ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Aquatic Microbiology
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1486189
This article is part of the Research TopicProtistan Phagotrophy and the Far-reaching ImplicationsView all articles
Identification and bioinformatics analysis of cilia-associated gene families in
Provisionally accepted
- Zunyi Medical University, Zunyi, China
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Ciliates are essential model organisms for exploring the protein composition and regulatory mechanisms involved in cellular processes. This study systematically analyzes the structure and function of cilia-associated genes in Euplotes amieti using next-generation sequencing (NGS) to sequence its macronuclear genome. We identified 418 cilia-associated genes through BLASTP analysis, revealing high homology with genes from the hypotrich ciliates Euplotes octocarinatus, Stylonychia lemnae, and Oxytricha trifallax. Among these, 44 genes are conserved across these species. The cilia-associated genes are categorized into kinases, dyneins, flagellin, tubulin, and autophagy-related proteins based on Non-Redundant function annotations. Pfam domain annotation predicted three conserved domains within these genes. Gene ontology (GO) analysis indicated significant enrichment in processes such as tubulin binding, cilia assembly, and microtubule-based movement. Additionally, pathway enrichment analysis highlighted their involvement in adenine ribonucleotide biosynthesis, glycolysis/gluconeogenesis, Wnt signaling, and AMP-activated protein kinase (AMPK) signaling pathways. These findings suggest that cilia-associated genes in ciliates play crucial roles in DNA replication, energy metabolism, intercellular communication, and morphogenesis. Furthermore, 39 hub genes are strongly associated with ciliopathies, potentially playing a key role in regulating ciliogenesis in ciliates. We conducted quantitative polymerase chain reaction (QPCR) analysis of the cilia-related gene family and found that most cilia-related proteins were significantly downregulated during mitosis. RNA interference targeting the ARL2BP and DYNLRB2 genes resulted in increased mortality and reduced motility in ciliates. Additionally, immunofluorescence staining revealed significant alterations in the arrangement of cortical microtubules associated with basal bodies.
Keywords: Euplotes amieti, Next-generation sequencing, cilia-associated genes, ciliopathy, Bioinformatics analysis
Received: 23 Sep 2024; Accepted: 14 Apr 2025.
Copyright: © 2025 SHEN, xiong, xv, liu, sheng and sheng. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: xin sheng, Zunyi Medical University, Zunyi, China
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