The Complete Chloroplast Genome of Tree Fern Cyathea delgadii and Its Comparison to Other Cyatheales

The chloroplast (cp) genome of the tree fern Cyathea delgadii Pohl ex Sternb. was assembled and annotated to investigate its structure and evolution within the Cyatheales order. The genome, sequenced using Oxford Nanopore Technologies, has a total size of 165,248 bp, comprising a large single-copy (LSC) region of 94,738 bp, a small single-copy (SSC) region of 22,012 bp, and two inverted repeat (IR) regions of 24,251 bp each. It contains 89 protein-coding genes, eight rRNAs, and 33 tRNAs. Comparative phylogenomic analyses involving 19 species of Cyatheales have revealed that the cp genome of C. delgadii shares similarities in gene content with other ferns of the Cyatheaceae family; however, it demonstrates variations in both genome size and GC content. Variations in cp genome size were observed across the Cyatheales species, ranging from 154,046 bp in Gymnosphaera denticulata (Baker) Copel to 168,244 bp in Dicksonia squarrosa (G.Forst) SW. Gene content analysis showed that most species have a conserved number of protein-coding genes, rRNAs, and tRNAs, suggesting structural stability. However, Cibotium spp. has a reduced number of protein-coding genes (87), possibly due to gene loss or transfer to the nuclear genome. Phylogenetic analyses using both whole genome and SNP data showed comparable clustering among Alsophila and Gymnosphaera species, while C. delgadii occupied a basal to intermediate position. The overall guanine-cytosine (GC) content of C. delgadii was calculated to be 40.95%, with a significantly higher content of 44.03% observed in the intragenic regions. An analysis of codon usage bias indicated a preference for codons ending with adenine or thymine, which aligns with the genome's adenine-thymine (AT) richness. This study provides valuable genomic resources and insights into the evolution of Cyatheales cp genomes, emphasizing both conserved features and specific adaptations within this group of ferns.