Order-level fern plastome phylogenomics: new insights from Hymenophyllales

PREMISE OF THE STUDY: Filmy ferns (Hymenophyllales) are a highly specialized lineage, having mesophyll one cell layer thick and inhabiting particularly shaded and humid environments. The phylogenetic placement of Hymenophyllales has been inconclusive, and while over 87 whole fern plastomes have been published, none was from Hymenophyllales. To better understand the evolutionary history of filmy ferns, we sequenced the first complete plastome for this order. METHODS: We compiled a plastome phylogenomic dataset encompassing all eleven fern orders, and reconstructed phylogenies using different data types (nucleotides, codons, and amino acids) and partition schemes (codon positions and loci). To infer the evolution of fern plastome organization, we coded plastomic features, including inversions, inverted repeat boundary shifts, gene losses, and tRNA anticodon sequences as characters, and reconstructed the ancestral states for these characters. KEY RESULTS: We discovered a suite of novel, Hy...研究背景：膜蕨目（Hymenophyllales）是一类高度特化的类群，其叶肉仅由单层细胞构成，且栖息于极端荫蔽湿润的生境中。目前膜蕨目的系统发育位置尚未明确，而已发表的蕨类完整质体基因组（plastome）已超过87个，但尚无膜蕨目的相关数据。为深入阐明膜蕨类植物的演化历史，我们首次对该目物种的完整质体基因组进行了测序。 方法：我们构建了涵盖全部11个蕨类目的质体基因组系统发育组学数据集，并采用不同数据类型（核苷酸、密码子（codon）、氨基酸（amino acids））及分区策略（密码子位点与基因座位）重建系统发育树。为推断蕨类质体基因组的结构演化，我们将质体基因组特征（包括倒位（inversions）、反向重复边界漂移、基因丢失、转运RNA（transfer RNA, tRNA）反密码子序列）作为性状进行编码，并重建了这些性状的祖先状态。 主要结果：我们发现了一系列全新的、膜蕨目（Hymenophyllales）特有的……