An investigation of a questionable orchid led to the discovery of a new genus and species Thuniopsis cleistogama, endemic to Yunnan province, China. It is characterized by having a subglobose corm, a spike-like (racemose) inflorescence, half opened and spurless flowers, a collar-shaped stigma and subglobose capsules. Based on DNA sequence data from three gene regions (nuclear ribosomal ITS, chloroplast matK and trnL), we investigated its phylogenetic position within the tribe Arethuseae. Phylogenies using maximum likelihood and Bayesian inference support the recognition of Thuniopsis as a distinct genus, and suggest its close relationship to the genera Bletilla, Dilochia, and Thunia. The new genus is circumscribed and a description and illustrations of the new species are provided. The phylogenetic relationships among the genera in Arethuseae are accessed. Moreover, our phylogeny also shed light on the phylogenetic positions of several genera which, to date, remain uncertain.

Dalbergia odorifera T. C. Chen (Leguminosae), a rare and endangered tree species endemic to Hainan Island of China, produces the most expensive and rarest wood in China. The wood characteristics of D. odorifera are remarkably similar to those of D. tonkinensis (a much less sought‐after species from Vietnam), and the DNA from wood is often highly degraded, making it very difficult to identify the two species using anatomical features or DNA barcoding based on regular DNA markers. To solve the confusion of identifying wood reliably from the two species, we built and analyzed the plastome library of 26 samples from 18 Dalbergia species, of which 12 samples from eight closely related species of D. odorifera are newly sequenced in this study. Phylogenomic analysis suggested that the relationships among the 26 samples are mostly well resolved, and conspecific individuals from different populations of D. odorifera and D. tonkinensis clustered together. Between the plastid genomes of the two species, we identified 129 indels and 114 single nucleotide polymorphisms. By assessing a subset of 20 nucleotide polymorphisms and 10 indels using 37 population‐level samples (20 samples of D. odorifera and 17 samples of D. tonkinensis), we recovered eight species‐specific barcode regions that could be suitable for identifying the wood D. odorifera and D. tonkinensis. To examine their utility in wood identification, we amplified the eight DNA barcodes using six wood samples and recovered an amplification success rate of 83.3%, demonstrating a reliable method for precise wood identification of the two species.

Molecular studies have shown thatLipariss.l. is polyphyletic, with the epiphyticLiparisalliance well separated from the clade representingLiparisin its restricted sense and further forming a phylogenetically heterogeneous assemblage. The generic status ofCestichis, as the key member of the epiphyticLiparisalliance, remains contentious, and the relationships betweenCestichis,StichorkisandPlatystyliparisare still unclear and in need of further studies. We herein employ DNA sequence data from nuclear ITS and plastidmatK regions to clarify the generic boundaries ofCestichisand its relationship to the allied genera. Results from both Bayesian inference and maximum likelihood analysis congruently indicate thatCestichisas currently circumscribed is not monophyletic. TheBlepharoglossumclade, corresponding to commonly recognized sect.Blepharoglossum, forms a monophyletic lineage closely related to the genusOberoniainstead of the coreCestichisclade. A re-evaluation of the diagnostic morphological characters reveals that this lineage represents a morphologically distinct group. Based on these results,Blepharoglossumis removed fromCestichisand elevated to generic status. Our study also sheds light on the homoplastic nature of some diagnostic morphological characters used traditionally in the taxonomy of the Malaxidinae.

