ArticleMolecular biology and evolution2017
Insights into Ciliary Genes and Evolution from Multi-Level Phylogenetic Profiling.
Article in Molecular biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 75 citations in OpenAlex.
- Primary cilia: sensors of biliary homeostasis and disease.Nature reviews. Gastroenterology & hepatology · 2026Review
- A high-resolution spatial map of cilia-associated proteins in the human fallopian tube.Nature communications · 2026Article
- Insights into Human Ciliopathies: Gene Silencing ofmicroPublication biology · 2026Article
- The evolutionary foundations of transcriptional regulation in animals.Nature reviews. Genetics · 2025Review
- Profylo: A Python Package for Phylogenetic Profile Comparison and Analysis.Journal of molecular evolution · 2025Article
- A Multi-level Perspective on the Evolution of Orthologs and Their Functions.Journal of molecular evolution · 2025Review
- Exploratory analysis of differences at the transcriptional interface between the maternal and fetal compartments of the sheep placenta and potential influence of fetal sex.Molecular and cellular endocrinology · 2025Article
- Identification and bioinformatics analysis of cilia-associated gene families inFrontiers in microbiology · 2025Article
- A subset of evolutionarily conserved centriolar satellite core components is crucial for sperm flagellum biogenesis.Theranostics · 2025Article
- CilioGenics: an integrated method and database for predicting novel ciliary genes.Nucleic acids research · 2024Article
- Matreex: Compact and Interactive Visualization for Scalable Studies of Large Gene Families.Genome biology and evolution · 2024Article
- The MBO2/FAP58 heterodimer stabilizes assembly of inner arm dyneinMolecular biology of the cell · 2024Article
- Different Host-Endogenous Retrovirus Relationships between Mammals and Birds Reflected in Genome-Wide Evolutionary Interaction Patterns.Genome biology and evolution · 2024Article
- A phylogenetic profiling approach identifies novel ciliogenesis genes in Drosophila and C. elegans.The EMBO journal · 2023Article
- WGS Revealed NovelInternational journal of molecular sciences · 2023Article
- Phylogenetic profiling in eukaryotes comes of age.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- 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
- Prenatal diagnosis and mRNA profiles of fetal tetralogy of Fallot.BMC pregnancy and childbirth · 2022Article
- Phylogenetic profiling and cellular analyses of ARL16 reveal roles in traffic of IFT140 and INPP5E.Molecular biology of the cell · 2022Article
- An updated SYSCILIA gold standard (SCGSv2) of known ciliary genes, revealing the vast progress that has been made in the cilia research field.Molecular biology of the cell · 2021Review
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cilia (flagella) are important eukaryotic organelles, present in the Last Eukaryotic Common Ancestor, and are involved in cell motility and integration of extracellular signals. Ciliary dysfunction causes a class of genetic diseases, known as ciliopathies, however current knowledge of the underlying mechanisms is still limited and a better characterization of genes is needed. As cilia have been lost independently several times during evolution and they are subject to important functional variation between species, ciliary genes can be investigated through comparative genomics. We performed phylogenetic profiling by predicting orthologs of human protein-coding genes in 100 eukaryotic species. The analysis integrated three independent methods to predict a consensus set of 274 ciliary genes, including 87 new promising candidates. A fine-grained analysis of the phylogenetic profiles allowed a partitioning of ciliary genes into modules with distinct evolutionary histories and ciliary functions (assembly, movement, centriole, etc.) and thus propagation of potential annotations to previously undocumented genes. The cilia/basal body localization was experimentally confirmed for five of these previously unannotated proteins (LRRC23, LRRC34, TEX9, WDR27, and BIVM), validating the relevance of our approach. Furthermore, our multi-level analysis sheds light on the core gene sets retained in gamete-only flagellates or Ecdysozoa for instance. By combining gene-centric and species-oriented analyses, this work reveals new ciliary and ciliopathy gene candidates and provides clues about the evolution of ciliary processes in the eukaryotic domain. Additionally, the positive and negative reference gene sets and the phylogenetic profile of human genes constructed during this study can be exploited in future work.
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