Using CoGe for the analysis of Plasmodium spp

1.1 Finding about the Plasmodium spp. genomes present in CoGe

The number of Plasmodium genomes available to the public increases yearly. Numerous research groups are working on completing the Plasmodium genome panorama, leading to reposition of diverse genome sequences under diverse levels of completion and originating from a variety of databases. A large number of Plasmodium genomes have been deposited on the National Center for Biotechnology Information (NCBI); however, additional databases such as PlasmoDB ([1]), GeneDB ([2]) and MalAvi ([3]) also carry addiional Plasmodium genome sequences.

In order to attain a better picture of Plasmodium spp. genome evolution, the CoGe platform can be used to perform diverse comparative analyses. