Martti Vasar "Developing a bioinformatics pipeline gDAT to analyse arbuscular mycorrhizal fungal communities using sequence data from different marker regions"

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Date:

18.08.2020 - 10:15 to 14:15

On 18 August at 10:15 Martti Vasar will defend her doctoral thesis "Developing a bioinformatics pipeline gDAT to analyse arbuscular mycorrhizal fungal communities using sequence data from different marker regions".

Supervisors:
Dr. Maarja Öpik, University of Tartu, Estonia
Prof. J. Peter W. Young, University of York, United Kingdom

Opponent:
Prof. Philippe Vandenkoornhuyse, University of Rennes, France

Summary:
Soils harbour vast numbers of microorganisms that play important roles in ecosystems. One important group of microorganisms is the arbuscular mycorrhizal (AM) fungi. AM is a type of mycorrhiza, where fungi forms a symbiosis with most of the herbaceous and woody plants including crop plants. AM fungi provide nutrients and water that are needed for plant growth and in exchange receive carbon fixed by the plant in photosynthesis. AM fungi also improve plant tolerance to stress, such as drought and pathogen attacks. This thesis analysed the efficiency of popular DNA sequencing marker regions (SSU, ITS, LSU) used with microorganisms and different sequencing platforms to identify AM fungi in environmental samples. Outcome of the thesis is a bioinformatics tool gDAT (graphical downstream analysis tool) with graphical interface that allows ecologists to easily analyse vast amounts of DNA sequence data. The main results and conclusions of the thesis are the following: 1) the SSU marker region is sufficiently variable to identify AM fungi; and the variation within species is lower than the variation between species; 2) newer sequencing technologies provide increased sequencing depth, but this does not increase species richness estimates per sample and produces similar community patterns compared to previous generation sequencing. Thus, the optimal sample sequencing depth has been achieved for AM fungal diversity assessments; 3) the ITS region can be used successfully to identify abundant AM fungal species; 4) the newly developed bioinformatics tool gDAT allows rapid and efficient analysis of AM fungi from sequenced DNA. This tool is not limited to AM fungi and is applicable for other organisms to be identified through DNA sequencing.

Location:

Room 218, 40 Lai Street, Tartu and MS Teams

Event category:

Defence

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Martti Vasar "Developing a bioinformatics pipeline gDAT to analyse arbuscular mycorrhizal fungal communities using sequence data from different marker regions"

May