Protist Genomics and the Darwin Tree of Life Project.

Wellcome logo

The Sanger Institute, along with a host of collaborators, are aiming to sequence ‘every’ eukaryotic species resident in Britain. In collaboration with the Earlham Institute and MBA Plymouth we are charged with preparing protist samples for genome sequencing. Working closely with CCAP and CABI we are preparing to sequence every protist sampled in the UK and maintained in a UK culture collection. Of course, this only covers a small minority of protistan diversity, as such we are continuing to work on single cell genome and transcriptome pipelines in order to begin a very large culture-free genome sequencing initiative with the aim of sequencing thousands of cells and their associated microbiomes.

Darwin Tree of Life logo

Examples of our work in this area:

  • Darwin Tree of Life Project Consortium. 2022. Sequence locally, think globally: The Darwin Tree of Life Project. Proceedings of the National Academy of Sciences 119:e2115642118. https://doi.org/10.1073/pnas.2115642118
  • Lawniczak MKN, Davey RP, Rajan J, Pereira-da-Conceicoa LL, Kilias E, Hollingsworth PM, Barnes I, Allen H, Blaxter M, Burgin J, Broad GR, Crowley LM, Gaya E, Holroyd N, Lewis OT, McTaggart S, Mieszkowska N, Minotto A, Shaw F, Richards TA, Sivess LAS, Darwin Tree of Life Consortium. 2022. Specimen and sample metadata standards for biodiversity genomics: a proposal from the Darwin Tree of Life project. Wellcome Open Research 7:187. https://doi.org/10.12688/wellcomeopenres.17605.1
  • Leonard G, Labarre A, Milner DS, Monier A, Soanes D, Wideman JG, Maguire F, Stevens S, Sain D, Grau-Bové X, Sebé-Pedrós A, Stajich JE, Paszkiewicz K, Brown MW, Hall N, Wickstead B, Richards TA. 2018. Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides. Open Biology 8:170184. https://doi.org/10.1098/rsob.170184
  • McGowan J, Kilias ES, Alacid E, Lipscombe J, Jenkins BH, Gharbi K, Kaithakottil GG, Macaulay IC, McTaggart S, Warring SD, Richards TA, Hall N, Swarbreck D. 2023. Identification of a non-canonical ciliate nuclear genetic code where UAA and UAG code for different amino acids. PLOS Genetics 19:e1010913. https://doi.org/10.1371/journal.pgen.1010913
  • McGowan J, Kilias ES, Lipscombe J, Alacid E, Barker T, Catchpole L, McTaggart S, Warring SD, Gharbi K, Richards TA, Hall N, Swarbreck D. 2025. Comparative single-cell genomics of two uncultivated Naegleria species harboring Legionella cobionts. mSphere 10:e00352-25. https://doi.org/10.1128/msphere.00352-25
  • McGowan J, Richards TA, Hall N, Swarbreck D. 2024. Multiple independent genetic code reassignments of the UAG stop codon in phyllopharyngean ciliates. PLOS Genetics 20:e1011512. https://doi.org/10.1371/journal.pgen.1011512
  • Wideman JG, Lax G, Leonard G, Milner DS, Rodríguez-Martínez R, Simpson AG, Richards TA. 2019. A single-cell genome reveals diplonemid-like ancestry of kinetoplastid mitochondrial gene structure. Philosophical Transactions of the Royal Society B 374:20190100. https://doi.org/10.1098/rstb.2019.0100
  • Wideman JG, Monier A, Rodríguez-Martínez R, Leonard G, Cook E, Poirier C, Maguire F, Milner DS, Irwin NA, Moore K, Santoro AE, Keeling PJ, Worden AZ, Richards TA. 2020. Unexpected mitochondrial genome diversity revealed by targeted single-cell genomics of heterotrophic flagellated protists. Nature Microbiology 5:154-165. https://doi.org/10.1038/s41564-019-0605-4