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Papaver setigerum  is an annual herb that is closely related to the opium poppy,  P. somniferum . Genetic resources for  P. setigerum  are scarce. In the present study, we assembled the complete chloroplast (cp) genome of  P. setigerum  based on genome skimming data, and we conducted comparative cp genome analyses to study the evolutionary pattern in Papaveraceae. The cp genome of  P. setigerum  is 152,862 bp in length with a typical quadripartite structure. Comparative analyses revealed no gene rearrangement in the Papaveraceae family, although differences were evident in genome size, gene losses, as well as inverted repeats (IR) region expansion and contraction. The  rps 15 gene has been lost from the genomes of  Meconopsis racemosa ,  Coreanomecon hylomeconoides ,  P. orientale ,  P. somniferum , and  P. setigerum , and the  ycf 15 gene is found only in  C. hylomeconoides . Moreover, 13 cpDNA markers, including  psb A- trn H,  rps 16- trn Q,  trn S- trn G,  trn C- pet N,  trn E- trn T,  trn L- trn F,  trn F- ndh J,  pet A- psb J,  ndh F- rpl 32,  rpl 32- trn L,  ccs A- ndh D,  ndh E- ndh G, and  rps 15- ycf 1, were identified with relatively high levels of variation within  Papaver , which will be useful for species identification in this genus. Among those markers,  psb A- trn H is the best one to distinguish  P. somniferum  and  P. setigerum .

The complete chloroplast genome of Papaver setigerum and comparative analyses in Papaveraceae