Estimating the rates and modes of creation of new genetic variation in plants using NGS technologies.

Supervisor : Michele Morgante

Structural variants (SVs) are an important source of genetic variation in plants. Molecular mechanisms underlying SVs are diverse and not fully understood yet. One of the known mechanisms for the generation of novel SVs involves transposable elements (TEs).

The activation of such elements could be strictly related to epigenetic regulation, in terms of silencing a TE region, resulting in different rates of creation of new genetic events.
This PhD project is aimed at the identification of SVs in Zea mays and Vitis vinifera to characterise the dispensable genome of the two species.

To reach this aim, paired-end and mate-pair data obtained from Illumina Next Generation Sequencing instruments will be used.

A substantial effort will be devoted to the improvement and development of methods for the detection of structural variants, e.g. deletions and insertions.

In particular it is foreseen the integration of mate-pair information to improve detection of deletions usually performed with paired end reads.

Also, efforts will be devoted to the development of novel methods for the detection of insertions of transposable elements (a task that is still very difficult from a bioinformatics point of view).
Finally, a part of the project will be devoted to the assessment of the performance of several tools for the detection of SVs using both real and simulated data.

Biography and contacts

Ettore Zapparoli was born in 1984 in Turin, Italy.

In 2013 graduated as MSc in Molecular Biotechnology (110/110 cum laude) at Molecular Biotechnology Center, University of Turin (Italy).

In 2014 he started the doctoral course at the PhD school “Agriculture Science and Biotechnology” at the University of Udine.

ezapparoli@appliedgenomics.org