• Research group

Clark Group

Genetic and genomic techniques to understand plant and microbe interactions.

Group leader
Matt Clark

Group activities.

The Clark group, in collaboration with EI's Pipelines and Platforms group, tests and develops new sequencing library techniques, automating high throughput pipelines for lower cost, and optimising assemble strategies  with data from different sequencing platforms such as Illumina short read, PacBio long reads and BioNano optical mapping. o We integrate these technologies to calibrate and refine our process for future projects.

We also test and develop new bioinformatics protocols, including low input and single cell transcriptomics. Our technical expertise is widely recognised, and we provide a consultancy service, working with biologists to better understand the exact nature of their questions and design optimised genomics approaches.

We have a particular focus upon understanding host-pathogen interactions; developing technologies to study plant and microbial interaction at great detail with spatial transcriptomics. In addition, develop pipelines to rapidly identify novel antibiotics from the genomes of new Actinomycetes bacteria species.

Some of our current projects include:

  • Novel Technology Testing and Development
  • Triticeae Genomics For Sustainable Agriculture
  • Solanaceae Genomics - Potatoes, Tomatoes, their relatives and pathogens
  • Ash Dieback - Resistant Trees and the Global Fungal Aggressor
  • Mauritius Pink Pigeon - Conservation Genomics
  • AirSeq - Environmental Genomics 
  • Spatial transcriptomics -  Plant Transcriptome Defense Responses

Tools.

Targeted Assembly Pipeline

GWASer - association mapping of complex genetic traits using CyVerse (formerly iPlant)

ADLA - Adapter Design and Library Analysis

LORIS - sequencing RNA samples with low starting material    

Data.

Wheat Genome TGAC v.1 (Clavijo et al)

Ash & Ash Dieback