Genomics projects  

Lead researcher: Prof Matt Loose 

Through the COVID-19 pandemic, Deep Seq together with members of Virology have contributed to the sequencing of SARS-CoV-2 genomes as part of the COG UK Consortium. The sequencing approach used was developed by the ARTIC Network and involved amplifying small overlapping fragments of the viral genome which could then be sequenced on the GridION X5. The scale of the group’s contribution to this project was made possible thanks to Future Food investment in both equipment and personnel. Deep Seq has now sequenced approximately 10,000 viral genomes, which have been used to identify patterns of transmission and emergence of variants at a local, national and global level.  

This project was funded by COG UK. 

Lead researchers: Prof David Salt, Assco Prof Gabriel Castrillo 

This project researches the different microbes present during cocoa fermentation. Cocoa bean fermentation is an on-farm process that significantly affects the flavours of chocolate, but which is largely uncontrolled. Researchers travelled to Colombia to conduct in-field sequencing using the hand-held Oxford MinION. They took samples from the leaves, pods, surrounding soils, worker’s hands, and the fermenting cocoa beans. They also measured the daily pH and temperature of the fermentation. 500 cocoa accessions have been sequenced using low coverage genome sequencing. The data was used in a Genome Wide Association Study (GWAS) to identify genes involved in heavy metal uptake and accumulation in the plants. 

This project was funded by Innovate UK.

Lead researchers: Dr Sean Mayes, Prof Festo Massawe

Bambara groundnut is a hardy drought resistant, but underutilised crop indigenous to sub-Saharan Africa. In order to produce a reference genome for bambara, Deep Seq has sequenced the genome using both long and short DNA reads produced on the GridION X5 and the NextSeq500, respectively. This was combined with Bionano optical maps and RNA-Seq data to produce an annotated reference genome. Scaffolds from the combined assembly were orientated and mapped to individual chromosomes through the position of DArT Seq markers across controlled crosses (n=500) to give a final 23 superscaffolds forming the pseudochromosomes. These data will help understanding of the genetic basis of some of bambara’s valuable traits, particularly drought tolerance and also help to direct breeding programs to allow this crop to be utilised to the fullest. 

 This project was funded by the Future Food Beacon. 

Lead researchers: Dr Sean Mayes and Prof Festo Massawe

Winged bean grows in hot humid equatorial regions of south and southeast Asia and has seed with a similar protein content to soybean. It is however still an underutilised crop despite being nutritious, and relatively disease resistant. Deep Seq has sequenced the genome of winged bean using both long and short DNA reads produced on the PromethION and HiSeq respectively. This has been combined with Bionano optical maps and RNA-Seq data to produce an annotated reference genome. Scaffolds were orientated and placed on the genetic map through the use of two DArT Seq controlled cross maps (n= 250). Like for Bambara this data will improve understanding of the genetic basis of traits and help improve breeding programs to select high protein and adaptation to mechanised harvesting. 

This project was funded by Crops for the Future Impact Fund. 

Lead researchers: Assco Prof Levi Yant & Dr Peter Emmerich 

Grass pea is a hardy crop grown in east Africa and Asia for both humans and livestock. Its drought resistance makes it particularly important as it will often survive when other crops have failed. However, the seeds contain a neurotoxin, which when consumed over a prolonged period can lead to a neurodegenerative disease. Deep Seq has sequenced grass pea DNA using Nanopore long read sequencing on the PromethION 24. This data has been added to Illumina short read data to produce a reference genome of grass pea. Having a grass pea genome sequence will help understanding how the toxin is produced and accumulates within the seeds and allow development of grass pea strains with reduced toxicity. 

This project was funded by a Future Food Beacon Innovation Grant and JIC.

Lead researchers: Prof Tracey Coffey and Prof James Leigh 

This was a project to produce genome assemblies for two cows from the Sutton Bonnington dairy herd. Using DNA extracted from milk Deep Seq sequenced the cow genomes using a combination of long read sequencing performed on the PromethION 24 together with linked read pseudo long read data produced using the 10X Chromium Controller. These reference genomes will be used as the basis for more detailed genetic analysis of the herd to help elucidate understanding of host-pathogen interaction, fertility, soundness, metabolism, nutrition, behaviour, and environmental emissions. Read more on the blog. 

This project was funded by the Future Food Beacon

Lead researchers: Dr Thomas Alcock, Dr Neil Graham and Prof Martin Broadley 

Pooled, high molecular weight DNA samples from Brassica rapa mutant plants segregating for either higher or lower leaf magnesium concentrations were sequenced by linked-read sequencing using the 10X Chromium Controller and the NextSeq500. The data were used in a bulked segregant analysis (BSA) to identify a mutation in schengen3 as responsible for the observed high magnesium accumulation. This data could potentially be used to improve the nutritional value of brassica crops both in human and livestock food systems.  

Funding for reagents required for high molecular weight DNA extraction was provided by the University of Nottingham Faculty of Science 4* REF Paper Enhancement Fund (PEF) awarded to Neil Graham and Thomas Alcock. Funding for performance of linked-read sequencing was provided by the UK Biotechnology and Biological Sciences Research Council (BBSRC) and the UK Natural Environment Research Council (NERC), through a Sustainable Agriculture Research and Innovation Club (SARIC) project, Magnesium Network (MAG-NET): Integrating Soil-Crop-Animal Pathways to Improve Ruminant Health [grant number BB/N004302/1], awarded to Martin Broadley. 

Lead researchers: Prof Andy Salter, Dr Carlos Lopez Viso 

As part of the Future Proteins Platform, Deep Seq has been sequencing the genome of the mealworm using both long DNA reads (sequenced on the GridION X5 and PromethION) and short DNA reads (sequenced on the NextSeq500). The mealworm has great potential as a sustainable protein source for animal feed. The project applies genetic silencing by RNA interference in order to modify the gene expression of mealworms to increase the protein and decrease the fat content. 

This project is funded by the Future Food Beacon.