State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China.
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China.
Mol Phylogenet Evol. 2020 Jun;147:106788. doi: 10.1016/j.ympev.2020.106788. Epub 2020 Mar 12.
Selaginellaceae have been shown to be monophyletic in previous studies, and include only the single genus Selaginella. However, the two most recent classifications of the genus disagree in terms of the number of subgenera recognized, and the position of problematic clades such as the "sanguinolenta" group, which has been resolved in quite different positions in different studies. Here, we performed a plastid-genome based phylogenomic analysis of Selaginellaceae to address this problem. The sanguinolenta group, represented here by three species, was resolved as sister to the remaining members of subg. Stachygynandrum. Additionally, subg. Exaltatae, subg. Ericetorum, and subg. Gymnogynum in clade A clustered into a well supported monophyletic clade but with conflicting topology between subgenera inside, which is possibly attributed to the early divergence among them. We uncovered substantial variation in both synonymous (dS) and nonsynonymous (dN) substitution rate, and GC content in plastomes of Selaginellaceae. The values of dS, dN, and GC content were significantly higher than those of other lycophytes (Isoetaceae and Lycopodiaceae). We observed a significant positive correlation between the high GC content, and the elevated dS and dN rates. In addition, the dS and dN values inferred among branches of Selaginellaceae were extremely variable. Our data indicate that this unevenly distributed substitution rate likely reflected relaxed or intensified selection among different lineages, which is possibly related to the inconsistency of the subgeneric phylogenetic topologies of Selaginellaceae.
卷柏科在以前的研究中被证明是单系的，仅包含一个属卷柏属。然而，最近的两次该属的分类在承认的亚属数量以及有问题的分支（如“sanguinolenta”组）的位置上存在分歧，该组在不同的研究中被解决在不同的位置。在这里，我们进行了基于质体基因组的卷柏科系统发育基因组学分析，以解决这个问题。以三个物种为代表的 sanguinolenta 组被解析为亚属 Stachygynandrum 其余成员的姐妹群。此外，亚属 Exaltatae、亚属 Ericetorum 和亚属 Gymnogynum 在 A 分支中聚类为一个支持良好的单系群，但内部亚属的拓扑结构存在冲突，这可能归因于它们之间的早期分化。我们发现卷柏科的质体基因组中同义（dS）和非同义（dN）替换率以及 GC 含量都有很大的变化。dS、dN 和 GC 含量的值均明显高于其他石松类植物（水韭科和木贼科）。我们观察到高 GC 含量与升高的 dS 和 dN 速率之间存在显著的正相关。此外，在卷柏科的分支之间推断出的 dS 和 dN 值变化极大。我们的数据表明，这种不均匀分布的替换率可能反映了不同谱系之间的放松或强化选择，这可能与卷柏科亚属系统发育拓扑结构的不一致有关。
