title: A paneukaryotic genomic analysis of the small GTPase RABL2 underscores the significance of recurrent gene loss in eukaryote evolution.
abstract: BACKGROUND
  The cilium (flagellum) is a complex cellular structure inherited from the last eukaryotic common ancestor (LECA). A large number of ciliary proteins have been characterized in a few model organisms, but their evolutionary history often remains unexplored. One such protein is the small GTPase RABL2, recently implicated in the assembly of the sperm tail in mammals.
  
  
  RESULTS
  Using the wealth of currently available genome and transcriptome sequences, including data from our on-going sequencing projects, we systematically analyzed the phylogenetic distribution and evolutionary history of RABL2 orthologs. Our dense taxonomic sampling revealed the presence of RABL2 genes in nearly all major eukaryotic lineages, including small "obscure" taxa such as breviates, ancyromonads, malawimonads, jakobids, picozoans, or palpitomonads. The phyletic pattern of RABL2 genes indicates that it was present already in the LECA. However, some organisms lack RABL2 as a result of secondary loss and our present sampling predicts well over 30 such independent events during the eukaryote evolution. The distribution of RABL2 genes correlates with the presence/absence of cilia: not a single well-established cilium-lacking species has retained a RABL2 ortholog. However, several ciliated taxa, most notably nematodes, some arthropods and platyhelminths, diplomonads, and ciliated subgroups of apicomplexans and embryophytes, lack RABL2 as well, suggesting some simplification in their cilium-associated functions. On the other hand, several algae currently unknown to form cilia, e.g., the "prasinophytes" of the genus Prasinoderma or the ochrophytes Pelagococcus subviridis and Pinguiococcus pyrenoidosus, turned out to encode not only RABL2, but also homologs of some hallmark ciliary proteins, suggesting the existence of a cryptic flagellated stage in their life cycles. We additionally obtained insights into the evolution of the RABL2 gene architecture, which seems to have ancestrally consisted of eight exons subsequently modified not only by lineage-specific intron loss and gain, but also by recurrent loss of the terminal exon encoding a poorly conserved C-terminal extension.
  
  
  CONCLUSIONS
  Our comparative analysis supports the notion that RABL2 is an ancestral component of the eukaryotic cilium and underscores the still underappreciated magnitude of recurrent gene loss, or reductive evolution in general, in the history of eukaryotic genomes and cells.
authors.affiliation: Department of Biology and Ecology, University of Ostrava, Faculty of Science, Chittussiho 10, 710 00, Ostrava, Czech Republic. marek.elias@osu.cz.
authors.forename: Marek
authors.initials: M
authors.lastname: Eliáš
authors.affiliation: Department of Biology and Ecology, University of Ostrava, Faculty of Science, Chittussiho 10, 710 00, Ostrava, Czech Republic. thorin0@seznam.cz.
authors.forename: Vladimír
authors.initials: V
authors.lastname: Klimeš
authors.affiliation: Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique UMR 8079, Université Paris-Sud, 91405, Orsay, France. romain.derelle@u-psud.fr.
authors.forename: Romain
authors.initials: R
authors.lastname: Derelle
authors.affiliation: Department of Biology and Ecology, University of Ostrava, Faculty of Science, Chittussiho 10, 710 00, Ostrava, Czech Republic. losssina@gmail.com.
authors.forename: Romana
authors.initials: R
authors.lastname: Petrželková
authors.affiliation: Department of Parasitology, Charles University in Prague, Faculty of Science, Viničná 7, 128 44, Prague 2, Czech Republic. jan.tachezy@natur.cuni.cz.
authors.forename: Jan
authors.initials: J
authors.lastname: Tachezy
mesh_terms: D002923:Cilia / Q000378:metabolism; D056890:Eukaryota / Q000145:classification* / Q000235:genetics*; D019143:Evolution, Molecular; D020559:Monomeric GTP-Binding Proteins / Q000235:genetics; D010802:Phylogeny
chemical_list: D020559:Monomeric GTP-Binding Proteins
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