Genomics and Next Generation Sequencing (NGS)

Featured project

The Blumeria graminis Sequencing Project

We have contributed to many projects relating to genomic studies and NGS analysis, varying from being members of international genome sequencing consortia through to development of in-house resources enabling genomic analysis for lab-based scientists.

Current projects

Cryptococcus neoformans sequencing

An evolutionary population genomics approach to determine the genetic basis of virulence in the pathogenic fungus Cryptococcus neoformans

Cryptococcus neoformans is one of the leading fungal causes of death and disease, affected individuals with impaired immune systems. This project is aiming to understand the genomic regions of Cryptoccoccus neoformans which affect virulence in humans. The BDSG are providing support and computational resources for the project personnel.

PI: Prof. Matthew Fisher

Funding Body: MRC

Grant Reference: MR/K000373/1

BDSG Contact: Dr. Sarah Butcher

Developing Rapid Responses to Emerging Virus Infections of Poultry

PI: Dr. Mike Skinner (Dept. of Medicine)

Funding Body: BBSRC

Grant Reference: BB/K002465/1

BDSG Contact: Geraint Barton

Selected completed projects

Blumeria Graminis Sequencing

This project set out to provide a better understanding of factors affecting virulence and host-specificity in the powdery mildew fungus Blumeria graminis f. sp. hordei. Please see the Featured Project page for full details.

PI: Prof. Pietro Spanu

Funding Body: BBSRC

Grant Reference: BB/E000983/1

BDSG Contact: Dr. James Abbott

Publications:

  • Spanu, P.D. James C. Abbott et al. (2010) Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism. Science, 10 December: 1540-1543.DOI:10.1126/science.11 94573
  • Pedersen C. et al (2012) Structure and evolution of barley powdery mildew effector candidates. BMC Genomics 2012, 13:694 doi:10.1186/1471-2164-13-694
  • Oberhaensli S et al (2010) Comparative sequence analysis of wheat and barley powdery mildew fungi reveals gene colinearity, dates divergence and indicates host-pathogen co-evolution. Fungal Genet Biol 48(3) 327-334 doi:10.1016/j.fgb.2010.10.003
  • Bindschedler L.V. et al (2009) In planta proteomics and proteogenomics of the biotrophic barley fungal pathogen Blumeria graminis f. sp. Hordei. Mol Cell Proteomics, Oct;8(10):2368-81. Epub 2009 Jul 14

 

MiPGR - The Microbial Population Genomics Resource

This is a 5 year Wellcome Trust funded (099202/Z/12/Z) project with Dr David Aanensen at the Department for Infectious Disease Epidemiology. The project aims to develop web applications focussing on data storage, processing and presentation of the genomes of very large populations of pathogens to communities of users.

PI: Dr. David Aanensen

Funding Body: Wellcome Trust

Grant Reference: 099202/Z/12/Z

BDSG Contact: Dr. Derek Huntley

Streptococcus pyogenes analysis

Sequence from 48 Streptococcus pyogenes isolates were assembled de-novo and analysis carried out via mapping to reference strains to identify sequence variation

PI: Prof. Shiranee Sriskandan

Funding Body: NIHR BRC

Publications: Turner et al., (2015) Emergence of a New Highly Successful Acapsular Group A Streptococcus Clade of Genotype emm89 in the United Kingdom; doi: 10.1128/mBio.00622-15

BDSG Contact: Dr. James Abbott

The Indian-Asian Genome

This project involved variant discovery amongst a population of 180 low-coverage human genomes and 170 exomes from the Indian-Asian subcontinent. The work was carried out on behalf of the Lolipop project.

PIs: Prof. John Chambers

BDSG Contact: Dr. James Abbott

Publications: 

  • Kato N et al (2015) Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation. Nat Genet doi:10.1038/ng.3405
  • Chambers J.C. et al (2015) Epigenome-wide association of DNA methylation markers in peripheral blood from Indian Asians and Europeans with incident type 2 diabetes: a nested case-control study. Lancet Diabetes Endocrinol. 3(7):526-534. doi:10.1016/S2213-8587(15)00127-8
  • Chambers JC, Abbott J, Zhang W, et al. (2014) The South Asian Genome. PLoS One. Aug 12;9(8):e102645. doi:10.1371/journal.pone.0102645. 

Tomato Genome

Our involvement in the Tomato Genome Project spanned two separate projects:

Tomato Chromosome IV sequencing

PI: Dr. Gerard Bishop

Funding Body: BBSRC

Grant Reference: BB/C509731/1

EU-SOL

PI: Dr Gerard Bishop

Funding Body: EU Framework 6

Grant Reference: FOOD-CT-2006-016214

Publications:

  • Ioannis Filippis, Rosa Lopez-Cobollo, James Abbott, Sarah Butcher, Gerard J. Bishop (2013) Using a periclinal chimera to unravel layer-specific gene expression in plants. The Plant Journal10.1111/tpj.12250
  • The Tomato Genome Consortium (including I. filippis, D. Buchan, S. Butcher, J. Abbott) (2012) The Tomato Genome Sequence Provides Insights into Fleshy Fruit Evolution. Nature 485, 635-641; doi:10.1038/nature11119
  • Lukas A Mueller et al (2009) A Snapshot of the Emerging Tomato Genome Sequence. The Plant Genome Vol. 2  No. 1  78-92

BDSG Contact: Dr Sarah Butcher