Background: The orchids of the subtribe Coelogyninae are among the most morphologically diverse and economically important groups within the subfamily Epidendroideae. Previous molecular studies have revealed that Coelogyninae is an unambiguously monophyletic group. However, intergeneric and infrageneric relationships within Coelogyninae are largely unresolved. There has been long controversy over the classification among the genera within the subtribe.Results: The complete chloroplast (cp.) genomes of 15 species in the subtribe Coelogyninae were newly sequenced and assembled. Together with nine available cp. genomes in GenBank from representative clades of the subtribe, we compared and elucidated the characteristics of 24 Coelogyninae cp. genomes. The results showed that all cp. genomes shared highly conserved structure and contained 135 genes arranged in the same order, including 89 protein-coding genes, 38 tRNAs, and eight rRNAs. Nevertheless, structural variations in relation to particular genes at the IR/SC boundary regions were identified. The diversification pattern of the cp. genomes showed high consistency with the phylogenetic placement of Coelogyninae. The number of different types of SSRs and long repeats exhibited significant differences in the 24 Coelogyninae cp. genomes, wherein mononucleotide repeats (A/T), and palindromic repeats were the most abundant. Four mutation hotspot regions (ycf1a,ndhF-rp132,psaC-ndhE, andrp132-trnL) were determined, which could serve as effective molecular markers. Selection pressure analysis revealed that three genes (ycf1a,rpoC2andycf2genes) might have experienced apparent positive selection during the evolution. Using the alignments of whole cp. genomes and protein-coding sequences, this study presents a well-resolved phylogenetic framework of Coelogyninae.Conclusion: The inclusion of 55 plastid genome data from a nearly complete generic-level sampling provide a comprehensive view of the phylogenetic relationships among genera and species in subtribe Coelogyninae and illustrate the diverse genetic variation patterns of plastid genomes in this species-rich plant group. The inferred relationships and informally recognized major clades within the subtribe are presented. The genetic markers identified here will facilitate future studies on the genetics and phylogeny of subtribe Coelogyninae.

The subtribe Malaxidinae encompasses diverse species, many of which possess remarkable medicinal properties that have been employed in traditional Chinese medicine for centuries. Although recent advancements have improved our understanding of the backbone phylogeny of Malaxidinae, clarifying the complex intergeneric relationships remains challenging, largely owing to limited genomic data. To address this gap and further investigate the genetic diversity and evolutionary patterns within this subtribe, we sequenced and assembled complete chloroplast (cp.) genomes from sixteen Malaxidinae species. These newly acquired genomic resources, combined with two previously published cp. genomes from closely related species, were incorporated into a comprehensive comparative genomic and phylogenomic analysis. The complete cp. genomes of all 18 Malaxidinae species were analyzed, revealing lengths ranging from 143,062 bp to 158,785 bp. Each genome contains 123–133 genes, including 74–86 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 1–8 pseudogenes. The chloroplast genomes of Malaxidinae species exhibit significant structural diversity, with particularly pronounced variations observed in the ndhF and ycf1 genes located at the IR/SSC boundary regions. In certain species, the SSC regions showed substantial size reduction, ranging from 10,224 to 15,582 bp. Notable variability in both gene loss and truncation patterns was observed in the ndh gene family across these species, accompanied by diverse modifications affecting the length, position, and pseudogenization of the ycf1 gene. Furthermore, our study identified genomic inversions and rearrangements occurring in both the LSC and SSC regions of specific species. The detection of abundant long dispersed repeats and SSRs provides valuable molecular markers for evaluating both intrageneric and interspecific polymorphism as well as genetic diversity patterns. Through codon usage bias analysis, we established that natural selection serves as the predominant evolutionary force shaping codon usage patterns in most Malaxidinae species. Detailed sequence alignment of the chloroplast genome revealed that structural variants are primarily concentrated within single-copy regions. Ten highly variable cpDNA markers were chosen as mutational hotspots, with the potential for development as DNA barcodes for Malaxidinae species. Our phylogenomic analysis clearly resolved the Malaxidinae into three well-supported major clades. Clade I comprises species of Liparis s.s., Malaxis, and Oberonioides. Clade II includes species of Crepidium, Dienia, Diteilis and Empusa. Clade III consists of species from the genera Blepharoglossum, Cestichis, Oberonia, Platystyliparis and Stichorkis. This research provides valuable insights into the unique characteristics of the chloroplast genome in Malaxidinae orchids, significantly advancing our comprehension of their evolutionary mechanisms and phylogenetic architecture. The acquired genomic data establish a crucial foundation to advance medical resources and aid in species differentiation.