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Epigenetics contribution to plant genome evolution

Primary Supervisor: Dr Marco Catoni, School of Biosciences

Secondary supervisor: TBC

PhD project title: Epigenetics contribution to plant genome evolution

University of Registration: University of Birmingham

Project outline:

The proposed project can focus in one of these areas:

1- Explore the links between genome stability and evolution, investigating how epigenetic marks affect genome plasticity, which directly control the speed of genome evolution. The candidate will learn how to handle efficiently large data sets, extract information and build biological model using informatics tools developed for the Linux environment and the R programming language. This role is for students with affinity to bioinformatics.

2- Investigate the bases of epigenetic variation, studying how epialleles (= genes with identical DNA sequence but different epigenetic marks) are generated, and which factors control their stability. The ideal candidate will develop a broad knowledge in all aspects of genomics studies, from molecular biology, genomics and data analysis, learning how to build models based on biological experiments. This role is ideal for a candidate who wishes to bridge wet lab experiments and bioinformatics.

3- Study the consequences of Transposable element (TE) mobilization. The aim of this approach is to discover, characterize and investigate the role of active TEs in plants, going beyond the concept of a single reference genome. The ideal candidate should have affinity with molecular biology and he/she will become familiar with cutting edge technologies such as third generation sequencing (PACBio or Nanopore) and CRISP-Cas9 editing system in plants.

References:

  1. Heard, E., and Martienssen, R.A. (2014). Transgenerational Epigenetic Inheritance: Myths and Mechanisms. Cell 157, 95–109.
  2. Lisch, D. (2013). How important are transposons for plant evolution? Nat. Rev. Genet. 14, 49–61.

BBSRC Strategic Research Priority: Sustainable Agriculture and Food: Plant and Crop Science

    Techniques that will be undertaken during the project:

    It is expected that a student will apply many techniques, which may vary depending on the project chosen. These techniques include genome wide library preparation for next generation sequencing (RNAseq, BS-DNASeq, DNAseq), and analysis of the acquired datasets (genome alignments, DNA methylation call, differentially methylated regions identification, differential gene expression analysis). This may include the preparation of libraries for long read sequencing (Pac Bio), de novo genome assembly and genome comparison studies. Data analysis will make large use of command line tools developed for Linux environments and the programming language R. In addition, cutting edge genetic technology (such as CRISP-CAS9 genome editing) will be applied, beside classic molecular biology techniques (cloning, plant transformation) and other genomics (DNA blot, transposon display, PCR), transcriptomic (Northern blot, quantitative RT-PCR) and proteomic (protein extraction, Western blot) approaches.

    Contact: Dr Marco Catoni, University of Birmingham