Complete plastome sequences of and and comparative analyses with and .

and have sympatric ranges and are closely related, but the differences between these species at the plastome level are unknown. To better understand the patterns of variation among plastomes, the complete plastomes of and were sequenced. Then, the plastomes were compared with the complete plastomes of and , which are closely and distantly related to the focal species, respectively. We also used these sequences to construct phylogenetic trees to determine the relationships among and between the four species as well as additional taxa from Pinaceae and other gymnosperms. Analysis of our sequencing data allowed us to identify 438 single nucleotide polymorphism (SNPs) point mutation events, 95 indel events, four inversion events, and seven highly variable regions, including six gene spacer regions (, , , , , and ) and one gene (). The highly variable regions are appropriate targets for future use in the phylogenetic reconstructions of closely related, sympatric species of as well as Pinaceae in general.