ArticleEvolution; international journal of organic evolution2014
Genome structure drives patterns of gene family evolution in ciliates, a case study using Chilodonella uncinata (Protista, Ciliophora, Phyllopharyngea).
Article in Evolution; international journal of organic evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 24 citations in OpenAlex.
- Bioinformatic, cell localization, and phylogenetic analyses reveal a novel family of putative lipases in Tetrahymena thermophila.G3 (Bethesda, Md.) · 2026Article
- Complex evolutionary patterns within the tubulin gene family of ciliates, unicellular eukaryotes with diverse microtubular structures.BMC biology · 2024Article
- From germline genome to highly fragmented somatic genome: genome-wide DNA rearrangement during the sexual process in ciliated protists.Marine life science & technology · 2024Article
- Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes.eLife · 2022Article
- Macronuclear development in ciliates, with a focus on nuclear architecture.The Journal of eukaryotic microbiology · 2022Review
- Transcriptomic Differences between Free-Living and ParasiticMicroorganisms · 2022Article
- Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study.Genome biology and evolution · 2020Article
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- Evolutionary origins and impacts of genome architecture in ciliates.Annals of the New York Academy of Sciences · 2019Review
- Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within "Nassophorea-Synhymenia-Phyllopharyngea" Assemblage.Frontiers in microbiology · 2019Article
- Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina.Genome biology and evolution · 2018Article
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- Hidden genetic variation in the germline genome of Tetrahymena thermophila.Journal of evolutionary biology · 2016Article
- Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates.Genome biology and evolution · 2015Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
In most lineages, diversity among gene family members results from gene duplication followed by sequence divergence. Because of the genome rearrangements during the development of somatic nuclei, gene family evolution in ciliates involves more complex processes. Previous work on the ciliate Chilodonella uncinata revealed that macronuclear β-tubulin gene family members are generated by alternative processing, in which germline regions are alternatively used in multiple macronuclear chromosomes. To further study genome evolution in this ciliate, we analyzed its transcriptome and found that (1) alternative processing is extensive among gene families; and (2) such gene families are likely to be C. uncinata specific. We characterized additional macronuclear and micronuclear copies of one candidate alternatively processed gene family-a protein kinase domain containing protein (PKc)-from two C. uncinata strains. Analysis of the PKc sequences reveals that (1) multiple PKc gene family members in the macronucleus share some identical regions flanked by divergent regions; and (2) the shared identical regions are processed from a single micronuclear chromosome. We discuss analogous processes in lineages across the eukaryotic tree of life to provide further insights on the impact of genome structure on gene family evolution in eukaryotes.
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