Global mitochondrial and chloroplast genome diversity in the threatened aquatic carnivorous plant Aldrovanda vesiculosa

The submerged aquatic carnivorous plant Aldrovanda vesiculosa (Droseraceae) is threatened by rapid deterioration of wetlands and oligotrophic lake habitats. Its native distribution spans four continents, but many historic populations are now extinct. Previous genetic studies found distinction between populations from Australia and those from the rest of the world, but due to limited genetic markers, neither detailed phylogenetic relationships nor the migration routes of A. vesiculosa populations were revealed. We used a de novo assembly of the A. vesiculosa mitochondrial genome and a previously published plastid genome as references for mapping short DNA sequence reads from 17 globally distributed populations. Phylogenetic trees were constructed based on detected polymorphisms. Genetic diversity of both the mitochondrial and plastid genome was low (Pi 0.55 × 10−4 and 0.7 × 10−4, respectively). Greater polymorphisms were found in the mitochondrial compared with the plastid genome, owing to its larger size (1.27 Mb). Australian populations formed a monophyletic clade in both plastid and mitochondrial trees, while the mitochondrial tree also distinguished populations from southern and northern Europe. Aldrovanda vesiculosa likely migrated to Australia and Africa from a southern European refuge during the last interglacial period∼100,000 years ago. When the last glaciation started, some populations could have survived in eastern Europe and moved north, when the continental glacier retreated. Aldrovanda vesiculosa experienced repeated population bottlenecks that reduced its genetic diversity. •Aquatic carnivorous Aldrovanda vesiculosa is threatened by deterioration of habitats.•Its native distribution spans four continents, but many populations are now extinct.•We analyzed complete mitochondrial and plastid genomes of 17 world populations.•A. vesiculosa likely migrated to Australia and Africa from Europe ∼ 100,000 years ago.•It experienced repeated population bottlenecks that reduced genetic diversity.