Myrmecophytes, characterized by specialized structures like hollow stems that facilitate mutualistic relationships with ants, serve as an important system for studying ant-plant interactions and the adaptation mechanisms. Caularthron and Myrmecophila are exemplary myrmecophytes within Orchidaceae. Previous studies suggested a genetic relationship between these two genera, placing them within Laeliinae (Epidendreae), yet the precise phylogenetic positioning remained uncertain. The absence of available plastome resources has hindered investigations into plastome evolution and phylogeny. In this study, we sequenced and assembled the complete plastomes of Caularthron bicornutum and Myrmecophila thomsoniana to elucidate their plastome characteristics and phylogenetic relationships. The determined plastome sizes were 150,557 bp for C. bicornutum and 156,905 bp for M. thomsoniana, with GC contents of 37.3% and 37.1%, respectively. Notably, M. thomsoniana exhibited a distinctive IR expansion and SSC contraction, with the SSC region measuring only 4532 bp and containing five genes (ccsA, ndhD, rpl32, psaC, and trnL-UAG), a unique feature observed for the first time in Epidendreae. Comparative analyses with species from the related genus Epidendrum revealed that C. bicornutum plastome exhibited conserved genome size, GC content, gene content, and gene order. A total of 32 and 33 long sequence repeats, 50 and 40 tandem repeats, and 99 and 109 SSRs were identified in the plastomes of C. bicornutum and M. thomsoniana, respectively. The RSCU analysis demonstrated a consistent pattern in both plastomes, with 29 out of 30 codons with RSCU values greater than 1 featuring A/U at the third codon position. Leucine was the most prevalent amino acid, while Cysteine was the least common. Four potential DNA barcoding regions with Pi values exceeding 0.07, namely ycf1, ccsA–psaC, petN–psbM, and accD–psaI, were identified for subsequent phylogenetic reconstructions within Laeliinae. Phylogenetic analysis underscored the close relationships among Caularthron, Epidendrum, and Myrmecophila. This study represents the first comprehensive analysis of the plastome characteristics of Caularthron bicornutum and Myrmecophila thomsoniana. Through our characterization and phylogenetic analyses, we unveiled the unique IR expansion/SSC contraction and further elucidated their phylogenetic positions. Our research contributes significant data and insights into the dynamic evolution of ant–orchid plastomes and the phylogeny of the Laeliinae.

Superoxide dismutase (SOD) enzymes are essential for reducing oxidative damage resulting from overabundant reactive oxygen species under abiotic stress. While the SOD gene family has been extensively studied in many species, research focusing on Cymbidium species remains limited. In this study, a comprehensive analysis of the SOD gene family in three Cymbidium genomes was conducted. A total of 23 SOD genes were identified, with nine SODs in C. sinense, eight in C. ensifolium, and six in C. goeringii. These SOD genes were categorized into three clades: Cu/Zn-SOD, Fe-SOD, and Mn-SOD, with the Cu/Zn-SOD being the most abundant in these three types. This classification was supported by analyses of conserved domains, motifs, and phylogenetic relationships. Cis-element prediction showed that stress-responsive elements were identified in most SODs. Transcriptomic data revealed that seven CsSODs exhibited a border expression in all sequenced tissues, while two exhibited undetectable expression levels. Further qRT-PCR analysis showed that all CsSODs were upregulated under salt stress, with some exhibiting significant changes in expression. These findings all highlight the crucial role of CsSODs in the salt stress response and provide valuable insights for further breeding salt-tolerance varieties of C. sinense.

The Coelogyne s.l. is one of the emblematic genera of the Asian orchids, with high horticultural and medicinal values. However, the phylogenetic relationships of the genus inferred from previous studies based on a limited number of DNA markers remain ambiguous. In this study, we newly sequenced and assembled the complete plastomes of seven Coelogyne species: C. bulleyia, C. fimbriata, C. flaccida, C. prolifera, C. tricallosa, C. uncata, and an unknown taxa, Coelogyne sp. The plastomes of Coelogyne exhibited a typical quadripartite structure, varying in length between 157,476 bp and 160,096 bp, accompanied by a GC content spanning from 37.3% to 37.5%. A total of 132 genes were annotated for each plastome, including 86 protein-coding genes, eight rRNA genes, and 38 tRNA genes. Among these, 19 genes underwent duplication within the inverted repeat (IR) regions, and 18 genes exhibited the presence of introns. Additionally, we detected 54 to 69 simple sequence repeats (SSRs) and 30 to 49 long repeats. In terms of codon usage frequency, leucine (Leu) emerged with the highest frequency, while cysteine (Cys) exhibited the lowest occurrence. Furthermore, eight hypervariable regions (atpB-rbcL, psbK-psbI, rps8-rpl14, rps16-trnQ^UUG, psaC-ndhE, ndhF-rpl32, psbB-psbT, and ycf1) were identified. Phylogenetic analyses using complete plastomes and protein-coding genes indicated that Coelogyne s.l. was monophyletic. Moreover, the results robustly supported the division of Coelogyne s.l. into five clades. This study provides a comprehensive analysis of the structural variation and phylogenetic analysis of the Coelogyne s.l. based on plastome data. The findings offer significant insights into the plastid genomic characteristics and the phylogenetic relationships of Coelogyne s.l., contributing to a deeper understanding of its evolutionary history.

Thyrsostachys is oligotypic genus of Bambusinae, while its phylogenetic position had been unclear. Here, the complete plastid genome of the type species, T. siamensis, was sequenced and analyzed in this work. The complete genome is a typical quadripartite structure with 139,522 bp in length, comprising of a large single-copy region (LSC, 83,032 bp), a small single-copy region (SSC, 12,892 bp), and a pair of invert repeats regions (IR, 21,799 bp). The genome contains 138 genes, 89 protein-coding genes, 41 tRNA genes, and 8 rRNA genes. The GC content of genome was 38.9%. Phylogenetic analysis indicated T. siamensis was sister to Dendrocalamus birmanicus within Bambusinae.

A new species of Anacardiaceae, Toxicodendron oligophyllum S. L. Tang, Liang Ma & S. P. Chen, from eastern Fujian Province, China, is described and illustrated. Morphologically, the leaf of T. oligophyllum includes only 3–5 leaflets which is the least number in all known species of Toxicodendron. Additionally, the length of inflorescence equal to which of the leaf can also be used as a well diagnostic characters to distinguish the new species from the other Toxicodendron. The phylogeny of Toxicodendron using the nuclear ribosomal internal transcribed spacer (nrITS) and chloroplast (trnL-F) sequences was reconstructed. The result showed the new species is sister to T. sylvestre (Sieb. & Zucc.) Kuntze.