For the past five years my research has focused on plant-fungal interactions. In my current postdoctoral position, I am investigating the genetic basis of the interaction between Phytophthora agathidicida and kauri (Agathis australis), a native tree of New Zealand having major social importance for Māori. Phytophthora agathidicida is an oomycete pathogen similar to the potato blight agent, Phytophthora infestans which caused the Irish Great Famine in 1845 killing over 1 million people. The goal of this research is to identify candidate effectors (small secreted proteins often essential for disease) using population genetics data, whole genome comparisons and transcriptomic analyses.
My previous research focused on the association between the fungal endophyte Epichloë festucae and perennial ryegrass, a key pasture grass in New Zealand, using bioinformatics and next generation sequencing approaches. These associations play an important role in forage improvement as the fungus protects its host against a wide range of pests (insects and pathogenic fungi), and enhances host drought tolerance. My research encompassed three main areas: lateral gene transfer between plant-associated fungi, host transcriptomic responses to endophyte infection, and transcriptomic comparison of mutualistic and pathogenic Epichloë-grass interactions. The study of lateral gene transfer between plant-associated fungi (pathogens, endophytes, mycorrhiza) was based on a genomic comparison of different fungi and started with the annotation of the gene models of Epichloë festucae and perennial ryegrass. My work on host responses to endophyte infection identified transcriptomic and metabolomic signatures of endophyte infection. The comparison of mutualistic and pathogenic interactions was performed on different mutant Epichloë strains that display a switch from a mutualistic to pathogen-like behaviour. A transcriptomic study comparing three of these mutants to the original wild-type association was performed and led to the discovery of a key set of fungal genes involved in symbiosis.
|Date of Birth||24/04/1984|
|Residency||Permanent New Zealand resident|
Bioinformatics consultant• Feb. 2018
I am very proud to join the Environmental Research Team at ESR in Christchurch in February.
Postdoctoral researcher• 2016 - Jan 2018
Time to fight back: harnessing molecular determinants of virulence and adaptation in kauri dieback pathogens - Massey University & the Bio-Protection Research Centre
Postdoctoral researcher• 2012 - 2016
Lateral gene transfer in fungi: Identifying the cross-species toolbox for metabolic innovation - Massey University & the Bio-Protection Research
PhD studentship • 2008 - 2011
INRA is the French National Agronomy Research Institute. Thesis on developing bioinformatics tools to combine information from metabolomics, transcriptomics and promotor studies to characterize metabolic pathways involved in liver cancers. This was in collaboration with the Polytechnic school (Palaiseau, France) and a IT startup company, Solusciences (Clermont-Ferrand, France) to develop software for biological pathway modelling and biochemical dynamics analysis.
Masters in Computational Biology • 2008
During my Masters, I worked on two different projects:
• Evaluation of a docking software (Autodock v.4) and development of an automatic procedure to compute docking of multiple ligands on kinase receptors using a computation cluster
• Development of software for visualization and detection of internal movements in biomolecules
Bachelor in Computer Sciences • 2007
I did this diploma in parallel with my first year of Masters
Bachelor in Biology, Geology and Earth Sciences • 2005
Diploma to become High School biology and geology teacher
Massey University Team Research Medal• 2015
Medal given to the Massey Bio-Protection Research Team for our research on "Decoding the molecular basis of fungal-plant interactions". Rosie Bradshaw, Murray Cox, Pierre-Yves Dupont, Carla Eaton, Austen Ganley and Barry Scott
Chromatin-level regulation of the fragmented dothistromin gene cluster in the forest pathogen Dothistroma septosporumChettri P, Dupont PY, Bradshaw RE. • Molecular Microbiology • 2017
Epichloë hybrida sp. nov., an emerging model system for investigating fungal allopolyploidyCampbell MA, Tapper BA, Simpson WR, Johnson RD, Mace W, Ram A, Lukito Y, Dupont PY, Johnson LJ, Scott DB, Ganley ARD, Cox MP • Mycologia • 2017
Genetic diversity of Phytophthora pluvialis, a pathogen of conifers, in New Zealand and the 2 west coast of the United States of AmericaBrar S, Tabima JF, McDougal RL, Dupont PY, Feau N, Hamelin RC, Panda P, LeBoldus JL, Grünwal NJ, Hansen EM, Bradshaw RE, Williams NM • Plant Pathology • 2017
