The complete chloroplast genome of Isoetes yunguiensis (Isoetaceae), a rare and endangered fern endemic to China

Isoetes yunguiensis is a rare and endangered fern endemic to Yunnan–Guizhou Plateau, China. The complete chloroplast genome sequence of I. yunguiensis was generated by de novo assembly using whole genome next-generation sequencing. The cp genome of I. yunguiensis was a circular structure and 145,355 bp in length, comprising a pair of inverted repeat (IR) regions of 26,130 bp, a large single copy (LSC) of 91,923 bp, and a small single copy (SSC) of 27,302 bp. The genome encoded 124 unique genes consisting of 82 protein-coding genes, 32 transfer RNA, four ribosomal RNA genes, and six pseudogenes. A maximum-likelihood phylogenetic analysis revealed that I. yunguiensis was closely related to I. butleri, I. engelmannii, I. flaccida, I. melanospora, and I. valida, with strong support values.