Horizontal Gene Transfer and Trait Acquisition in the Eukaryotes

Royal Society

We have a long-term interest in testing the hypothesis that horizontal gene transfer has played a role in adding traits to eukaryotic lineages. Our work in this area has shown that horizontal gene transfer has been an important factor in the evolution of plant parasitic protists, specifically amending the secretome of oomycetes. Our work in this area also studies the evolution of transporter encoding genes and the role of ‘transporter-HGT’ in eukaryotic evolution, specifically fungi. We are currently testing the hypothesis that this is important for evolution of pathogenesis in the fungi. We are also interested in tracking down vectors for HGT in eukaryotes including the role of viruses in moving genes important for cellular phenotypes between lineages.

Phylogeny illustrating seven transfers of predicted transporter-encoding genes. Phylogeny of published genomes showing proximate points of HGT origin and acquisition for the seven primary HGTs identified. The species phylogeny was calculated from an alignment of 79 taxa and 134,948 characters based on the JGI-1086 hidden Markov models link, using a maximum-likelihood approach in IQ-Tree v1.5.4 with LG model and 1,000 ultrafast bootstraps.

Examples of our work in this area:

  • Leonard G, Labarre A, Milner DS, Monier A, Soanes D, Wideman JG, Maguire F, Stevens S, Sain D, Grau-Bové X. 2018. Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides. Open biology 8:170184.
  • Milner DS, Attah V, Cook E, Maguire F, Savory FR, Morrison M, Müller CA, Foster PG, Talbot NJ, Leonard G. 2019. Environment-dependent fitness gains can be driven by horizontal gene transfer of transporter-encoding genes. Proceedings of the National Academy of Sciences 116:5613-5622.
  • Monier A, Chambouvet A, Milner DS, Attah V, Terrado R, Lovejoy C, Moreau H, Santoro AE, Derelle É, Richards TA. 2017. Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton. Proceedings of the National Academy of Sciences 114:E7489-E7498.
  • Richards TA, Leonard G, Soanes DM, Talbot NJ. 2011. Gene transfer into the fungi. Fungal Biology Reviews 25:98-110.
  • Richards TA, Soanes DM, Foster PG, Leonard G, Thornton CR, Talbot NJ. 2009. Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi. The Plant Cell 21:1897-1911.
  • Richards TA, Soanes DM, Jones MD, Vasieva O, Leonard G, Paszkiewicz K, Foster PG, Hall N, Talbot NJ. 2011. Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. Proceedings of the National Academy of Sciences 108:15258-15263.
  • Richards TA, Talbot NJ. 2013. Horizontal gene transfer in osmotrophs: playing with public goods. Nature Reviews Microbiology 11:720-727.
  • Savory F, Leonard G, Richards TA. 2015. The role of horizontal gene transfer in the evolution of the oomycetes. PLoS Pathog 11:e1004805.
  • Savory FR, Milner DS, Miles DC, Richards TA. 2018. Ancestral function and diversification of a horizontally acquired oomycete carboxylic acid transporter. Molecular Biology and Evolution 35:1887-1900.
  • Soanes D, Richards TA. 2014. Horizontal gene transfer in eukaryotic plant pathogens. Annual Review of Phytopathology 52:583-614.