State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Mol Biol Evol. 2024 Aug 2;41(8). doi: 10.1093/molbev/msae153.
Selaginellaceae, originated in the Carboniferous and survived the Permian-Triassic mass extinction, is the largest family of lycophyte, which is sister to other tracheophytes. It stands out from tracheophytes by exhibiting extraordinary habitat diversity and lacking polyploidization. The organelle genome-based phylogenies confirmed the monophyly of Selaginella, with six or seven subgenera grouped into two superclades, but the phylogenetic positions of the enigmatic Selaginella sanguinolenta clade remained problematic. Here, we conducted a phylogenomic study on Selaginellaceae utilizing large-scale nuclear gene data from RNA-seq to elucidate the phylogeny and explore the causes of the phylogenetic incongruence of the S. sanguinolenta clade. Our phylogenetic analyses resolved three different positions of the S. sanguinolenta clade, which were supported by the sorted three nuclear gene sets, respectively. The results from the gene flow test, species network inference, and plastome-based phylogeny congruently suggested a probable hybrid origin of the S. sanguinolenta clade involving each common ancestor of the two superclades in Selaginellaceae. The hybrid hypothesis is corroborated by the evidence from rhizophore morphology and spore micromorphology. The chromosome observation and Ks distributions further suggested hybridization accompanied by polyploidization. Divergence time estimation based on independent datasets from nuclear gene sets and plastid genome data congruently inferred that allopolyploidization occurred in the Early Triassic. To our best knowledge, the allopolyploidization in the Mesozoic reported here represents the earliest record of tracheophytes. Our study revealed a unique triad of phylogenetic positions for a hybrid-originated group with comprehensive evidence and proposed a hypothesis for retaining both parental alleles through gene conversion.
卷柏科起源于石炭纪，在二叠纪-三叠纪大灭绝中幸存下来，是石松类植物中最大的科，与其他维管束植物为姐妹群。它通过表现出非凡的生境多样性和缺乏多倍化而与维管束植物区别开来。基于细胞器基因组的系统发育分析证实了卷柏属的单系性，六个或七个亚属分为两个超类群，但神秘的卷柏属血红色群的系统发育位置仍然存在问题。在这里，我们利用来自 RNA-seq 的大规模核基因数据对卷柏科进行了系统基因组学研究，以阐明系统发育并探讨血红色群系统发育不一致的原因。我们的系统发育分析确定了血红色群的三个不同位置，这三个位置分别得到了三个核基因集的支持。基因流测试、物种网络推断和质体基因组系统发育的结果一致表明，血红色群可能涉及卷柏科两个超类群的每个共同祖先，存在杂种起源。杂种假说得到了根状茎形态和孢子微形态的证据的支持。染色体观察和 Ks 分布进一步表明，杂交伴随着多倍化。基于核基因集和质体基因组数据的独立数据集的分歧时间估计一致推断，异源多倍化发生在早三叠世。据我们所知，这里报道的中生代异源多倍化代表了维管束植物最早的记录。我们的研究揭示了一个杂种起源的组具有独特的三重系统发育位置，并提出了一个通过基因转换保留双亲等位基因的假说。
