We are recruiting for a BBSRC DTP PhD studentship to improve analysis of Oxford Nanopore Technology (ONT) sequencing data. Long-read sequencing technologies, such as ONT, can capture structural variation in genomes as well as sequence variation, and identify full-length and alternatively-spliced transcripts. In this project we will develop improved analytical methods for ONT data and apply methods such as machine learning to increase the efficiency of ONT’s real-time selective sequencing and adapt it for large genome crops. These new methods will be used to improve an Amaranthus cruentus genome annotation and drive characterisation and use of an Amaranth diversity collection.
Amaranths hold significant potential for sustainable development. These leafy vegetables are eaten across Sub-Saharan Africa and typically harvested from the wild. They have high nutrient content and can be grown on poor soil with low inputs. They are C4 plants with enhanced resilience to water deficit. Amaranth cultivation by smallholder farmers (rather than wild harvesting) would provide greater control over availability and enhance consumption for nutritional benefits. In addition, amaranth can deliver household income, because of its high value, and build climate-resilience into smallholder agriculture. However, scaling-up cultivation of amaranth requires improved varieties with higher robust yield.
This is a collaborative project with Dr Runxuan Zhang and Dr Wenbin Guo at the James Hutton Institute, Dundee.
Please see FindaPhD for more details and to apply. Deadline is Jan 10th 2021.
Systems Biology of Plant Disease Resistance 