Phylogenetic Analysis of Rare Crepis Species of the Crimean Flora (C. purpurea (Willd.) M. Bieb. and C. callicephala Juz.) Through Plastid Genome Reconstruction

One of the largest genera within the Cichorieae tribe of the Asteraceae family is Crepis, comprising ∼200 species. The diversity of numerous local forms is of interest for adaptation studies. There are two rare closely related species within the Lagoseris clade of the genus Crepis which occupy highly divergent habitats—C. callicephala Juz. and C. purpurea (Willd.) M. Bieb.—both occurring in the Crimean Peninsula. The habitats differ in environmental conditions and are isolated by location and altitude, restricting opportunities for gamete exchange. The species are similar morphologically but demonstrate different phenological patterns, representing a notable natural model for investigating how isolation and habitat conditions may shape genetic differentiation and local adaptation. We sequenced the total DNA of C. callicephala and C. purpurea. Relying on both short-read and long-read data, we assembled plastid genomes of these species and reconstructed the phylogeny of the subtribe Crepidinae. The assembled plastid genomes are 149,980 bp (C. callicephala) and 150,007 bp (C. purpurea), and the two species were recovered as a closely related pair on a long common branch within the sampled Crepidinae. We also noted an unusual structural rearrangement in the rbcL–psaI locus shared by the studied accessions of both species, affecting the accD gene (encoding the β-carboxyltransferase subunit of acetyl-CoA carboxylase), which has not been reported in other members of Cichorioideae. Together with the shifts in the inverted-repeat boundaries, these features provide molecular data relevant to the taxonomic status and relationship of C. callicephala and C. purpurea.