Dr Darren Soanes
Postdoctoral Research Fellow (Bioinformatics)
D.M.Soanes@exeter.ac.uk
RILD Building L3/24 RILD South
University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
Overview
After graduating from Oxford, Darren trained to be a science teacher and then spent four years teaching at a secondary school in Eastbourne. Darren moved to Exeter in 1996, where he completed an M.Sc. before studying for a Ph.D. with Professor Nick Talbot entitled “Regulation of the pathogenicity gene MPG1 in the rice blast fungus Magnaporthe grisea”.
Darren stayed in Professor Talbot’s group as a research fellow where he specialised in bioinformatics. Darren worked on several projects involving comparative genomics of fungal phytopathogens, as well as transcriptional regulation in Magnaporthe grisea. Darren spent a year working for the Exeter Sequencing Service before moving to the Complex Disease Epigenetics Group in 2019, working under the supervision of Professor Katie Lunnon.
In 2023, Darren joined the NIHR Exeter Biomedical Research Centre as a bioinformatician within the neurodegeneration theme.
Qualifications
- B.A. Biochemistry – (1991, University of Oxford)
- P.G.C.E. Secondary Science – (1992, University of Sussex)
- M.Sc. Biological Research Methods – (1997, University of Exeter)
- Ph.D. Molecular Genetics – (2000, University of Exeter)
Research
Research interests
Darren has had many years’ experience of using sequence data to answer biological questions. In the first part of his career, he studied the comparative genomics and transcriptomics of fungal phytopathogens. His current research is in the area of neurodegeneration.
His most recent project involved analysing transcriptomic data, sequenced from patient blood samples, to identify genes that may be important in the progression from mild cognitive impairment to Alzheimer’s disease and the role of inflammation in this process. He is now looking at how long-read sequence data produced by Oxford Nanopore can be used to study patterns of epigenetic modification in a number of neurodegenerative diseases.
Publications
Journal articles
Fones HN, Soanes D, Gurr SJ (2023). Epiphytic proliferation of Zymoseptoria tritici isolates on resistant wheat leaves. Fungal Genet Biol, 168 Abstract. Author URL.
Latorre SM, Were VM, Foster AJ, Langner T, Malmgren A, Harant A, Asuke S, Reyes-Avila S, Gupta DR, Jensen C, et al (2023). Genomic surveillance uncovers a pandemic clonal lineage of the wheat blast fungus. PLoS Biol, 21(4). Abstract. Author URL.
Smith AR, Soanes D, Moore K, Jeffries A, Lunnon K (2023). New mitochondrial DNA methylation profiling method confirms epigenetic marker in the brain. Alzheimer's & Dementia, 19(S12).
Tang B, Yan X, Ryder LS, Bautista MJA, Cruz-Mireles N, Soanes DM, Molinari C, Foster AJ, Talbot NJ (2023). Rgs1 is a regulator of effector gene expression during plant infection by the rice blast fungus Magnaporthe oryzae. Proc Natl Acad Sci U S A, 120(12). Abstract. Author URL.
Wheildon G, Smith AR, Soanes D, Smith RG, Moore K, O'Neill P, Morgan K, Thomas AJ, Love S, Francis PT, et al (2023). Targeted bisulfite sequencing analysis of Alzheimer’s disease candidate genes reveals differential methylation across neurofibrillary tangle burden in the prefrontal cortex. Alzheimer's & Dementia, 19(S12).
Wheildon G, Smith AR, Soanes D, Southern F, Devall M, Moore K, O'Neill P, Troakes C, Lunnon K (2022). DNA methylation of mitochondrial DNA shows variation in human brain. Alzheimer's and Dementia, 18(S4). Abstract.
Devall M, Soanes DM, Smith AR, Dempster EL, Smith RG, Burrage J, Iatrou A, Hannon E, Troakes C, Moore K, et al (2022). Genome-wide characterization of mitochondrial DNA methylation in human brain. Front Endocrinol (Lausanne), 13 Abstract. Author URL.
Glover G, Voliotis M, Łapińska U, Invergo BM, Soanes D, O’Neill P, Moore K, Nikolic N, Petrov PG, Milner DS, et al (2022). Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. Communications Biology, 5(1). Abstract.
Wheildon G, Smith AR, Soanes D, Smith RG, Moore K, O'Neill P, Morgan K, Thomas AJ, Francis PT, Love S, et al (2022). Targeted bisulfite sequencing analysis of candidate genes associated with Alzheimer’s disease. Alzheimer's & Dementia, 18(S4).
