This is the report from a BSPP Junior Fellowship.
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I am very grateful to the BSPP for accepting my application for the Junior Fellowship Award. The award enabled me to visit from Canada in the lab of Dr Megan McDonald at the University of Birmingham. During my stay I learned bioinformatic and comparative genomic techniques and further explored the role of transposons in the evolution of pathogen virulence.
When I started my PhD I was extremely fortunate to have Dr McDonald included on my advisory committee, providing excellent guidance and mentorship. After publishing my first major article and passing my comprehensive exams, Dr McDonald invited me to join her over-seas to have a period of focused work and learning in order to rapidly advance the next stages of my research.
My trip began in the Austrian Alps, in Innsbruk, where the 16th European Conference on Fungal Genetics was being held (pictured below). At this event I presented a poster, saw many exciting talks, and networked with other scientists and learned of their interesting research. After four days in Innsbruk, I travelled by train to Birmingham. However, first I stopped in Munich and Brussels for a few days to do some sight seeing. Upon my arrival in Birmingham, we immediately got to work on my project.
Pyrenophora tritici-repentis is a foliar pathogen of wheat and part of the leaf-spot disease complex. In Europe, Zymoseptoria tritici is the dominant leaf-spot pathogen, but in North America P. tritici-repentis is more common. Previously, it had been shown that an important necrosis inducing protein produced by the ToxA gene was present within a hAT transposon. This transposon had facilitated the horizontal movement of ToxA between species in the leaf-spot complex. In the first part of my PhD, I showed that this ToxA containing hAT transposon was nested within another much larger mobile element called a Starship. Starship transposons are a new class of super-large mobile genetic elements recently classified in fungi. Due to their massive size, a Starship can contain many ‘cargo’ genes (and other transposons) which travel along with the Starship.
Dr McDonald and another student had also discovered ToxA within a Starship in another leaf-spot pathogen. During my time in the UK we performed comparative genomics between these Starships and between species. Our hope here is to further understand the potential mobility of ToxA, as it is already known to have jumped between species, its introduction into another could contribute to a future pathogen emergence.
Another important virulence gene in P. tritici-repentis is the chlorosis inducing effector gene ToxB. Perhaps due to its multi-copy nature it has been less intensively studied than ToxA. However, with long-read sequencing, investigating the evolution of this gene becomes tractable as the separate copies can be assembled clearly. While in Dr McDonalds lab we also utilised eight newly assembled long-read genomes to explore possible mechanisms behind ToxB replication. The genomes consisted of isolates with the inactive homolog toxb, single ToxB carriers, and multi-copy ToxB carriers. Using comparative alignments, BLAST searches, ORF identifiers, and known transposon databases we identified a candidate for the replicative unit of ToxB.
Finally, P. tritici-repentis is known to produce a third effector ToxC. The exact identity of ToxC has eluded the leaf-spot community for decades. Utilising a large collection of short-read sequenced genomes originally used for creating a pangenome, we were able to attempt a genome-wide association study to link the ToxC phenotype with a SNP. While I had performed the SNP calls prior to my trip, in Birmingham I was able to refine my filtering methods and test multiple algorithms for GWAS using GAPIT.
The end result of this trip was significant progress on three avenues of my research. I am indebted to both the BSPP and Dr McDonald for making this learning experience happen. I hope to maintain ties with the UK research community throughout my career and this visit was an excellent opportunity for solidifying collaboration.
The University of Lethbridge, Canada