ArticleGigaScience2018
Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns.
Article in GigaScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- The Dayhoff Exchange Score: A New Metric to Quantify Entropic Site Saturation in Amino Acid Data Sets Prior to Phylogenetic Analysis.Systematic biology · 2026Article
- Cryptocaulaceae: a new and deeply diverged branch within the fern tree of life.Journal of plant research · 2026Article
- Repeated loss of plastid NDH during evolution of land plants.Annals of botany · 2026Review
- Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls.Nature plants · 2025Article
- The chromosome-level genome assembly of Broad-Leaf Fern (Dipteris shenzhenensis).Scientific data · 2025Article
- The Possible Earliest Allopolyploidization in Tracheophytes Revealed by Phylotranscriptomics and Morphology of Selaginellaceae.Molecular biology and evolution · 2024Article
- Patterns in Genome-Wide Codon Usage Bias in Representative Species of Lycophytes and Ferns.Genes · 2024Article
- Review
- Differential expression and co-localization of transcriptional factors during callus transition to differentiation for shoot organogenesis in the water fern Ceratopteris richardii.Annals of botany · 2024Article
- Whole Genome Duplication Events Likely Contributed to the Aquatic Adaptive Evolution of Parkerioideae.Plants (Basel, Switzerland) · 2024Article
- Comprehensive analysis of theFrontiers in plant science · 2024Article
- Dynamic evolution of MADS-box genes in extant ferns via large-scale phylogenomic analysis.Frontiers in plant science · 2024Article
- Chloroplast genome structure analysis ofFrontiers in plant science · 2024Article
- Variations in Rhizospheric and Endophytic Root Fungal Communities of Scrophularia ningpoensis in Different Producing Areas.Current microbiology · 2023Article
- First Fossil Record ofLife (Basel, Switzerland) · 2023Article
- Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae).Plants (Basel, Switzerland) · 2023Article
- Revisiting ancient polyploidy in leptosporangiate ferns.The New phytologist · 2023Article
- Editorial: Biology, systematics, and evolution of ferns and lycophytes in the omics era.Frontiers in plant science · 2023Article
- Filmy Ferns (Hymenophyllaceae) and Associated Spike-Mosses (Selaginellaceae) from the Mid-Cretaceous Kachin Amber, Myanmar.Biology · 2022Article
- Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses.Pathogens (Basel, Switzerland) · 2022Article
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Background: Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. Results: With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata. Conclusions: Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants.
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