| Title of Project |
| Genome Assembly and Prediction of Metabolic and Functional Trait Profiles of Pectobacterium Species Isolated from Soft Rotting Potato Tubers |
| This project going to be… |
| Remote/virtual |
| Full Name of Supervisor |
| Dr Ciara Keating |
| Institution Department and Address |
| Bower Building, University Avenue, University of Glasgow Glasgow, Lanarkshire G12 8QQ United Kingdom Map It |
| Telephone |
| 07454844802 |
| ciara.keating@glasgow.ac.uk |
| Position held |
| Post Doctoral Research Associate |
| Full name of the day to day supervisor and/or arrangements for supervision |
| Dr Keating will co-supervise and deliver training to the student with Dr Ijaz (Reader in Bioinformatic Engineering: http://userweb.eng.gla.ac.uk/umer.ijaz/). They will be integrated into the Environmental Omics Lab and the cross-disciplinary Blackleg Hub team (https://www.blackleghub.ac.uk). Training and daily meetings will be held on Teams/Zoom which will cover plans for the week and training on techniques. The student will attend weekly project meetings where they will show Powerpoint slides of their progress. – Skills: Dr Keating has co-supervised 13+ computational MSc projects with Dr Ijaz from 2020-2022. |
| Date of Project Commencement |
| 09/05/2022 |
| Duration (weeks) |
| 10 |
| Brief Description of Project |
| Background The potato is one of the most popular vegetables in the UK. The potato grower industry suffers losses in excess of £50M per year from potato blackleg disease. Blackleg disease is a soft rot disease whereby pathogenic bacteria (Pectobacterium spp) produce enzymes (cellulases and pectinases for example) that allow them to degrade the plant cell walls. This capability is actually quite interesting in terms of biotechnology. Food, plant and paper mill waste contain high volumes of cellulose and lignocellulose. A biotechnological process – termed anaerobic digestion can be applied to degrade these wastes and convert them to renewable energy in the form of methane gas. However, the initial break-down of cellulose is often a rate-limiting step in the process and leads to poor methane yields. Yet, Pectobacterium breaks down plant cell walls relatively easily. In this studentship, we will analyse the genomes of Pectobacterium species, with a particular focus on the metabolic functions and their contribution to biogeochemical cycling (e.g. the carbon cycle) using state of the art bioinformatics software.Objectives Therefore the aims and objectives of this studentship are to: • Assemble the genomes of 20+ novel Pectobacterium isolates with demonstrated ability to initiate soft rot infection in five potato varieties from multiple agricultural field sites (Week 1 – Week 3). • Annotate the genomes to recover metabolic function in particular focusing on major biogeochemical pathways such as Carbon, Nitrogen and Sulfur, and other nutrient cycles (Week 4 – Week 6). • Compare the genomes (SNPs, genes) to existing genomes of Pectobacterium species available in public repositories such as NCBI (Week 7 – Week 10)Supervision and Benefit to the Student This will be a remote computational research project. The student should have basic computational skills. I will co-supervise and deliver training to the student with Dr Ijaz (Reader in Bioinformatic Engineering: http://userweb.eng.gla.ac.uk/umer.ijaz/). They will be integrated into the Environmental Omics Lab and the cross-disciplinary Blackleg Hub team (https://www.blackleghub.ac.uk). The student will also attend the wider grant consortium meetings (held on a bi-monthly basis) where updates from all the involved institutes are shown. Importantly, these meetings have all the staff from the project from across the UK and key industry contacts such as potato growers, SASA, and other stakeholders. We anticipate that these findings will form part of a short research or perspective article citing that Pectobacterium may be adaptable for biotechnological solutions. |
| Attach the recommended reading for the project |
| Literature related to blackleg disease and Pectobacterium: Wolf, J.M., Acuña, I., Boer, S.H.D., Brurberg, M.B., Cahill, G., Charkowski, A.O., Coutinho, T., Davey, T., Dees, M.W., Degefu, Y. and Dupuis, B., 2021. Diseases caused by Pectobacterium and Dickeya species around the world. In Plant diseases caused by Dickeya and Pectobacterium species (pp. 215-261). Springer, Cham. Toth, I.K., Barny, M.A., Brurberg, M.B., Condemine, G., Czajkowski, R., Elphinstone, J.G., Helias, V., Johnson, S.B., Moleleki, L.N., Pirhonen, M. and Rossmann, S., 2021. Pectobacterium and Dickeya: environment to disease development. In Plant Diseases Caused by Dickeya and Pectobacterium Species (pp. 39-84). Springer, Cham. Skelsey, P., Humphris, S.N., Campbell, E.J. and Toth, I.K., 2018. Threat of establishment of non-indigenous potato blackleg and tuber soft rot pathogens in Great Britain under climate change. PLoS One, 13(10), p.e0205711. Literature related to computational methods that will be used in this project: Stratakos, A.C., Ijaz, U.Z., Ward, P., Linton, M., Kelly, C., Pinkerton, L., Scates, P., McBride, J., Pet, I., Criste, A. and Stef, D., 2020. In vitro and in vivo characterisation of Listeria monocytogenes outbreak isolates. Food Control, 107, p.106784. Page, A.J., Cummins, C.A., Hunt, M., Wong, V.K., Reuter, S., Holden, M.T., Fookes, M., Falush, D., Keane, J.A. and Parkhill, J., 2015. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics, 31(22), pp.3691-3693. Brynildsrud, O., Bohlin, J., Scheffer, L. and Eldholm, V., 2016. Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome biology, 17(1), pp.1-9. Zhou, Z., Tran, P.Q., Breister, A.M., Liu, Y., Kieft, K., Cowley, E.S., Karaoz, U. and Anantharaman, K., 2022. METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. Microbiome, 10(1), pp.1-22. Li, X., Ma, Y., Liang, S., Tian, Y., Yin, S., Xie, S. and Xie, H., 2018. Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle. BMC genomics, 19(1), pp.1-22. |