Analysis of simple sequence repeat (SSR) structure and sequence within Epichloë endophyte genomes reveals impacts on gene structure and insights into ancestral hybridization eventsClayton W, Eaton CJ, Dupont PY, Gillanders T, Cameron N, Saikia S, Scott B • PLoS ONE • 2017
Evolution of polyketide synthesis in a Dothideomycete forest pathogenOzturk IK, Chettri P, Dupont PY, Barnes I, McDougal RL, Moore GG, Sim A Bradshaw RE • Fungal Genetics and Biology • 2017
Host tissue environment directs activities of an Epichloë endophyte, while it induces systemic hormone and defense responses in its native perennial ryegrass hostShmid J, Day R, Zhang N, Dupont PY, Cox MP, Schardl CL, Minards N, Truglio M, Moore N, Harris DR, Zhou Y • Molecular Plant-Microbe Interactions • 2017
Genomic data quality impacts automatic detection of lateral gene transfer in fungiDupont PY and Cox MP • Genes | Genomes | Genetics • 2017
Fungal endophyte infection of ryegrass reprogrammes host metabolism and alters developmentDupont PY, Eaton CJ, Wargent JJ, Fechtner S, Solomon P, Schmid J, Day RC, Scott B, Cox MP • New Phytologist • 2015
A core gene set describes the molecular basis of mutualism and antagonism in Epichloë spp.Eaton CJ, Dupont PY, Solomon P, Clayton W, Scott B, Cox MP • Molecular Plant-Microbe Interactions • 2015
HyLiTE: accurate and flexible analysis of gene expression in allopolyploid speciesDuchemin W, Dupont PY, Campbell MA, Ganley A, Cox MP • BMC Bioinformatics • 2015
Computational identification of transcriptionally co-regulated genes, validation with the four ANT isoform genesDupont PY, Guttin A, Issartel JP, Stepien G • BMC Genomics • 2012
Description and assessment of a model for GSK-3β database virtual screening Ventimila N, Dupont PY, Laguerre M, Dessolin J • Journal of Enzyme Inhibition and Medicinal Chemistry • 2010
Genomes of plant-associated clavicipitaceaeSchardl CL, Young CA, Moore N, Krom N, Dupont PY, Pan J, Farman ML • Advances in Botanical Research • 2014
Time to fight back: Harnessing molecular determinants of virulence and adaptation in kauri dieback pathogens2017 Healthy Trees Healthy Future Symposium • Scion Rotorua • 2017 • Oral presentation
Time to fight back: Harnessing molecular determinants of virulence and adaptation in kauri dieback pathogensFungal effectors symposium • Massey University • 2016 • Oral presentation
Insights into the molecular mechanisms underlying grass-endophyte symbiosisPlant-fungal interactions symposium • The Samuel Roberts Noble Foundation • March 2015 • Oral presentation
Fungal endophyte infection of ryegrass reprograms host metabolism and alters development28th Fungal Genetics Conference • March 2015 • Poster
Endophyte infection of ryegrass alters metabolism, development and response to stressQueenstown Molecular Biology Conference • August 2014 • Two oral presenations (plant satellite and main meeting)
Cold Spring Harbor Laboratory, Computational & Comparative Genomics workshopCold Spring Harbor Laboratory • February 2015
I have been involved in teaching to both undergraduate students and academic staff. I have been in charge of teaching Microarray analysis to third year students at Massey University in 2015 and to medical students in Clermont-Ferrand University, France in 2010 and 2011. I also created an introductory course to Unix and Python programming for Massey University staff (2013-2014). I have also given numerous tutorials on a variety of computer-related topics including SVN and GIT, Ruby on Rails and Lisp. Finally, I am train and mentor PhD students and confirmed researchers for statistical analyses and the use of bioinformatics tools in the space or transcriptomics, phylogenetics, next-generation sequencing and comparative genomics.
This database is a Ruby on Rails web application linked to a MySQL server. It contains the results of automatic annotations for 9000 Epichloë festucae genes models as well as transcriptomics results and manual annotations. It is used both by national and international researchers. It was publically announced in Eaton et al. (2015).
This database is based on the same framework as the Epichloë festucae database and contains automatic annotations of about 50.000 gene models. It was publically announced in Dupont et al. (2015).
HyLiTE is a software allowing the analysis of high-throughput transcriptome data from allopolyploid species
Geneprom is a Ruby on Rails web application developped during my PhD. It allowed me to study regultory elements present in gene promoters.
It is a Java plugin for VANTED. It allows the integration of data from different biological analysis methods to have a better understanding of metabolic pathways and their regulation.
I also worked on the developement of a propriatary information system for academic research (written in C++) during my PhD.
100%Python + BioPython
90%R + Bioconductor
80%HTML5 / CSS3
70%Ruby on Rails