A phylotranscriptome study using silica gel-dried leaf tissues produces an updated robust phylogeny of Ranunculaceae

Abstract

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 Ranunculaceae to test whether silica-dried plant tissues could be used for RNA extraction and subsequent phylogenomic studies. We sequenced 27 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 this data, we conducted phylogenomic analyses, including concatenated- and coalescent-based phylogenetic reconstruction, molecular dating, coalescent simulation, phylogenetic network estimation, and whole genome duplication (WGD) inference. The resulting phylogeny was consistent with previous studies with higher resolution and statistical support. The 11 core Ranunculaceae tribes grouped into two chromosome type clades (T- and R-types), with high support. Discordance among gene trees is likely due to hybridization and introgression, ancient genetic polymorphism and incomplete lineage sorting. Our results strongly support one ancient hybridization event within the R-type clade and three WGD events in Ranunculales. 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.

Mahonia vs. Berberis Unloaded: Generic Delimitation and Infrafamilial Classification of Berberidaceae Based on Plastid Phylogenomics

“…The late Cretaceous origins of the three subfamilies of Berberidaceae estimated in present study are consistent with recent studies of temperate eudicots (e.g., Hypericaceae, Juglandaceae, and Ranunculaceae) in which major lineage diversification had occurred during the Late Cretaceous and Paleocene ( Nürk et al, 2015 ; He et al, 2021 ; Zhang et al, 2021 ). Considering the paleoclimate of the Cretaceous, our dating estimation also suggests that the early lineages of Berberidaceae should have adapted to warmer environments, implying niche shifts experienced by extant species ( Folk et al, 2020 ).…”

Phylogenomic analyses of Alismatales shed light into adaptations to aquatic environments

“…During the Late Cretaceous, the Tethys seas provided vast shallow water areas (Larkum et al 2018), which are suitable for the origination of seagrasses. On the contrary, most of the aquatic taxa in terrestrial orders originated during the Late Cenozoic and later, thus are younger than the existence of the Tethys seas, (e.g., aquatic Ranunculus (He et al 2022)). Therefore, the aquatic taxa in terrestrial orders had fewer chances of adaptation to the sea.…”

Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere

“…To measure the goodness‐of‐fit of the coalescent model with ILS explaining the gene tree discordance adequately, we performed a coalescent simulation analysis following the methods in previous studies (Wang et al, 2018; Yang et al, 2020; He et al, 2021; Morales‐Briones et al, 2021). Briefly, if the simulated gene trees based on the coalescent model correspond well to the empirical gene trees, the gene tree discordance may be explained by ILS.…”

“…Cytonuclear discordance at various levels was detected in Malus s.l. (Figure 6); coalescent simulation was also used for evaluating the importance of ILS in explaining cytonuclear discordance (Rose et al, 2020; He et al, 2021). We used the R package Phybase v. 1.5 to simulate 10,000 gene trees based on the ASTRAL species tree from SCN genes under MSC model.…”