf, flower size, and a mid-lobe of the lip with densly distinct crystalline papillae and wrinkled 3–5 crest lines in middle. Molecular phylogeny analyses based on the nrITS and plastid DNA (matK and trnL-F) reveal that D. yongjiaense is a member of sect. Stachyobium, and genetically similar to D. monticola.