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

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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.

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The results here presented are part of the Ph.D. thesis of EIOM under the advisory of SILC. We thank the financial support of the following: CONACyT graduate studies scholarship 290575 to EIOM, CONACyT sabbatical scholarship 232839 to SILC, Coordinación de la Investigación Científica (UMSNH), Project 8.16. NSF award number 1120080 to JMP. Curators from herbaria RSA, BIGU, EBUM, ENCB, IEB, MEXU and UAMIZ. We are thankful for the collection assistance of Arnulfo Blanco, Anna Paizanni, Brenda Bedolla, Cesar Alfaro, Justino Olvera, Manuel Ramírez, Sergio Zamudio and Mario Veliz (BIGU) for aiding in the Guatemala collection. Mario Hernández for allowing collection of fresh leaf material at the Botanical Garden “Charco del Ingenio” in San Miguel de Allende, Guanajuato. And Heather Blume for facilitating collections at the Cabrillo College Environmental Horticulture Center & Botanic Gardens.

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Grant T. Godden, J. Mark Porter, and Sabina I. Lara-Cabrera were involved in conceptualization of the study; Grant T. Godden, J. Mark Porter, and Sabina I. Lara-Cabrera contributed to methodology; material preparation and data collection were performed by Grant T. Godden, J. Mark Porter, Sabina I. Lara-Cabrera and Edgar I. Olvera-Mendoza. All authors contributed to analysis, investigation and writing, review and editing of the manuscript. All authors read and approved the final manuscript.

Correspondence to Sabina I. Lara-Cabrera.

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Olvera-Mendoza, E.I., Godden, G.T., Montero-Castro, J.C. et al. Chloroplast and nuclear ribosomal cistron phylogenomics in a group of closely related sections in Salvia subg. Calosphace. Braz. J. Bot (2020).

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  • Lamiaceae
  • Lamiales
  • Nuclear ribosomal cistron
  • Nucleotide diversity
  • Plastid genome