The complete chloroplast genome sequence of American elm (Ulmus americana) and comparative genomics of related species

American elm, Ulmus americana L., was widely cultivated in the USA and Canada as a landscape tree. Despite its importance in landscaping and horticulture, its genome is poorly characterized. We assembled the chloroplast genomes of two American elm genotypes (RV16 and Am. 57845); to our knowledge, this is the first description of sequencing and assembly of this species. The complete chloroplast genome of U. americana ranged from 158,935 to 158,993 bp and it contains 127 genes, namely 85 protein-coding genes, 34 tRNA genes, and 8 rRNA genes. Between the two American elm chloroplasts we sequenced, we identified 240 high-quality sequence variants (SNPs and indels). To evaluate the phylogeny of American elm, we compared the chloroplast genomes of the two American elms with seven Asian elm species and twelve other chloroplast genomes available through the NCBI database. As expected, Ulmus was closely related to Morus and Cannabis, as all three genera are assigned to the Urticales. We clarified the timing of the divergence of American elm from the available Asian elms, the divergence within these Asian elms, and all the species’ relative ages. Comparison of the chloroplasts of American elm with the available Asian elms revealed that trnH was absent from American elm but not most Asian elms; conversely, petB, petD, psbL, trnK, and rps16 are present in the American elm but absent from all Asian elms analyzed. ycf15 was present in both American and Asian elms but absent from members of closely related genera. The complete chloroplast genome of U. americana will provide useful genetic resources for characterizing the genetic diversity of U. americana and potentially help to conserve natural populations of American elm.