Chloroplast and nuclear ribosomal cistron phylogenomics in a group of closely related sections in Salvia subg. Calosphace

Sage phylogenies have not resolved many shallow level clades within problematic Salvia subgenus Calosphace, hindered by the difficulty in finding sufficiently variable loci. We assembled fifteen chloroplast genomes and nuclear ribosomal cistrons from non-target reads of a nuclear hybrid enrichment project to assess the phylogenetic utility for a closely related group of mainly Mexican sections. Chloroplast synteny is confirmed with 10 Lamiales chloroplasts, supporting a map to reference assembly. Salvia miltiorrhiza Bunge chloroplast was used as a reference for assemblies, averaging 25,970 reads with mean depth of 20.71 reads; genomes ranged from 141,451 to 150,339 bp. The S. carduacea Benth. nuclear ribosomal cistron (18S, ITS1, 5.8S, ITS2 and 26S) was used as a reference for assembly, averaging 66,387 reads and mean depth of 1508 reads. We evaluated several partitioning schemes for plastid, plastid and nrDNA and reduced sampling, to assess whether these would render the same phylogenetic inferences. Maximum likelihood inferences resulted with high bootstrap support and two main clades with interspersed species from Salvia sect. Scorodoniae: clade A with species from S. sects. Atratae and Mitratae and clade B from S. sects. Sigmoideae and Uricae. Only S. sect. Uricae is monophyletic in every analysis supporting its identity, not merged into S. sect. Scorodoniae; S. sect. Sigmoideae is inferred monophyletic only if the ribosomal DNA sequences are included. Greater resolution and higher branch support are obtained with the entire plastome and nrDNA, rather than subsampling highly variable regions; thus we recommend this approach with expanded taxon sampling, coupled with a morphological review to better solve sectional circumscription in closely related S. subgenus Calosphace species.