Chloroplast phylogenomics resolves key relationships in ferns

Studies on chloroplast genomes of ferns and lycophytes are relatively few in comparison with those on seed plants. Although a basic phylogenetic framework of extant ferns is available, relationships among a few key nodes remain unresolved or poorly supported. The primary objective of this study is to explore the phylogenetic utility of large chloroplast gene data in resolving difficult deep nodes in ferns. We sequenced the chloroplast genomes from Cyrtomium devexiscapulae (eupolypod I) and Woodwardia unigemmata (eupolypod II), and constructed the phylogeny of ferns based on both 48 genes and 64 genes. The trees based on 48 genes and 64 genes are identical in topology, differing only in support values for four nodes, three of which showed higher support values for the 48-gene dataset. Equisetum was resolved as the sister to the clade of Psilotales-Ophioglossales, and the clade of Equisetales-Psilotales-Ophioglossales was sister to the clade of the leptosporangiate and marattioid ferns. T...

相较于种子植物，蕨类与石松植物叶绿体基因组（chloroplast genomes）的相关研究仍较为匮乏。尽管目前已构建现存蕨类的基础系统发育框架（phylogenetic framework），但部分关键分支节点的演化关系仍未得到解析，或支持度偏低。本研究的核心目标，在于探究大规模叶绿体基因数据集在解析蕨类疑难深层分支节点时的系统发育应用价值。本研究对披针叶贯众（Cyrtomium devexiscapulae，eupolypod I）与单芽狗脊蕨（Woodwardia unigemmata，eupolypod II）的叶绿体基因组进行了测序，并基于48个基因与64个基因两套数据集构建了蕨类的系统发育树。基于48基因与64基因数据集构建的系统发育树拓扑结构完全一致，仅在4个分支节点的支持度上存在差异：其中3个节点在48基因数据集下呈现出更高的支持度。系统发育分析显示，木贼属（Equisetum）与松叶蕨目-瓶尔小草目类群构成姊妹群；而木贼目-松叶蕨目-瓶尔小草目类群，则与薄囊蕨类（leptosporangiate ferns）及合囊蕨类（marattioid ferns）类群互为姊妹群。T...