Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway

PLoS Genetics
Eduard Ocaña-PallarèsIñaki Ruiz-Trillo

Abstract

Genes and genomes can evolve through interchanging genetic material, this leading to reticular evolutionary patterns. However, the importance of reticulate evolution in 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 eukaryotic nitrate assimilation pathway is an ideal object of investigation, as previous results revealed a patchy distribution and suggested that the nitrate assimilation cluster of dikaryotic fungi (Opisthokonta) could have been originated and transferred from a lineage leading to Oomycota (Stramenopiles). We studied the origin and evolution of this pathway through both multi-scale bioinformatic and experimental approaches. Our taxon-rich genomic screening shows that nitrate assimilation is present in more lineages than previously reported, although being restricted to autotrophs and osmotrophs. The phylogenies indicate a pervasive role of HGT, with three bacterial transfers contributing to the pathway origin, and at least seven well-supported transfers between eukaryotes. In particular, we propose a distinct and more complex HGT path between Opisthokonta and Stramenop...Continue Reading

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Citations

Sep 19, 2019·Nature Microbiology·Marina Marcet-Houben, Toni Gabaldón
Aug 31, 2019·Genes·Yaqing Ou, James O McInerney
Aug 30, 2019·Current Opinion in Genetics & Development·Jason C Slot, Emile Gluck-Thaler
Jan 28, 2021·Proceedings of the National Academy of Sciences of the United States of America·Nils RädeckerChristian R Voolstra
Mar 9, 2021·Genome Biology and Evolution·Małgorzata OrłowskaAnna Muszewska

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Methods Mentioned

BETA
RNAseq
phylogenetic profiles
PCR

Software Mentioned

TREE
prok
ModelFinder
ProtTest
PfamScan
MAFFT
Newick
iQ5
hmmsearch
TBLASTN

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