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.

中文翻译：

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Salvia subg 中一组密切相关的部分中的叶绿体和核核糖体顺反子系统基因组学。钙质面

鼠尾草系统发育尚未解决有问题的鼠尾草亚属 Calosphace 中的许多浅层进化枝，因为难以找到足够多的可变位点。我们从核杂交富集项目的非目标读数中组装了 15 个叶绿体基因组和核核糖体顺反子，以评估主要是墨西哥部分的密切相关组的系统发育效用。叶绿体同线性由 10 个唇形目叶绿体证实，支持参考组装图。Salvia miltiorrhiza Bunge 叶绿体用作组装的参考，平均 25,970 个读数，平均深度为 20.71 个读数；基因组范围从 141,451 到 150,339 bp。S. carduacea Benth。核糖体顺反子（18S、ITS1、5.8S、ITS2 和 26S）用作组装参考，平均 66,387 个读数和 1508 个读数的平均深度。我们评估了质体、质体和 nrDNA 的几种分区方案并减少了采样，以评估这些是否会产生相同的系统发育推断。最大似然推断产生了高自举支持和两个主要进化枝，其中散布着来自鼠尾草派的物种。Scorodoniae：进化枝 A，具有来自 S. sects 的物种。来自 S. sects 的 Attratae 和 Mitratae 和进化枝 B。Sigmoideae和Uricae。只有 S. 教派。Uricae 在支持其身份的每项分析中都是单系的，而不是合并到 S. sect 中。蝎子科；S. 教派。仅当包含核糖体 DNA 序列时，才推断 Sigmoideae 是单系的。使用整个质体和 nrDNA 获得更高的分辨率和更高的分支支持，而不是对高度可变的区域进行二次采样；因此我们推荐这种扩展分类单元抽样的方法，