Premise of research. Previous studies based on plastid fragments and/or nuclear ribosomal DNA have had limited success resolving relationships within the genus Salvia. This study evaluates the efficacy of complete plastome sequences for phylogenetic inference within Salvia, using the recently established Salvia subg. Glutinaria as a case study. We use these plastomes to identify hypervariable and simple sequence repeat (SSR) regions for future studies within Salvia. Methodology. In order to produce a phylogenetic backbone for Salvia, we sequenced and assembled complete plastomes for six species of Salvia. These plastomes were combined with 11 plastomes (10 species) of Salvia from GenBank for analyses. This sampling represented seven of the 10 subgenera of Salvia. Genome features of these plastomes were analyzed, and hypervariable regions, SSRs, and longer repeats were identified. Phylogenetic relationships of 16 Salvia species were investigated using maximum likelihood and Bayesian methods based on four different data sets. Pivotal results. All of the 17 Salvia plastomes displayed a typical quadripartite structure, and 114 different genes were identified in each accession. In addition, a total of 18 hypervariable regions and 626 SSRs were identified. The monophyly of Salvia and Salvia subg. Glutinaria was supported in our phylogenetic analyses. Conclusions. Complete plastome sequences are promising for phylogenetic reconstruction of Salvia and likely other clades within Lamiaceae. In addition, we identified 18 hypervariable regions that should be useful as plastid phylogenetic markers for phylogenetic inferences within the genus and potentially as bar code markers for identifying different species of Salvia. The extended analysis of SSRs will be helpful for future population genetics studies and in elucidating the genetic diversity of Salvia and its relatives.

中文翻译：

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丹参叶绿体基因组：基因组特征和系统发育分析

研究的前提。以前基于质体片段和/或核糖体 DNA 的研究在解决鼠尾草属内的关系方面取得了有限的成功。本研究使用最近建立的 Salvia subg 评估了完整的质体序列对 Salvia 系统发育推断的功效。Glutinaria 作为案例研究。我们使用这些塑性体来识别高变和简单序列重复 (SSR) 区域，以供将来在鼠尾草内进行研究。方法。为了产生鼠尾草的系统发育骨架，我们对六种鼠尾草进行了测序并组装了完整的塑性体。这些塑性体与来自 GenBank 的丹参的 11 个塑性体（10 种）结合进行分析。该采样代表了鼠尾草 10 个亚属中的 7 个。分析了这些塑性体的基因组特征，并分析了高变区、SSR、并确定了更长的重复。使用基于四个不同数据集的最大似然和贝叶斯方法研究了 16 种丹参物种的系统发育关系。关键结果。所有 17 个丹参塑性体都显示出典型的四方结构，并且在每个种质中鉴定了 114 个不同的基因。此外，共鉴定了 18 个高变区和 626 个 SSR。丹参和丹参 subg 的单系。我们的系统发育分析支持了Glutinaria。结论。完整的塑性体序列有望用于鼠尾草和唇形科内其他进化枝的系统发育重建。此外，我们确定了 18 个高变区，它们应该可用作该属内系统发育推断的质体系统发育标记，并可能作为识别不同丹参物种的条形码标记。SSRs 的扩展分析将有助于未来的种群遗传学研究和阐明鼠尾草及其亲属的遗传多样性。