Peroxisomes are widespread eukaryotic organelles that show a high diversity in terms of metabolic functions. To explain their evolutionary origin, several endosymbiotic hypotheses have been put forward that suggest various possible prokaryotic ancestors. An alternative view proposes a scenario in which peroxisomes originated from the Endoplasmic Reticulum. Recently, an actinobacterial origin of peroxisomes have been proposed based on phylogenetic analysis of Pex1/6 proteins and the results of sequence comparisons of peroxisomal and bacterial proteins. Here we re-examine these data and show that the phylogenetic clustering of Pex1/6 proteins with actinobacterial proteins is likely the result of a long branch attraction artifact. Moreover, a statistical test shows that the phylogeny presented to support an actinobacterial origin is not significantly more supported than an alternative topology grouping Pex proteins with their Endoplasmic Reticulum homologs. We therefore conclude that there is a lack of phylogenetic support for a supposed actinobacterial origin of peroxisomes. Challenges for assessing the evolutionary origins of these intriguing organelles are discussed.

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