Background
Oomycetes is a group of Eukaryotic microorganisms that includes many different pathogens. One of these pathogens, Phytophtora infestans, is the most destructive pathogen of many different crops, in particular potato - an integral part of much of the world’s food supply. The species P. infestans and other Oomycetes are therefore important to study, and their ability to invade host species make the them interesting to study from an industrial perspective.
Potato leaflet infected by P. infestans. By Howard F. Schwartz, Colorado State University, United States
Several genes of oomycetes have been studies before, and specifically chitin synthase (CHS), an enzyme involved in building up the cell walls. In order to get a better understanding of these genes, the genome of the species of interest needs to be assembled, and the species on which we will focus is P. andina which has been proved to be a hybrid of P. infestans and other unknown Phytophtora species.
The data
In order to assemble the genome of P. andina, sequencing data is needed. Provided in this project is sequencing data deposited att UppMax (cluster-based super computer in Uppsala) including both Illumina reads and CHS genes.
The goal
Using the deposited sequence data, our goal is to assemble contigs based on the data, identify CHS genes and then compare these genes to those of P. infestans. Additionally, the aim is to compare the largest obtained contigs in the assembly, with the corresponding parts of the P. infestans genome published in 2009. Lastly, we aim to determine whether P. andina, as mentioned a hybrid between P. infestans and other Phytophtora species, can contribute with information to the study.