Using phylogenomics to reconstruct phylogenetic relationships within tribe Polygonateae (Asparagaceae), with a special focus on Polygonatum

Polygonatum is a widespread temperate genus with approximately 75 species centered in the Eastern Himalaya and Indo-Burma biodiversity hotspots. A complete assessment of the remarkable diversity of Polygonatum in these areas requires an accurate circumscription of the genus, as well as a clear understanding of generic and infrageneric relationships, both of which have been problematic in the past. In this study, we reconstruct phylogenetic relationships within Polygonatum and test its monophyly using a phylogenomic approach. For that, we built a comprehensive dataset that includes complete or nearly-complete plastid genomes of 19 species of Polygonatum, one of Disporopsis, and four of Heteropolygonatum. Their plastid genomes do not present any major structural differences and range from 153,821 to 155,580 bp in length. Molecular phylogenetic analyses of the chloroplast coding regions indicate that Polygonatum and Heteropolygonatum are monophyletic, providing support for their recognition as distinct genera and corroborating recent adjustments of their circumscriptions. An expanded analysis with higher species sampling using the petA-psbJ plastid gene region combined with the nuclear ribosomal ITS provided support for the recognition of three distinct sections within Polygonatum. These same sections are further supported by chromosome data: Polygonatum sect. Sibirica (x = 12); Polygonatum sect. Polygonatum (x = 9–11); and, Polygonatum sect. Verticillata (x = 13–15). Populations of P. multiflorum from northwestern Himalaya are here shown to be best treated as a separate taxon, P. govanianum. Furthermore, P. verticillatum is shown to be polyphyletic, indicating that it represents a species-complex that includes multiple Asiatic species. Despite that, additional studies are still needed until the proper nomenclatural adjustments can be made.