Plastid Genome of from the Atacama Desert, Chile and the Relationships of Based on Frequently Used Plastid Genes and Network Analysis.

The modern pteridophyte genus is the only survivor of Sphenopsida, an ancient clade known from the Devonian. This genus, of nearly worldwide distribution, comprises approximately 15 extant species. However, genomic information is limited. In this study, we assembled the complete chloroplast genome of the giant species from a metagenomic sequence and compared the plastid genome structure and protein-coding regions with information available for two other species using network analysis. chloroplast genomes showed conserved traits of quadripartite structure, gene content, and gene order. Phylogenetic analysis based on plastome protein-coding regions corroborated previous reports that is monophyletic, and that is more closely related to than to . Single-gene phylogenetic estimation and haplotype analysis showed that belonged to the subgenus . Single-gene haplotype analysis revealed that , , , and resolved more than one haplotype per species, suggesting the presence of a high diversity or a high mutation rate of the corresponding nucleotide sequence. Sequences from appeared as a distinct group of haplotypes representing the subgenus that diverged from and . In addition, the taxa that were frequently located at the joint region of the map were and , suggesting the presence of some plastome characters among the subgenera.