Phylogenetic relationships of Aquilaria and Gyrinops (Thymelaeaceae) revisited: evidence from complete plastid genomes

The agarwood-producing genera, Aquilaria and Gyrinops, have been treated as sister genera in Thymelaeaceae (Aquilarieae, Malvales). However, there are differing opinions about their taxonomic positions. Using new evidence from complete plastid genome (plastome) sequences of 12 Aquilaria spp. and seven Gyrinops spp., corresponding to more than half the total number of species recognized in each genus, we reconstructed a phylogenetic tree of Aquilarieae. Members of both genera shared similar sequence variations at the plastome level. The phylogenetic relationships of the two genera were completely resolved using the complete plastome sequences. Gyrinops was paraphyletic to Aquilaria, i.e. Aquilaria nested in Gyrinops. Overlapping clustering patterns were observed from topology-clustering analysis using the complete plastome and the protein-coding gene sequences, which further reinforced the paraphyletic link. The maximum-likelihood-based RelTime analysis suggested that Aquilarieae and Daphneae diverged c. 44 Mya during the Eocene, followed by a rapid divergence event in Aquilarieae, with the split between G. vidalii and G. walla c. 1.24 Mya during the Pleistocene. Our new phylogenetic estimation demonstrates the relationship between the two genera, which will aid in future taxonomic revisions involving members of Aquilarieae.