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Origin and extension of the IFT complex in early eukaryotic evolution


The intraflagellar transport (IFT) complex is an ancient protein complex that facilitates active trafficking of proteins and molecules across the eukaryotic cilium. Based on similar domain compositions Avidor-Reiss et al. (2004) and Jékely et al. (2006) postulated that the IFT originates from an ancestral proto-coatomer complex that also gave rise to vesicle coating complexes (e.g. COPI, COPII, Clathrin) and the Nuclear Pore Complex. Using comparative genomics we provide direct phylogenetic evidence of the proto-coatomer origin of the IFT.


We identified the COPIα, -β2 and –ε subunits as closest paralogs to 12 IFT subunits comprising all three sub-complexes (IFT-A, -B and the BBSome). Our analysis suggests that IFT-A and the BBSome arose from an IFT-B like proto-IFT complex by intra-complex duplication of subunits. We show that the BBSome is a modular component that is lost in eukaryotic species as a precursor to ciliary loss in organisms such as fungi, apicomplexa and plants.


Identification of the proto-coatomer origin and subsequent evolution of the IFT complex strengthens the suspected involvement of IFT components in vesicle transport and provides a rationale for its mechanism. Expansion of ancestral subunits by duplication as well as co-evolution of specific subunits provides some insight on modularity and internal structure of the IFT complex.

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Correspondence to J van Dam.

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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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van Dam, J., Field, M. & Huynen, M. Origin and extension of the IFT complex in early eukaryotic evolution. Cilia 1 (Suppl 1), P56 (2012).

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  • Subsequent Evolution
  • Comparative Genomic
  • Nuclear Pore Complex
  • Vesicle Transport
  • Similar Domain