Chloroplast genome structure analysis of Equisetum unveils phylogenetic relationships to ferns and mutational hotspot region

is one of the oldest extant group vascular plants and is considered to be the key to understanding vascular plant evolution. is distributed almost all over the world and has a high degree of adaptability to different environments. Despite the fossil record of horsetails ( , Equisetaceae) dating back to the Carboniferous, the phylogenetic relationship of this genus is not well, and the chloroplast evolution in remains poorly understood. In order to fill this gap, we sequenced, assembled, and annotated the chloroplast genomes of 12 species of , and compared them to 13 previously published vascular plants chloroplast genomes to deeply examine the plastome evolutionary dynamics of . The chloroplast genomes have a highly conserved quadripartite structure across the genus, but these chloroplast genomes have a lower GC content than other ferns. The size of plastomes ranges from 130,773 bp to 133,684 bp and they encode 130 genes. Contraction/expansion of IR regions and the number of simple sequences repeat regions underlie large genomic variations in size among them. Comparative analysis revealed we also identified 13 divergence hotspot regions. Additionally, the genes and can be used as potential DNA barcodes for the identification and phylogeny of the genus . Twelve photosynthesis-related genes were specifically selected in . Comparative genomic analyses implied divergent evolutionary patterns between and other ferns. Phylogenomic analyses and molecular dating revealed a relatively distant phylogenetic relationship between and other ferns, supporting the division of pteridophyte into Lycophytes, Equisetaceae and ferns. The results show that the chloroplast genome can be used to solve phylogenetic problems within or between species, and also provide genomic resources for the study of systematics and evolution.