Osés-Ruiz M, Cruz-Mireles N, Martin-Urdiroz M, Soanes DM, Eseola AB, Tang B, Derbyshire P, Nielsen M, Cheema J, Were V, et al (2021). Appressorium-mediated plant infection by Magnaporthe oryzae is regulated by a Pmk1-dependent hierarchical transcriptional network. Nat Microbiol, 6(11), 1383-1397. Abstract. Author URL.
Ryder LS, Dagdas YF, Kershaw MJ, Venkataraman C, Madzvamuse A, Yan X, Cruz-Mireles N, Soanes DM, Oses-Ruiz M, Styles V, et al (2019). A sensor kinase controls turgor-driven plant infection by the rice blast fungus. Nature, 574(7778), 423-427. Abstract. Author URL.
Gupta DR, Avila CSR, Win J, Soanes DM, Ryder LS, Croll D, Bhattacharjee P, Hossain MS, Mahmud NU, Mehebub MS, et al (2019). Cautionary Notes on Use of the MoT3 Diagnostic Assay for Magnaporthe oryzae Wheat and Rice Blast Isolates. Phytopathology, 109(4), 504-508. Abstract. Author URL.
Kershaw MJ, Basiewicz M, Soanes DM, Yan X, Ryder LS, Csukai M, Oses-Ruiz M, Valent B, Talbot NJ (2019). Conidial Morphogenesis and Septin-Mediated Plant Infection Require Smo1, a Ras GTPase-Activating Protein in Magnaporthe oryzae. Genetics, 211(1), 151-167. Abstract. Author URL.
Armaleo D, Müller O, Lutzoni F, Andrésson ÓS, Blanc G, Bode HB, Collart FR, Dal Grande F, Dietrich F, Grigoriev IV, et al (2019). The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata. BMC Genomics, 20(1). Abstract. Author URL.
Sakulkoo W, Osés-Ruiz M, Garcia EO, Soanes DM, Littlejohn GR, Hacker C, Correia A, Valent B, Talbot NJ (2018). A single fungal MAP kinase controls plant cell-to-cell invasion by the rice blast fungus. Science, 359(6382), 1399-1403. Abstract.
Foster AJ, Martin-Urdiroz M, Yan X, Wright HS, Soanes DM, Talbot NJ (2018). CRISPR-Cas9 ribonucleoprotein-mediated co-editing and counterselection in the rice blast fungus. Sci Rep, 8(1). Abstract. Author URL.
Leonard G, Labarre A, Milner DS, Monier A, Soanes D, Wideman JG, Maguire F, Stevens S, Sain D, Grau-Bové X, et al (2018). Comparative genomic analysis of the 'pseudofungus' Hyphochytrium catenoides. Open Biol, 8(1). Abstract. Author URL.
Gladieux P, Condon B, Ravel S, Soanes D, Maciel JLN, Nhani A, Chen L, Terauchi R, Lebrun M-H, Tharreau D, et al (2018). Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae. mBio, 9(1). Abstract. Author URL.
Gentekaki E, Curtis BA, Stairs CW, Klimeš V, Eliáš M, Salas-Leiva DE, Herman EK, Eme L, Arias MC, Henrissat B, et al (2017). Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis. PLoS Biol, 15(9). Abstract. Author URL.
Sambles C, Middelhaufe S, Soanes D, Kolak D, Lux T, Moore K, Matoušková P, Parker D, Lee R, Love J, et al (2017). Genome sequence of the oleaginous yeast Rhodotorula toruloides strain CGMCC 2.1609. Genomics Data, 13, 1-2.
Samalova M, Mélida H, Vilaplana F, Bulone V, Soanes DM, Talbot NJ, Gurr SJ (2017). The β-1,3-glucanosyltransferases (Gels) affect the structure of the rice blast fungal cell wall during appressorium-mediated plant infection. Cell Microbiol, 19(3). Abstract. Author URL.
Galhano R, Illana A, Ryder LS, Rodríguez-Romero J, Demuez M, Badaruddin M, Martinez-Rocha AL, Soanes DM, Studholme DJ, Talbot NJ, et al (2017). Tpc1 is an important Zn(II)2Cys6 transcriptional regulator required for polarized growth and virulence in the rice blast fungus. PLoS Pathog, 13(7). Abstract. Author URL.
