Genome sequencing of 10 novel Cyanidiales strains

The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics that impact our understanding regarding the origin of metabolic processes and the role of organelles in cellular evolution. We addressed this issue by analyzing 10 novel Cyanidiales genomes and determined that 1% of their gene inventory is HGT-derived. The majority of HGT candidates encodes functions related to polyextremophily and originated from extremophilic prokaryotes that live in similar habitats as the Cyanidiales. HGT candidates differ from native genes in GC-content, number of splice sites, and gene expression. These genes are prone to loss, which may explain the lack of a eukaryotic pan-genome. The maintenance of 1% HGTs, even under selection for genome reduction underlines the importance of non-endosymbiosis related foreign gene acquisition. Therefore, absence of a pan-genome and cumulative effects fail to provide a substantive argument against our hypothesis of recurring HGT followed by differential loss in eukaryotes.