| Summary: | The modern pteridophyte genus <i>Equisetum</i> 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 <i>Equisetum xylochaetum</i> from a metagenomic sequence and compared the plastid genome structure and protein-coding regions with information available for two other <i>Equisetum</i> species using network analysis. <i>Equisetum</i> 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 <i>Equisetum</i> is monophyletic, and that <i>E. xylochaetum</i> is more closely related to <i>E. hyemale</i> than to <i>E. arvense</i>. Single-gene phylogenetic estimation and haplotype analysis showed that <i>E. xylochaetum</i> belonged to the subgenus <i>Hippochaete</i>. Single-gene haplotype analysis revealed that <i>E. arvense</i>, <i>E. hyemale</i>, <i>E. myriochaetum</i>, and <i>E. variegatum</i> 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 <i>E. bogotense</i> appeared as a distinct group of haplotypes representing the subgenus <i>Paramochaete</i> that diverged from <i>Hippochaete</i> and <i>Equisetum</i>. In addition, the taxa that were frequently located at the joint region of the map were <i>E. scirpoides</i> and <i>E. pratense</i>, suggesting the presence of some plastome characters among the <i>Equiseum</i> subgenera.
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