Alam I, Cornell M, Soanes DM, Hedeler C, Wong HM, Rattray M, Hubbard SJ, Talbot NJ, Oliver SG, Paton NW, et al (2016). A Methodology for Comparative Functional Genomics. Journal of Integrative Bioinformatics, 4(3), 112-122.
Islam MT, Croll D, Gladieux P, Soanes DM, Persoons A, Bhattacharjee P, Hossain MS, Gupta DR, Rahman MM, Mahboob MG, et al (2016). Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae. BMC Biol, 14(1). Abstract. Author URL.
Corrochano LM, Kuo A, Marcet-Houben M, Polaino S, Salamov A, Villalobos-Escobedo JM, Grimwood J, Álvarez MI, Avalos J, Bauer D, et al (2016). Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication. Current Biology, 26(12), 1577-1584. Abstract.
Kilaru S, Schuster M, Studholme D, Soanes D, Lin C, Talbot NJ, Steinberg G (2015). A codon-optimized green fluorescent protein for live cell imaging in Zymoseptoria tritici. Fungal Genet Biol, 79, 125-131. Abstract. Author URL.
Thornton CR, Ryder LS, Le Cocq K, Soanes DM (2015). Identifying the emerging human pathogen Scedosporium prolificans by using a species-specific monoclonal antibody that binds to the melanin biosynthetic enzyme tetrahydroxynaphthalene reductase. Environmental Microbiology, 17(4), 1023-1048.
Penn TJ, Wood ME, Soanes DM, Csukai M, Corran AJ, Talbot NJ (2015). Protein kinase C is essential for viability of the rice blast fungus Magnaporthe oryzae. Mol Microbiol, 98(3), 403-419. Abstract. Author URL.
Stairs CW, Eme L, Brown MW, Mutsaers C, Susko E, Dellaire G, Soanes DM, Van Der Giezen M, Roger AJ (2014). A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia. Current Biology, 24(11), 1176-1186. Abstract.
bin Yusof MT, Kershaw MJ, Soanes DM, Talbot NJ (2014). FAR1 and FAR2 regulate the expression of genes associated with lipid metabolism in the rice blast fungus Magnaporthe oryzae. PLoS One, 9(6). Abstract. Author URL.
Bielska E, Schuster M, Roger Y, Berepiki A, Soanes DM, Talbot NJ, Steinberg G (2014). Hook is an adapter that coordinates kinesin-3 and dynein cargo attachment on early endosomes. J Cell Biol, 204(6), 989-1007. Abstract. Author URL.
Soanes D, Richards TA (2014). Horizontal gene transfer in eukaryotic plant pathogens. Annu Rev Phytopathol, 52, 583-614. Abstract. Author URL.
Read BA, Kegel J, Klute MJ, Kuo A, Lefebvre SC, Maumus F, Mayer C, Miller J, Monier A, Salamov A, et al (2013). Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature, 499(7457), 209-213. Abstract. Author URL.
Campbell SE, Williams TA, Yousuf A, Soanes DM, Paszkiewicz KH, Williams BAP (2013). The Genome of Spraguea lophii and the Basis of Host-Microsporidian Interactions. PLoS Genet, 9(8). Abstract. Author URL.
Soanes DM, Chakrabarti A, Paszkiewicz KH, Dawe AL, Talbot NJ (2012). Genome-wide transcriptional profiling of appressorium development by the rice blast fungus Magnaporthe oryzae. PLoS Pathog, 8(2). Abstract. Author URL.
He M, Kershaw MJ, Soanes DM, Xia Y, Talbot NJ (2012). Infection-associated nuclear degeneration in the rice blast fungus Magnaporthe oryzae requires non-selective macro-autophagy. PLoS One, 7(3). Abstract. Author URL.
Ryder LS, Harris BD, Soanes DM, Kershaw MJ, Talbot NJ, Thornton CR (2012). Saprotrophic competitiveness and biocontrol fitness of a genetically modified strain of the plant-growth-promoting fungus Trichoderma hamatum GD12. Microbiology, 158(Special issue of Trichoderma: from basic biology to biotechnology), 84-97.
Ryder LS, Harris BD, Soanes DM, Kershaw MJ, Talbot NJ, Thornton CR (2012). Saprotrophic competitiveness and biocontrol fitness of a genetically modified strain of the plant-growth-promoting fungus Trichoderma hamatum GD12. Microbiology (Reading), 158(Pt 1), 84-97. Abstract. Author URL.
Richards TA, Leonard G, Soanes DM, Talbot NJ (2011). Gene transfer into the fungi. Fungal Biology Reviews, 25(2), 98-110. Abstract.
