Du Xin-Yu, Kuo Li-Yaung, Zuo Zheng-Yu, Li De-Zhu, Lu Jin-Mei
Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan.
Front Plant Sci. 2022 May 2;13:862772. doi: 10.3389/fpls.2022.862772. eCollection 2022.
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 and 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 , and 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.
质体基因组（质体基因组）的结构变异，尤其是大型倒位和基因丢失，可为植物的深层系统发育提供关键证据。在本研究中，我们在系统发育背景下研究了蕨类植物质体基因组的结构变异。总共采集了代表蕨类植物50个公认科和11个目的127个质体基因组，使其成为迄今为止对蕨类植物谱系最全面的质体基因组分析。样本包括15个科的42个新质体基因组，重点是膜蕨目和里白目。我们重建了所有现存蕨类植物科的一个得到充分支持的系统发育树，检测到显著的结构共衍征，包括9个大型倒位、7个反向重复区域（IR）边界移位、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个密码子插入缺失（插入或缺失），这些跨越蕨类植物的深层系统发育，特别是在主干节点上。新鉴定的倒位V5，连同新推断的IR边界R5的扩展，可以被确定为一个由双扇蕨科、瘤足蕨科、莎草蕨目和核心薄囊蕨类组成的分支的共衍征，而独特的倒位V4，连同IR边界R4的扩展，被确认为里白科的共衍征。这一结构证据支持了我们的系统发育推断，从而为膜蕨目的并系性提供了关键见解。V5和V7的倒位共同填补了一个关键空白，即现存大多数蕨类植物（莎草蕨目和核心薄囊蕨类）所特有的IR区域中“反向”基因方向是如何从木贼目和紫萁目中保留的推断祖先类型进化而来的。tRNA基因 和 被认为是早期分化的蕨类植物谱系的遗迹，但在大多数水龙骨目，特别是真水龙骨类中是完整的；蕨类植物质体基因组中tRNA基因 、 和 的丢失比以前认为的更为普遍。我们还在核心薄囊蕨类的蛋白质编码基因中鉴定了几个密码子插入缺失，这些可能被确定为特定科或更高分类等级的共衍征。本研究提供了一个整合质体基因组的结构和序列信息以解决植物深层系统发育的实证案例。
