Rapid turnover of mitogenomic repeats and congruent phylogenomic signal among Digitalideae genomes

Digitalideae (Plantaginaceae) comprises ~25 species of foxgloves in two genera (Digitalis and the monotypic Erinus). Several species are notable as garden ornamentals or for their medical benefits and toxic side-effects, yet their genomic resources are limited to plastid genomes from two species. We assembled sequencing data from six Digitalideae species to evaluate the structural and functional evolution of their organellar genomes and to evaluate the phylogenetic signal of these organellar genomes and nuclear rDNA. Digitalideae plastomes are virtually identical among species, exhibiting invariant gene and intron content, a collinear gene order, and very similar sizes and repeat structures. The mitochondrial genomes are nearly identical in terms of gene and intron content but exhibit variation in size, substantial structural rearrangements, and extensive turnover of large repeat content. Comparison of large mitogenomic repeats is consistent with a turnover model, whereas plastomic inverted repeat content is consistent with a retention model, demonstrating distinctly different rates of repeat turnover between the organellar genomes. Phylogenetic trees constructed from entire plastomes, mitochondrial genes and introns, or nuclear rDNA are fully congruent among Digitalideae and other Plantaginaceae, and the results reveal some taxonomic uncertainties regarding Digitalideae systematics and possible species misidentifications in the existing data.