Navigating Artemis using the example of pathogenicity islands with Dr. Anna Protasio
In this Step, we will use Artemis. We will isolate a region of interest in the Salmonella typhi genome. We will analyse this region and save it in various file formats.
In order to reinforce our learning, there is an exercise for you to try before or after watching the video.
We will use the genome (St.dna) and annotation (St.tab) introduced in earlier steps. If you need to download these files, you can do so now: ftp://ftp.sanger.ac.uk/pub/resources/coursesandconferences/Online_Courses/Course3/data/S_typhi.dna and ftp://ftp.sanger.ac.uk/pub/resources/coursesandconferences/Online_Courses/Course3/data/S_typhi.tab
You may need to copy and paste the links in your internet browser and download the files using your browser. We recommend use of Chrome or Firefox browsers for downloading data files.
Still having problems with FTP download?
Most popular browsers no longer support download of data from FTP sites. If you are having trouble downloading the files from the FTP site, we advice you to use a FTP client such as cyberduck (https://cyberduck.io). It is Free and there are versions for Mac and Windows operating systems.
Open the St.dna file and load the annotation from the St.tab file. Use the Navigation to go to position 4409511. The region we are looking at is defined as a Salmonella pathogenicity island (SPI). SPI-7, or the major Vi pathogenicity island, is ~134 kb in length and contains ~30 kb of integrated bacteriophage. The region you should be looking at is shown below and is a classical example of a Salmonella pathogenicity island (SPI).
The definitions of what constitutes a pathogenicity island are quite diverse. However, below is a list of characteristics which are commonly seen within these regions, as described by Hacker et al., 1997 in their review Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. https://onlinelibrary.wiley.com/doi/epdf/10.1046/j.1365-2958.1997.3101672.x
- Often inserted alongside stable RNAs
- Atypical G+C contents.
- Carry virulence-related functions
- Often carry genes encoding transposase or integrase-like proteins
- Unstable and capable of changing location in the genome (jumping DNA)
- Of limited phylogenetic distribution
Pathogenicity islands are important genomic regions. They contain genes that contribute to the virulence of the bacterium. These genes can have a direct effect by making bacteria more virulent or by controlling the expression of genes found outside the pathogenicity islands.
In order to study this pathogenicity island in depth, we will isolate the region that contains its sequence and its annotation.
Watch the screencast above to learn how to do these steps and learn more about pathogenicity islands.
Bacterial Genomes II: Accessing and Analysing Microbial Genome Data Using Artemis
Bacterial Genomes II: Accessing and Analysing Microbial Genome Data Using Artemis
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