| Popis: |
The utility of transcriptome data in plant phylogenetics has gained popularity in recent years. However, because RNA degrades much more easily than DNA, the logistics of obtaining fresh tissues has become a major limiting factor for widely applying this method. Here, we used the plant family Ranunculaceae to test whether silica-dried plant tissues could be used for RNA extraction and subsequent phylogenomic studies. We sequenced 27 Ranunculales transcriptomes, 21 from silica gel-dried (SD-samples) and six from liquid nitrogen-preserved (LN-samples) leaf tissues, and downloaded 27 additional transcriptomes from GenBank. Our results showed that although the LN-samples produced slightly better reads than the SD-samples, there were no significant differences in RNA quality and quantity, assembled contig lengths and numbers, and BUSCO comparisons between two treatments. Using the newly generated and the GenBank data, we conducted phylogenomic analyses, including concatenated- and coalescent-based phylogenetic reconstruction, molecular dating, coalescent simulation, and phylogenetic network estimation to address nuclear gene conflicts and cyto-nuclear discordance, as well as whole genome duplication (WGD). The resulting phylogenetic framework was consistent with results of previous molecular phylogenetic studies, but with higher resolution and statistical support. The 11 core Ranunculaceae tribes grouped into two chromosome type clades (T- and R-types), with high support. Cyto-nuclear discordance was detected concerning Adonideae, and it may be likely resulted from ancient hybridization and introgression. Discordance among nuclear gene trees is most likely due to ancient genetic polymorphism and incomplete lineage sorting. Our results strongly support one ancient hybridization event within the R-type clade and three WGD events, one at the Ranunculales stem and two within Ranunculaceae. Evolution of the three Ranunculaceae chromosome types is likely not directly related to WGD events. By clearly resolving the Ranunculaceae phylogeny, we demonstrated that SD-samples can be used for RNA-seq and phylotranscriptomic studies of angiosperms. |
