Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes.
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.
State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, China.
Ren
R
Ren
Department of Biology, Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Intercollege Graduate Program in Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University.
Yazhou
Y
Sun
Intercollege Graduate Program in Cell and Developmental Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University.
Yue
Y
Zhao
Department of Plant Pathology, The Pennsylvania State University.
David
D
Geiser
State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, China zhouxiaofan1983@gmail.com hongma@fudan.edu.cn.
Hong
H
Ma
Department of Biology, Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Intercollege Graduate Program in Cell and Developmental Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University Present address: Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235 zhouxiaofan1983@gmail.com hongma@fudan.edu.cn.
Xiaofan
X
Zhou
D017124:Conserved Sequence; D019143:Evolution, Molecular; D005800:Genes, Fungal; D016814:Microsporidia / Q000145:classification / Q000235:genetics; D009687:Nuclear Proteins / Q000235:genetics; D010802:Phylogeny
D009687:Nuclear Proteins
eukaryotic phylogeny; fungal phylogeny; phylogenomics; single-copy genes