Genomic analysis of marine Halophythophthoras and comparison of their genetic capacity and gene organization with terrestrial relatives

Phytophthora and Pythium are well known and studied groups of oomycetes, fungus-like microorganisms. They are common in terrestrial habitats and many species have a high impact on the economy as they are plant pathogens, for example Phytophthora infestans is the cause of potato blight. Marine Halophythophthoras, on the contrary, are hardly studied. Some species have been described and their phylogeny studied based on three gene markers, but knowledge on the functional and ecological traits remains minimal. Some researchers consider them saprophytes while others think they are pathogens.

The aim of the project is to analyse shotgun metagenomic high throughput sequences  of two isolated strains (cultured in the laboratories of University of Algarve) in order to investigate if Halophythophthoras can have an impact on marine macrophytes. After assessing if the genome sequences are, as we expect them to be, from two different strains, the data will be used to reconstruct the mitochondrial genome and, as much as possible, the nuclear genome as well. In addition, the reconstructed genomes will be compared to sequenced terrestrial oomycetes to investigate the phylogenetic position of the new isolates, the similarity in genomic capacity and gene organization between terrestrial and marine species (main focus on pathogenic genes). If enough data is available a metabolic model will be constructed identifying what metabolic capacities the isolates have. Lastly, the microbiome composition and function associated with the isolates will be explored. The analysis will be carried out using online (meta)genomic softwares; an introduction to genomic approaches will be carried out before the beginning of the analysis.

Additional costs to be covered by the student: