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Plant and Microbial Genomics

About

The Plant and Microbial Genomics Team specialises in the application of genomic and genetic techniques to tackle a variety of biological questions in the fields of plant and microbial genomics. The team use a multidisciplinary approach, combining expertise in genomics, genetics, plant biology, cell biology and bioinformatics – often developing approaches based around novel molecular biology techniques. The team are fortunate to be able to collaborate with many other technical experts at TGAC, and biological system experts on the wider Norwich Research Park e.g. JIC, TSL, UEA and IFR.

Plants and microbes are fundamental to all ecological environments and indeed every agricultural system. Food security requires the continual improvement in the efficiency of agricultural systems so that we can meet the challenges of human population growth, climate change and plant pathogens which threaten yields. Improving the scientific understanding of how plants and microbes interact is therefore of utmost importance.

Strong selective pressures and short generation time lead to microbes overcoming genetic e.g. host resistances and synthetic approaches e.g. chemical treatments. By better understanding host-pathogen interactions, at the genetic level, we can design better approaches to swiftly diagnose, characterise and respond to emerging threats. The ability to overcome chemical treatments is exemplified by the rise of antibiotic resistance in bacteria that threaten our health, and that of our livestock. With collaborators the team are developing pipelines to rapidly identify novel antibiotics by from the genomes of new Actinomycetes bacteria species – a proven source of such compounds.

Activities
  • Testing and developing new sequencing library techniques
  • Automation, high throughput and low cost sequencing approaches
  • Low input and single cell transcriptomics
  • Improved genome assemblies – optimising paired end, mate pair, long read sequencing (PacBio & nanopores) and optical mapping data.
  • Testing and developing new bioinformatics protocols
  • Understanding host-pathogen interactions
  • Population genetics using genotyping by sequencing approaches e.g. RADseq.
  • Expert technical advice – working with biologists to better understand the exact nature of their biological questions, and design optimised genomics approaches.
Current Grants
  • BBSRC NCG - sequencing technology development
  • BBSRC LoLa - Triticeae Genomics for Sustainable Agriculture.
  • BBSRC RM - Use of a self-compatible diploid potato for mutagenesis and forward genetic studies
  • BBSRC IPA - Controlling important diseases in potato by cloning functional NB-LRR-type resistance genes
  • BBSRC & DEFRA - Nornex consortium – A genomics response to the threat of Ash dieback disease
  • ELSA (NRP) pump priming - Population genetics of a broad spectrum plant pathogen Albuga candida
Other Projects
  • Genomic approaches to tackling Honeybee colony collapse disorder (with Universities of Swansea and Warwick).
  • Discovering novel antibiotics in Actinomycetes bacterial genomes (with JIC)
  • Understanding the population genetics of endangered species – the Mauritius Pink Pigeon (with UEA)
Group
  • Matthew D. Clark - Group Leader at TGAC, Honorary Lecturer at UEA School of Biological Sciences
  • Walter Verweij - Senior Researcher Scientist (single cell sequencing)
  • Lawrence Percival-Alwyn - Researcher Associate (improved sequencing techniques)
  • Mark McMullan - Researcher Associate (population genomics)
  • TBA - Senior Researcher Scientist (transcriptional response dynamics)
Alumni
  • Darren Heavens - Pipelines and Production Team Leader, TGAC, UK
  • Fiorella Cugliandolo  - Pipelines and Production Technician, TGAC, UK
  • Deepali Vasoya - Bioinformatician, Roslin Institute, Edinburgh, Scotland
  • Robert Shore - PhD student, University of St Andrews, Scotland
  • Nicole Gkatza - Ph.D. Student, Wellcome Trust Stem Cell Institute, Cambridge, UK
  • Johanna Marsian - Ph.D. Student, John Innes Centre, Norwich, UK
  • Nicole Dawney - Final year undergraduate student, University of York, UK
  • Visit BBSRC website
  • Visit South Norfolk Council website
  • Visit Norwich City Council website
  • Visit Norfolk County Council website
  • Visit Greater Norwich Development Partnership website