Phylotranscriptomics of Theaceae: generic-level relationships, reticulation and whole-genome duplication

Abstract

Background and Aims Theaceae, with three tribes, nine genera and more than 200 species, are of great economic and ecological importance. Recent phylogenetic analyses based on plastomic data resolved the relationships among the three tribes and the intergeneric relationships within two of those tribes. However, generic-level relationships within the largest tribe, Theeae, were not fully resolved. The role of putative whole genome duplication (WGD) events in the family and possible hybridization events among genera within Theeae also remains to be tested further. Methods Transcriptomes or low-depth whole-genome sequencing of 57 species of Theaceae, as well as additional plastome sequence data were generated. Using a dataset of low-copy nuclear genes, we reconstructed phylogenetic relationships using concatenated, species tree and phylogenetic network approaches. We further conducted molecular dating analyses and inferred possible WGD events by examining the distribution of the number of synonymous substitutions per synonymous site (KS) for paralogs in each species. For plastid protein-coding sequences (CDS), phylogenies were reconstructed for comparison with the results obtained from analysis of the nuclear dataset. Results Based on the 610 low-copy nuclear genes (858,606 bp in length) investigated, Stewartieae was resolved as sister to the other two tribes. Within Theeae, the Apterosperma-Laplacea clade grouped with Pyrenaria, leaving Camellia and Polyspora as sister. The estimated ages within Theaceae were largely consistent with previous studies based mainly on plastome data. Two reticulation events within Camellia and one between the common ancestor of Gordonia and Schima were found. All members of the tea family shared two WGD events, an older At-γ and a recent Ad-β; both events were also shared with the outgroups (Diapensiaceae, Pentaphylacaceae, Styracaceae and Symplocaceae). Conclusions Our analyses using low-copy nuclear genes improved understanding of phylogenetic relationships at the tribal and generic levels previously proposed based on plastome data, but the phylogenetic position of the Apterosperma-Laplacea clade needs more attention. There is no evidence for extensive intergeneric hybridization within Theeae or for a Theaceae-specific WGD event. Land bridges (e.g. the Bering land bridge) during the Late Oligocene may have permitted the intercontinental plant movements that facilitated the putative ancient introgression between the common ancestor of Gordonia and Schima.

Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants

“…whole lamina shape, apex, margin shape and serration, and areole composition), which is in accordance with their close relationships in the phylogenetic tree. The phylogenetic tree constructed in the present study does not support the polyphyletic nature of section Camellia as proposed by the ITS and nuclear gene‐based trees reported previously (Vijayan et al., 2009; Zhang et al., 2022). The section Camellia is observed to be monophyletic in our transcriptome‐based tree, which stands in line with the finding based on morphology data (Lu et al., 2012; Ming, 1998).…”

“…The well‐resolved Camellia phylogeny consists of seven groups and supports the combinations of section Glaberrima and section Thea , section Paracamellia and section Oleifera , section Pseudocamellia and section Tuberculata , and section Eriandria and section Theopsis , which is consistent with the treatments of Ming's taxonomical system (Ming & Bartholomew, 2007), as well as previous findings base on ITS and recent nuclear gene sequences (Vijayan et al., 2009; Zhang et al., 2022). The accuracy of constructed phylogeny of genus Camellia was also supported by the phenotypic data of Camellia plants (Hong, 2011; Lu et al., 2012), especially in some important and complex lineages (Table S17).…”

“…In addition, the results also show an almost identical topology of the phylogeny of genus Camellia constructed using coalescent‐based and ortholog‐concatenation methods (Figure S9). A surprising result of the close relationship was observed between species from section Luteoflora and section Tuberculata , which is totally different from the treatments of Ming and Chang's taxonomical system (Chang, 1981, Ming & Bartholomew, 2007) but consistent with recent findings from nuclear genes (Zhang et al., 2022). Furthermore, it was also found that section Brachyandra and Corallina are positioned at the base of Camellia phylogeny (Zhang et al., 2022), whereas the present study revealed that section Chrysantha is actually the basal section of genus Camellia (Table S18), which agrees with the ancient nature of Chrysantha species in genus Camellia (Jiang et al., 2010; Ming & Zhang, 1993).…”

Phylogenomics Resolves the Phylogeny of Theaceae by Using Low-Copy and Multi-Copy Nuclear Gene Makers and Uncovers a Fast Radiation Event Contributing to Tea Plants Diversity

“…multisepala and Pyrenaria pingpienensis differentiated successively in LCGT. However, they were sister groups of each other in MCGT, which is consistent with a previous study in 2021 [19].…”

“…The ages of the MRCA of the genus Camellia and section Thea were estimated at 21.8 and 13.2 Mya, respectively. The age estimation of Theaceae in our study is the general consensus with previous studies by different inference methods [18,19].…”