Gain and loss of elongation factor genes in green algae

Background: Two key genes of the translational apparatus, elongation factor-1 alpha (EF-1 alpha) and elongation factor-like (EFL) have an almost mutually exclusive distribution in eukaryotes. In the green plant lineage, the Chlorophyta encode EFL except Acetabularia where EF-1 alpha is found, and the Streptophyta possess EF-1 alpha except Mesostigma, which has EFL. These results raise questions about evolutionary patterns of gain and loss of EF-1 alpha and EFL. A previous study launched the hypothesis that EF-1 alpha was the primitive state and that EFL was gained once in the ancestor of the green plants, followed by differential loss of EF-1 alpha or EFL in the principal clades of the Viridiplantae. In order to gain more insight in the distribution of EF-1 alpha and EFL in green plants and test this hypothesis we screened the presence of the genes in a large sample of green algae and analyzed their gain-loss dynamics in a maximum likelihood framework using continuous-time Markov models. Results: Within the Chlorophyta, EF-1 alpha is shown to be present in three ulvophycean orders (i.e., Dasycladales, Bryopsidales, Siphonocladales) and the genus Ignatius. Models describing gene gain-loss dynamics revealed that the presence of EF-1 alpha, EFL or both genes along the backbone of the green plant phylogeny is highly uncertain due to sensitivity to branch lengths and lack of prior knowledge about ancestral states or rates of gene gain and loss. Model refinements based on insights gained from the EF-1 alpha phylogeny reduce uncertainty but still imply several equally likely possibilities: a primitive EF-1 alpha state with multiple independent EFL gains or coexistence of both genes in the ancestor of the Viridiplantae or Chlorophyta followed by differential loss of one or the other gene in the various lineages. Conclusion: EF-1 alpha is much more common among green algae than previously thought. The mutually exclusive distribution of EF-1 alpha and EFL is confirmed in a large sample of green plants. Hypotheses about the gain-loss dynamics of elongation factor genes are hard to test analytically due to a relatively flat likelihood surface, even if prior knowledge is incorporated. Phylogenetic analysis of EFL genes indicates misinterpretations in the recent literature due to uncertainty regarding the root position