Phylogenomics of Salvia L. subgenus Calosphace (Lamiaceae)

Abstract

The evolutionary relationships of Salvia have been difficult to estimate. In this study, we used the Next Generation Sequencing method Hyb-Seq to evaluate relationships among 90 Lamiaceae samples, including representatives of Mentheae, Ocimeae, Salvia subgenera Audibertia, Leonia, Salvia, and 69 species of subgenus Calosphace, representing 32 of Epling's sections. A bait set was designed in MarkerMiner using available transcriptome data to enrich 119 variable nuclear loci. Nuclear and chloroplast loci were assembled with hybphylomaker (HPM), followed by coalescent approach analyses for nuclear data (ASTRAL, BEAST) and a concatenated Maximum Likelihood analysis of chloroplast loci. The HPM assembly had an average of 1,314,368 mapped reads for the sample and 527 putative exons. Phylogenetic inferences resolved strongly supported relationships for the deep-level nodes, agreeing with previous hypotheses which assumed that subgenus Audibertia is sister to subgenus Calosphace. Within subgenus Calosphace, we recovered eight monophyletic sections sensu Epling, Cardinalis, Hastatae, Incarnatae, and Uricae in all the analyses (nDNA and cpDNA), Biflorae, Lavanduloideae, and Sigmoideae in nuclear analyses (ASTRAL, BEAST) and Curtiflorae in ASTRAL trees. Network analysis supports deep node relationships, some of the main clades, and recovers reticulation within the core Calosphace. The chloroplast phylogeny resolved deep nodes and four monophyletic Calosphace sections. Placement of S. axillaris is distinct in nuclear evidence and chloroplast, as sister to the rest of the S. subg. Calosphace in chloroplast and a clade with “Hastatae clade” sister to the rest of the subgenus in nuclear evidence. We also tested the monophyly of S. hispanica, S. polystachia, S. purpurea, and S. tiliifolia, including two samples of each, and found that S. hispanica and S. purpurea are monophyletic. Our baits can be used in future studies of Lamiaceae phylogeny to estimate relationships between genera and among species. In this study, we presented a Hyb-Seq phylogeny for complex, recently diverged Salvia, which could be implemented in other Lamiaceae.

Chromosome-scaleSalvia hispanicaL. (Chia) genome assembly reveals rampantSalviainterspecies introgression

“…The fragmentation could be present due to different ancestry of Chia pinta and S. officinalis . As Salvia is a polyphyletic genus (Lara-Cabrera et al, 2021), this could be indicative of how distantly related these two species are. An alternative hypothesis is that they share a common ancestor, but the divergence time between species is so long that conserved genetic regions have been differentially fractionated (i.e.…”

“…A phylogeny of Salvia, based on 91 nuclear genes, places Chia within Salvia sect. Potiles in a monophyletic clade (Lara-Cabrera et al, 2021). However, the Salvia genus has yet to be fully resolved and remains polyphyletic with S. tiliifolia being placed within two separate clades: the Angulatae and Polystachyae (Lara-Cabrera et al, 2021).…”

“…Potiles in a monophyletic clade (Lara-Cabrera et al, 2021). However, the Salvia genus has yet to be fully resolved and remains polyphyletic with S. tiliifolia being placed within two separate clades: the Angulatae and Polystachyae (Lara-Cabrera et al, 2021). Therefore, additional phylogenetic analyses are necessary to achieve a comprehensive resolution of the Salvia genus.…”

Chemical constituents of Salvia urica Epling, and their antihyperglycemic and antipropulsive effects

“…The species of the Salvia genus have broad traditional medicinal uses in Mexico, which include treating digestive and gynecological problems, and affections of the nervous system (Jenks & Kim 2013). Previous reports have explored the phylogenetic relationships of species from Salvia subgenus Calosphace based on nuclear and plastid markers (ITS, trnL-trnF, and trnH-psbA) (Fragoso-Martínez et al, 2018;González-Gallegos et al 2018), and nuclear loci from massive sequencing data (Lara-Cabrera et al 2021). Using the phylogeny of Salvia subgenus Calosphace as a tool to target specific metabolites as proposed by Ortiz-Mendoza et al (2022), we decided explore the phytochemistry of key species; since we analyzed a species that was closely related to S. amarissima, which belongs to a taxon that has shown a wide variety of metabolites, which include neo-clerodanes, 9,10-seco-neo-clerodanes, and amarissanes (Bautista et al 2016).…”

Perspectives in plant evolutionary genetics: A field guide in 15 “easy steps” to modern tools in evolutionary genetics and genomics

“…The idea of using genomic data to obtain better resolved and more robust phylogenies has been in the air for a while (see for instance Conte et al 2008, Cibrián-Jaramillo et al 2010, Lee et al 2011), but the recent massive parallel sequencing, along with different reduced representation methods has boosted their use (see for instance the recent studies of McKain et al 2018, Hipp et al 2019, Leebens-Mack et al 2019, Kapli et al 2020, Cruz-Nicolás et al 2021, and Lara-Cabrera et al 2021.…”