Written by Palesa Madupe at the University of Pretoria. This is the report from a BSPP Grace Waterhouse Fellowship. Click here to read more/apply for one yourself.
Xanthomonas is bacterial genus that belongs to the gamma division of the Proteobacteria family. All species in this genus are plant pathogens. One of them is Xanthomonas vasicola (Xv) which is a pathogen of various monocot plants, including Banana (Banana Xanthomonas wilt) which is currently threatening crops in East Africa. Recently a strain of Xv causing an outbreak of blight and dieback in Eucalyptus grandis was reported and this was the first time this pathogen was found to infect a dicot plant.
The genome of an Xv strain had been sequenced in Pretoria using the Illumina MiSeq platform. During my fellowship, I spent a month at the University of Exeter working with Dr David J Studholme, where I performed quality control, using TrimGalore and the FastX Toolkit and re-analysed the sequencing. Velvet and SPAdes genome assemblers were used. We thus managed to improve the genome assembly. A BWA alignment was undertaken in order to find genomic differences in the E. grandis isolate compared to other X. vasicola strains. The programme MUMmer was used to compare the assemblies and Harvest for the whole-genome phylogenetic analysis. From this data we observed that the isolate from E. grandis groups together with the sugarcane isolates. There was a unique region that that was not found in any of the other X. vasicola strains, those from sugarcane, maize, banana and sorghum. Based on NCBI nt BLAST analysis 43% of this region matched with X. campestris pv. vesicatoria plasmid pXC183.
The skills I attained during my visit included learning to work within the Linux command line which can easily be extrapolated into various computational explorations. I feel that any further analyses of next generation sequence data will be done more easily and with confidence. The skills I learnt will be shared with others in my Department at the University of Pretoria. I thoroughly enjoyed my visit to the University of Exeter. As this was my first overseas trip, I valued the cultural experience in both Exeter and London. This was truly a once in a life time experience.
I would like thank everyone at the computational biology unit at the University of Exeter, with a special thanks to Jamie Harrison, and to Dr. David Studholme for giving his time to assist me and his patience teaching me new skills. Finally, I am truly grateful to the BSPP for giving me this opportunity to gain experience at the University of Exeter which has enhanced my genomic analysis skills.
Palesa Madupe
University of Pretoria