Amselem J, Cuomo CA, van Kan JAL, Viaud M, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS, Fillinger S, et al (2011). Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet, 7(8). Abstract. Author URL.
Richards TA, Soanes DM, Jones MDM, 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. Proc Natl Acad Sci U S A, 108(37), 15258-15263. Abstract. Author URL.
Leonard G, Soanes DM, Stevens JR (2011). Resolving the question of trypanosome monophyly: a comparative genomics approach using whole genome data sets with low taxon sampling. Infect Genet Evol, 11(5), 955-959. Abstract. Author URL.
Li Y, Liang S, Yan X, Wang H, Li D, Soanes DM, Talbot NJ, Wang Z, Wang Z (2010). Characterization of MoLDB1 required for vegetative growth, infection-related morphogenesis, and pathogenicity in the rice blast fungus Magnaporthe oryzae. Mol Plant Microbe Interact, 23(10), 1260-1274. Abstract. Author URL.
Green S, Studholme DJ, Laue BE, Dorati F, Lovell H, Arnold D, Cottrell JE, Bridgett S, Blaxter M, Huitema E, et al (2010). Comparative genome analysis provides insights into the evolution and adaptation of Pseudomonas syringae pv. aesculi on Aesculus hippocastanum. PLoS One, 5(4). Abstract. Author URL.
Soanes DM, Talbot NJ (2010). Comparative genome analysis reveals an absence of leucine-rich repeat pattern-recognition receptor proteins in the kingdom Fungi. PLoS One, 5(9). Abstract. Author URL.
Spanu PD, Abbott JC, Amselem J, Burgis TA, Soanes DM, Stüber K, Ver Loren van Themaat E, Brown JKM, Butcher SA, Gurr SJ, et al (2010). Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science, 330(6010), 1543-1546. Abstract. Author URL.
Rispail N, Soanes DM, Ant C, Czajkowski R, Grünler A, Huguet R, Perez-Nadales E, Poli A, Sartorel E, Valiante V, et al (2009). Comparative genomics of MAP kinase and calcium-calcineurin signalling components in plant and human pathogenic fungi. Fungal Genet Biol, 46(4), 287-298. Abstract. Author URL.
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.
Soanes DM, Alam I, Cornell M, Wong HM, Hedeler C, Paton NW, Rattray M, Hubbard SJ, Oliver SG, Talbot NJ, et al (2008). Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis. PLoS One, 3(6). Abstract. Author URL.
Soanes DM, Talbot NJ (2008). Moving targets: rapid evolution of oomycete effectors. Trends Microbiol, 16(11), 507-510. Abstract. Author URL.
Alam, I. Soanes, D.M. Wong, H.M. (2007). Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification of the fungi. Genome Research, 17, 1809-1822.
Wang Z-Y, Soanes DM, Kershaw MJ, Talbot NJ (2007). Functional analysis of lipid metabolism in Magnaporthe grisea reveals a requirement for peroxisomal fatty acid beta-oxidation during appressorium-mediated plant infection. Mol Plant Microbe Interact, 20(5), 475-491. Abstract. Author URL.
Richards, T.A. Talbot, N.J. (2007). Insights from sequencing fungal and oomycete genomes: What can we learn about plant disease and the evolution of pathogenicity?. The Plant Cell, 19, 3318-3326.
Hedler C, Wong HM, Cornell MJ, Alam I, Soanes DM, Rattray M, Hubbard SJ, Talbot NJ, Oliver SG, Paton N, et al (2007). e-Fungi: a Data Resource for Comparative Analysis of Fungal Genomes. BMC Genomics, 8
Soanes DM, Talbot, N.J. (2006). Comparative genomic analysis of phytopathogenic fungi using expressed sequence tag (EST) collections. Molecular Plant Pathology, 7, 61-70.
Wang, Z.Y. Talbot, N.J. (2006). Peroxisomal carnitine acetyl transferase is required for elaboration of penetration hyphae during plant infection by Magnaporthe grisea. Molecular Microbiology, 61, 46-60.
Soanes DM, Talbot NJ (2005). A bioinformatic tool for analysis of EST transcript abundance during infection-related development by Magnaporthe grisea. Mol Plant Pathol, 6(5), 503-512. Abstract. Author URL.
Talbot, N.J. Ebbole, D.J. (2005). The genome sequence of the rice blast fungus Magnaporthe grisea. Nature, 434, 980-986.
