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Can transposons promote plant genome evolution?

Primary Supervisor: Dr Marco Catoni, School of Biosciences

Secondary supervisor: Dr Peter Lund

PhD project title: Can transposons promote plant genome evolution?

University of Registration: University of Birmingham

Project outline:

Evolution is the process that allow organisms to adapt to new environments, and it is based on changes of heritable traits and their selection over successive generations. Considering that heritable traits are encoded in genes, the mutation of the DNA sequence is a prerequisite to evolve new features. Nonetheless, an increased mutation rate can have tremendous effect on fitness of eukaryote organisms with a long generational time, while it could be relatively tolerated by prokaryotic life. Consequently, genome stability appears to be proportionally more important in complex and larger genomes, and we have now evidences that epigenetics mechanisms are able to regulate the degree of genome plasticity, potentially affecting genome evolution. One of the main feature typical of large genome is the abundance of “parasitic” DNA elements call transposons or Transposable elements (TEs). TEs are able to move from their original position in the genome to a new chromosomal location, multiplying their copies similarly to viruses. Plant genomes are rich in TEs, which account for the most variable portion of the genome. As consequence of their apparent selfish behaviour, TEs have been initially associated to “junk” DNA, but growing evidences are now demonstrating their contribution to the evolution of genes responsible for agricultural traits (Lisch, 2013). However, it is still unclear if TEs (at least some of them) evolved specific mechanisms to facilitate gene evolution, or if the generated traits are just the result of selection of a pool of rare rearranged TE integration events.

The proposed work aims to address this fundamental question with two complementary projects, which can be chosen depending by student background and interests:

1- A pool of well-characterized plant TEs will be artificially moved from their original genome into the alga Chlamydomonas reinhardtii. The “naive” genome of this eukaryotic alga is relatively small with little TE content (Philippsen et al., 2016). However, the extreme fast growing and the unicellular behaviour of this organism allow microevolution studies, similarly to bacteria. Therefore, the generated “TE-enriched” alga strains will be exposed to stress conditions (heat, light, toxic chemicals) for several generations, to test their ability to adapt to a new environment, and investigate the mechanisms involved in the adaptation process. This work will made use of synthetic biology, new generation sequencing approaches (Nanopore, Illumina) and genetic mapping, and the ideal candidate should have a good affinity to both microbiology and bioinformatics.

2- DNA methylation is a powerful epigenetic mark controlling TE expression, and we previously developed a population of Arabidopsis thaliana plants with reduced DNA methylation in the genome, inducing the mobilization of many TEs. Among them, we observed a new TE family with the ability to shuffle coding exons across the genome, with a strong attitude to generate new genes (Catoni et al., 2019). With this project, we will investigate if the mobilization of this TEs can “speed up” evolution, increasing the adaption speed. We will grow several generations of plants in presence of environmental stresses, selecting only most performant individuals for seeds collection. The selected “adapted” plants will be profiled to characterize the genome variants associated to the improved fitness. The candidate will learn how to handle genomics data and perform genetic mapping, and should have affinity to plant science and molecular biology.

References:

  1. Catoni, M., et al. (2019). Mobilization of Pack-CACTA transposons in Arabidopsis suggests the mechanism of gene shuffling. Nucleic Acids Res. 47, 1311–1320.
  2. Lisch, D. (2013). How important are transposons for plant evolution? Nat. Rev. Genet. 14, 49–61.
  3. Philippsen, G.S., et al. (2016). Distribution patterns and impact of transposable elements in genes of green algae. Gene 594, 151–159.

BBSRC Strategic Research Priority: Understanding the Rules of Life: Plant Sciences

    Techniques that will be undertaken during the project:

    It is expected that a student will apply many techniques, which may vary depending by the chosen project. These techniques include genome wide library preparation for next generation sequencing (RNAseq, BS-DNASeq, DNAseq), and analysis of the produced datasets (genome alignments, variants calling, differentially methylated regions identification, differential gene expression analysis). This will also include the preparation of libraries for long read sequencing (Nanopore), 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, the projects will include classic molecular biology techniques (cloning, plant and algae 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