Data_Sheet_1_Structural Variation of Plastomes Provides Key Insight Into the Deep Phylogeny of Ferns.PDF

Structural variation of plastid genomes (plastomes), particularly large inversions and gene losses, can provide key evidence for the deep phylogeny of plants. In this study, we investigated the structural variation of fern plastomes in a phylogenetic context. A total of 127 plastomes representing all 50 recognized families and 11 orders of ferns were sampled, making it the most comprehensive plastomic analysis of fern lineages to date. The samples included 42 novel plastomes of 15 families with a focus on Hymenophyllales and Gleicheniales. We reconstructed a well-supported phylogeny of all extant fern families, detected significant structural synapomorphies, including 9 large inversions, 7 invert repeat region (IR) boundary shifts, 10 protein-coding gene losses, 7 tRNA gene losses or anticodon changes, and 19 codon indels (insertions or deletions) across the deep phylogeny of ferns, particularly on the backbone nodes. The newly identified inversion V5, together with the newly inferred expansion of the IR boundary R5, can be identified as a synapomorphy of a clade composed of Dipteridaceae, Matoniaceae, Schizaeales, and the core leptosporangiates, while a unique inversion V4, together with an expansion of the IR boundary R4, was verified as a synapomorphy of Gleicheniaceae. This structural evidence is in support of our phylogenetic inference, thus providing key insight into the paraphyly of Gleicheniales. The inversions of V5 and V7 together filled the crucial gap regarding how the “reversed” gene orientation in the IR region characterized by most extant ferns (Schizaeales and the core leptosporangiates) evolved from the inferred ancestral type as retained in Equisetales and Osmundales. The tRNA genes trnR-ACG and trnM-CAU were assumed to be relicts of the early-divergent fern lineages but intact in most Polypodiales, particularly in eupolypods; and the loss of the tRNA genes trnR-CCG, trnV-UAC, and trnR-UCU in fern plastomes was much more prevalent than previously thought. We also identified several codon indels in protein-coding genes within the core leptosporangiates, which may be identified as synapomorphies of specific families or higher ranks. This study provides an empirical case of integrating structural and sequence information of plastomes to resolve deep phylogeny of plants.

叶绿体基因组（叶绿体群）的结构变异，尤其是大型倒位和基因丢失，可为植物深部分枝系统提供关键的证据。在本研究中，我们以系统发育的背景探讨了蕨类植物叶绿体群的结构变异。共采集了代表50个已识别蕨类植物科和11个目的127个叶绿体群样本，这使得本项研究成为迄今为止对蕨类植物谱系最全面的叶绿体组分析。样本中包括15个科的42个新的叶绿体群，重点关注鳞毛蕨目和adder's-tongue目。我们重建了所有现存蕨类植物科的稳健系统发育树，检测到显著的结构共祖特征，包括9个大型倒位、7个逆转重复区域（IR）边界移动、10个蛋白质编码基因丢失、7个tRNA基因丢失或反密码子变化以及19个密码子插入或删除，这些特征在蕨类植物的深部分枝系统，尤其是在主干节点上。新识别的V5倒位，连同新推断的IR边界R5的扩张，可以被视为由Dipteridaceae、Matoniaceae、Schizaeales和核心薄壁孢子植物组成的类群的共祖特征，而独特的V4倒位，连同IR边界R4的扩张，被验证为adder's-tongue目的共祖特征。这一结构证据支持了我们的系统发育推断，从而为我们提供了关于adder's-tongue目的旁系同源的深刻见解。V5和V7倒位共同填补了关于大多数现存蕨类植物（adder's-tongue目和核心薄壁孢子植物）中IR区域“反转”基因取向如何从保留在Equisetales和Osmundales中的推断的祖先类型演化的关键空缺。tRNA基因trnR-ACG和trnM-CAU被认为是早期分歧的蕨类植物谱系的遗迹，但在大多数Polypodiales，尤其是真鳞毛蕨科中完整保留；而tRNA基因trnR-CCG、trnV-UAC和trnR-UCU在蕨类植物叶绿体群中的丢失比先前认为的要普遍得多。我们还识别了核心薄壁孢子植物蛋白质编码基因内的几个密码子插入或删除，这些可能被识别为特定科或更高阶的共祖特征。本研究为将叶绿体群的结构和序列信息整合起来，以解决植物的深部分枝系统提供了经验案例。