Abstract
Photosynthetic diatom plastids have long been suggested to have originated by the secondary endosymbiosis of a red alga. However, recent phylogenomic studies report a high number of diatom nuclear genes phylogenetically related to green algal and green plant genes. These were interpreted as endosymbiotic gene transfers (EGT) from a cryptic green algal endosymbiosis. We reanalyzed this issue using a larger set of red algal genomic data. We show that previous studies suffer from a taxonomic sampling bias and point out that a majority of gene phylogenies are either poorly resolved or do not describe EGT events. We finally show that genes having a complete descent from cyanobacteria to diatoms through primary and secondary EGTs have been mostly transferred via a red alga. We conclude that, even if some diatom genes still support a putative green algal origin, these are not sufficient to argue for a cryptic green algal secondary endosymbiosis.