Reticulate evolution in eukaryotes: origin and evolution of the nitrate assimilation pathway
2018
Genes and genomes can evolve through interchanging genetic material, this leading to reticular evolutionary patterns. However, the importance of
reticulate evolutionin
eukaryotes, and in particular of
horizontal gene transfer(HGT), remains controversial. Given that metabolic pathways with taxonomically-patchy distributions can be indicative of HGT events, the
eukaryoticnitrate assimilation pathway is an ideal object of investigation, as previous results revealed a patchy distribution and suggested one crucial HGT event. We studied the evolution of this pathway through both multi-scale bioinformatic and experimental approaches. Our taxon-rich genomic screening shows this pathway to be present in more lineages than previously proposed and that nitrate assimilation is restricted to autotrophs and to distinct osmotrophic groups. Our phylogenies show a pervasive role of HGT, with three bacterial transfers contributing to the pathway origin, and at least seven well-supported transfers between
eukaryotes. Our results, based on a larger dataset, differ from the previously proposed transfer of a nitrate assimilation cluster from Oomycota (Stramenopiles) to
Dikarya(Fungi, Opisthokonta). We propose a complex HGT path involving at least two cluster transfers between Stramenopiles and Opisthokonta. We also found that gene fusion played an essential role in this evolutionary history, underlying the origin of the canonical
eukaryotic
nitrate reductase, and of a novel
nitrate reductasein Ichthyosporea (Opisthokonta). We show that the ichthyosporean pathway, including this novel
nitrate reductase, is physiologically active and transcriptionally
co-regulated, responding to different nitrogen sources; similarly to distant
eukaryoteswith independent HGT-acquisitions of the pathway. This indicates that this pattern of transcriptional control evolved convergently in
eukaryotes, favoring the proper integration of the pathway in the metabolic landscape. Our results highlight the importance of
reticulate evolutionin
eukaryotes, by showing the crucial contribution of HGT and gene fusion in the evolutionary history of the nitrate assimilation pathway.
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