Wang Z-Y, Jenkinson JM, Holcombe LJ, Soanes DM, Veneault-Fourrey C, Bhambra GK, Talbot NJ (2005). The molecular biology of appressorium turgor generation by the rice blast fungus Magnaporthe grisea. Biochem Soc Trans, 33(Pt 2), 384-388. Abstract. Author URL.
Talbot NJ, Gilbert MJ, Soanes DM, Barooah M, Wang ZY, Ahmad S, Veneault-Fourrey C, Jenkinson JM, Holcombe LJ, Bhambra G, et al (2004). Functional genomics of plant infection by the rice blast fungus Magnaporthe grisea. , 2004(Fall).
Giles PF, Soanes DM, Talbot NJ (2003). A relational database for the discovery of genes encoding amino acid biosynthetic enzymes in pathogenic fungi. Comp Funct Genomics, 4(1), 4-15. Abstract. Author URL.
Soanes DM, Skinner W, Keon J, Hargreaves J, Talbot NJ (2002). Genomics of phytopathogenic fungi and the development of bioinformatic resources. Mol Plant Microbe Interact, 15(5), 421-427. Abstract. Author URL.
Soanes DM, Kershaw MJ, Cooley RN, Talbot NJ (2002). Regulation of the MPG1 hydrophobin gene in the rice blast fungus Magnaporthe grisea. Mol Plant Microbe Interact, 15(12), 1253-1267. Abstract. Author URL.
Chapters
Foster AJ, Littlejohn GR, Soanes DM, Talbot NJ (2016). Strategies for Nutrient Acquisition by Magnaporthe Oryzae During the Infection of Rice. In (Ed) Host - Pathogen Interaction: Microbial Metabolism, Pathogenicity and Antiinfectives, 93-108. Abstract.
Jenkinson JM, Wilson RA, Cartwright Z, Soanes DM, Kershaw MJ, Talbot NJ (2007). Functional genomics of plant infection by the rice blast fungus magnaporthe grisea. In (Ed) Fungi in the Environment, 227-254. Abstract.
Soanes, D.M. Barooah, M.J. Talbot, N.J. (2005). Investigating the evolution of fungal virulence by functional genomics. In Brown AJP (Ed) The Mycota Vol XII. Fungal Genomics, Berlin: Springer-Verlag.
Gilbert MJ, Soanes DM, Talbot NJ (2004). 14 Functional Genomic Analysis of the Rice Blast Fungus Magnaporthe grisea. In (Ed) Fungal Genomics, Elsevier, 331-352.
Soanes, D. Talbot, N.J. (2004). Functional Genomics of the rice blast fungus Magnaporthe grisea. In Elsevier BV (Ed) Fungal Genomics, Applied Mycology and Biotechnology Volume 4.
Conferences
Oses-Ruiz M, Martin-Urdiroz M, Soanes D, Kershaw MJ, Littlejohn G, Cruz-Mireles N, Derbyshire P, Menke FLH, Talbot NJ (2019). A hierarchical transcriptional network controls appressorium development in the rice blast fungus Magnaporthe oryzae in response to surface hydrophobicity. Author URL.
Yan X, Were VM, Ryder LS, Tang B, Oses-Ruiz M, Soanes D, Menke FLH, Talbot NJ (2019). Global novel effector-mining in the rice blast fungus Magnaporthe oryzae. Author URL.
Herrero CR, Martin-Urdiroz M, Yan X, Kershaw MJ, Soanes D, Talbot NJ (2019). Studying effector secretion by the rice blast fungus Magnaporthe oryzae. Author URL.
Griffin CD, Foster A, Soanes D, Plessis A, Hanley ME, Talbot NJ, Littlejohn G (2019). The role of circadian entrainment in the outcome of rice blast infection. Author URL.
Were VM, Mwongera DT, Foster A, Yan X, Soanes D, Mutiga SK, Rotich F, Kershaw MJ, Zhou B, Ouedraogo I, et al (2019). Using population level diversity of the rice blast fungus Magnaporthe oryzae to identify new resistant varieties of rice for Sub-Saharan Africa. Author URL.
Richards T, Soanes DM, Foster PG, Leonard G, Talbot NJ (2009). The role of horizontal gene transfer in the evolution of trophic mechanisms across the eukaryotes. Author URL.
Teaching
In the past I have taught on the following modules:Undergraduate
- BIO2077
Postgraduate
- BIOM504 (module co-ordinator)
- BIOM506
Modules
2023/24
Information not currently available
