Research

Project A3

The interpretation of distribution of epigenetic modification, and sequence-level analysis of polyploid genome evolution

Lead Partners 7: CLC (SME) 1: QMUL (University)

State-of-the-Art Problem and its Solution
Most of the world’s major crop and biomass species are polyploids (they contain duplicated genome copies, sometimes derived from more than one parental species). Understanding epigenetic modification and the effects of mutation, introgression and selection on these genomes is essential for understanding their evolution, and for genomically-informed crop breeding. However, sequence analysis of polyploid genomes is highly challenging, and few methods are available for high throughput sequence analysis of their genomes. This project will pioneer polyploid genome analysis in biomass genus Betula, and develop a module for the CLC genomics workbench that can be applied to all polyploid species.

Suggested reading:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030906
http://www.cell.com/current-biology/abstract/S0960-9822(11)01404-7
http://www.nature.com/ng/journal/v23/n4/abs/ng1299_452.html
Objectives
  • Analyze genome-wide epigenetic data and genetic mutation, selection and introgression data in Betula species at a population level
  • Development of new methods for analysis of polyploid genomes.
  • Supply genome-wide data to CLC as an aid to software development.
Methodology
The two ESR fellows will work together in the development and application of biological data, bioinformatics tools and statistical methods to study epigenetic modifications of polyploid genomes and the evolution of polyploid genomes through the mechanisms of mutation, selection and introgression. Particular attention will be paid to data generated by widely-used methods of genome sequence sub-sampling, such as RAD-sequencing. Much of the initial development will be based on data from diploid and polyploid Betula (birch) species, generated by the ESR based at Queen Mary University of London.
ESRs training by research
Fellow 1 (INTERCROSSING position #4) will be based at CLC Bio, Aarhus, Denmark, with a six month outplacement at Queen Mary University of London. He/she will research and develop bioinformatics methods for the analysis of polyploid genomes, including genome mapping, identification of SNPs, gene losses, epigenetic modifications, and copy number variations. Fellow 1 will collaborate with Fellow 2 in the practical application of these methods. The main supervisor if this Fellow will be Dr Roald Forsberg, Director of Research and Development at CLC Bio.

Fellow 2 (INTERCROSSING position #5) will be based at Queen Mary University of London, with a six month outplacement at CLC Bio, Denmark. He/she will generate whole genome and genome-wide sub-sampled data from diploid and polyploid species of Betula (Birch). He/she will analyze genomic and geographic patterns of introgressive hybridisation and genome evolution in natural populations using bioinformatics methods developed in collaboration with Fellow 1. The main supervisor of this Fellow will be Dr Richard Buggs, Senior Lecturer at QMUL.

They two fellows and their supervisors will jointly work on public release of the tools that result.
Job description 4
Job description 5