Nelumbonaceae: Systematic position and species diversification revealed by the complete chloroplast genome

Nelumbonaceae is a morphologically unique family of angiosperms and was traditionally placed in Nymphaeales; more recently, it was placed in Proteales based on molecular data, or in an order of its own, Nelumbonales. To determine the systematic position of the family and to date the divergence time of the family and the divergence time of its two intercontinentally disjunct species, we sequenced the entire chloroplast genome of Nelumbo lutea and most of the chloroplast genes of N. nucifera. We carried out phylogenetic and molecular dating analyses of the two species and representatives of 47 other plant families, representing the major lineages of angiosperms, using 83 plastid genes. The N. lutea genome was 163 510 bp long, with a total of 130 coding genes and an overall GC content of 38%. No significant structural differences among the genomes of N. lutea, Nymphaea alba, and Platanus occidentalis were observed. The phylogenetic relationships based on the 83 plastid genes revealed a close relationship between Nelumbonaceae and Platanaceae. The divergence times were estimated to be 109 Ma between the two families and 1.5 Ma between the two Nelumbo species. The estimated time was only slightly longer than the age of known Nelumbo fossils, suggesting morphological stasis within Nelumbonaceae. We conclude that Nelumbonaceae holds a position in or close to Proteales. We further conclude that the two species of Nelumbo diverged recently from a common ancestor and do not represent ancient relicts on different continents.