ArticleGenome biology and evolution2016
Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes.
Article in Genome biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Species evolution: cryptic species and phenotypic noise with a particular focus on fungal systematics.Frontiers in cellular and infection microbiology · 2025Review
- Identification of hidden associations among eukaryotic genes through statistical analysis of coevolutionary transitions.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade.Frontiers in bioinformatics · 2022Review
- Gene Duplications Trace Mitochondria to the Onset of Eukaryote Complexity.Genome biology and evolution · 2021Article
- Repeated Evolution of Inactive Pseudonucleases in a Fungal Branch of the Dis3/RNase II Family of Nucleases.Molecular biology and evolution · 2021Article
- Fungal evolution: cellular, genomic and metabolic complexity.Biological reviews of the Cambridge Philosophical Society · 2020Article
- MetaEuk-sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics.Microbiome · 2020Article
- SUMOylation in fungi: A potential target for intervention.Computational and structural biotechnology journal · 2020Review
- Fungal evolution: diversity, taxonomy and phylogeny of the Fungi.Biological reviews of the Cambridge Philosophical Society · 2019Article
- Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi.BMC genomics · 2018Article
- Comparative genomics of nuclear envelope proteins.BMC genomics · 2018Article
- Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria.Protoplasma · 2018Article
- Phylogenetic taxon definitions forIMA fungus · 2018Article
- Origin and evolution of fungal HECT ubiquitin ligases.Scientific reports · 2018Article
- Cytochrome P450 diversity in the tree of life.Biochimica et biophysica acta. Proteins and proteomics · 2018Article
- Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences.Protoplasma · 2018Article
- The Conservation of the Germline Multipotency Program, from Sponges to Vertebrates: A Stepping Stone to Understanding the Somatic and Germline Origins.Genome biology and evolution · 2017Article
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
A comprehensive and reliable eukaryotic tree of life is important for many aspects of biological studies from comparative developmental and physiological analyses to translational medicine and agriculture. Both gene-rich and taxon-rich approaches are effective strategies to improve phylogenetic accuracy and are greatly facilitated by marker genes that are universally distributed, well conserved, and orthologous among divergent eukaryotes. In this article, we report the identification of 943 low-copy eukaryotic genes and we show that many of these genes are promising tools in resolving eukaryotic phylogenies, despite the challenges of determining deep eukaryotic relationships. As a case study, we demonstrate that smaller subsets of ∼20 and 52 genes could resolve controversial relationships among widely divergent taxa and provide strong support for deep relationships such as the monophyly and branching order of several eukaryotic supergroups. In addition, the use of these genes resulted in fungal phylogenies that are congruent with previous phylogenomic studies that used much larger datasets, and successfully resolved several difficult relationships (e.g., forming a highly supported clade with Microsporidia, Mitosporidium and Rozella sister to other fungi). We propose that these genes are excellent for both gene-rich and taxon-rich analyses and can be applied at multiple taxonomic levels and facilitate a more complete understanding of the eukaryotic tree of life.
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