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.