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

Phragmipedium kovachii 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 P. kovachii (GenBank accession number OR348669) and assembled its complete chloroplast genome. The complete chloroplast genome of P. kovachii 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 P. kovachii and P. besseae. This study contributes to the understanding of the phylogenetic relationships of the monophyletic group Cypripedioideae.