Complete Chloroplast Genome and Phylogenomic Analysis of Davallia trichomanoides (Polypodiaceae)

Background/Objectives: Chloroplast genomes (plastomes) are valuable for fern systematics, yet the epiphytic lineages have remained underexplored. Methods: The Davallia trichomanoides plastome was de novo assembled from Illumina data and annotated. Results: The plastome measures 154,217 bp with a GC content of 40.82% and contains 115 genes. Comparative analysis reveals two inverted repeat (IR) size classes (~24.0-24.6 kb vs. ~27.4-27.5 kb) and lineage-specific shifts at the IR junctions. For instance, the ndhF gene remains in the small single copy (SSC) region in D. trichomanoides and Drynaria acuminata, but it crosses into the IRb region in other species. We observed nucleotide diversity hotspots in the large single copy (LSC) and SSC regions. The IR regions are highly conserved. The ratios of nonsynonymous to synonymous substitutions (Ka/Ks) are mostly less than 1, indicating purifying selection. Phylogenetic analysis places D. trichomanoides as the sister to D. acuminata. Conclusions: This study highlights the stable plastome structure of D. trichomanoides and identifies candidate loci for barcoding. It also supports the stable placement of Davallia within the epiphytic Polypodiineae.