Phylotranscriptomic analyses reveal a deep gene tree discordance of Camellia (Theaceae) and the possible ancestral origin of cultivated C. oleifera

An increasing use of genomic data has forced molecular phylogeneticists to confront gene tree discordance. Multiple factors can result in incongruence among genes, such as introgression, incomplete lineage sorting (ILS), gene duplication or loss, and the influence of incomplete sampling through assembly errors and filtering criteria. <em>Camellia</em>, the largest genus in Theaceae s.str., has controversial taxonomy and systematics due in part to a complex evolutionary history including interspecific gene flow. Here, we used 60 transcriptomes of 55 species, which represented 15 sections of <em>Camellia</em> to investigate its phylogeny and the possible causes of gene tree discordance. We conducted gene tree discordance analysis based on 1,617 orthologous low-copy nuclear genes, primarily using coalescent species trees and polytomy tests for hard vs. soft conflict. In order to assess the impact of selective pressure on phylogenetic topology reconstruction, we also performed a selective pressure analysis. Our results detected different levels of gene tree discordance in the backbone of <em>Camellia</em>, and recovered rapid diversification as one of the possible causes of gene discordance. Furthermore, we confirmed that none of the currently proposed sections from <em>Camellia</em> was monophyletic and discuss the possible ancestral origin of cultivated <em>C. oleifera</em>. Combing all orthologous genes could provide an improved phylogenetic resolution and minimize the incongruence between gene trees and species tree of <em>Camellia</em>.