| Summary: | <i>Aragoa</i>, comprising 19 high-altitude North Andean species, is one of three genera in the Plantagineae (Plantaginaceae, Lamiales), along with <i>Littorella</i> and <i>Plantago</i>. Based primarily on plastid data and nuclear ITS, <i>Aragoa</i> is sister to a clade of <i>Littorella</i> + <i>Plantago</i>, but Plantagineae relationships have yet to be assessed using multigene datasets from the nuclear and mitochondrial genomes. Here, complete mitogenomes were assembled for two species of <i>Aragoa</i> (<i>A. abietina</i> and <i>A. cleefii</i>). The mitogenomes of both species have a typical suite of genes for 34 proteins, 17 tRNAs, and three rRNAs. The <i>A. abietina</i> mitogenome assembled into a simple circular map, with no large repeats capable of producing alternative isoforms. The <i>A. cleefii</i> mitogenomic map was more complex, involving two circular maps bridged by a substoichiometric linear fragment. Phylogenetics of three mitochondrial genes or the nuclear rRNA repeat placed <i>Aragoa</i> as sister to <i>Littorella</i> + <i>Plantago</i>, consistent with previous studies. However, <i>P. nubicola</i>, the sole representative of subg. <i>Bougueria</i>, was nested within subg. <i>Psyllium</i> based on the mitochondrial and nuclear data, conflicting with plastid-based analyses. Phylogenetics of the nuclear rRNA repeat provided better resolution overall, whereas relationships from mitochondrial data were hindered by extensive substitution rate variation among lineages.
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