High-throughput sequencing yields the complete plastid genome of the endemic species <i>Phragmipedium kovachii</i> (Orchidaceae) from northeastern Peru

<i>Phragmipedium kovachii</i> is a species of orchid endemic to the Amazonas and San Martín regions. Unfortunately, its excessive extraction has made it a critically endangered species. In this study, we performed next-generation sequencing of <i>P. kovachii</i> (GenBank accession number OR348669) and assembled its complete chloroplast genome. The complete chloroplast genome of <i>P. kovachii</i> is A + T-rich (64.3%), measuring 152,918 bp in length. This plastid genome contains a total of 124 genes (77 protein-coding genes, 39 tRNAs, and eight rRNAs) and five pseudogenes, including a pair of inverted repeats (IRs) 25,116 bp in size and separated by a large single-copy (LSC) region of 89,216 bp and a small single-copy (SSC) region of 13,470 bp. This genome has a typical quadripartite organization following the structure of other Orchidaceae plastomes. Phylogenetic analyses revealed the close relationship between <i>P. kovachii</i> and <i>P. besseae.</i> This study contributes to the understanding of the phylogenetic relationships of the monophyletic group Cypripedioideae.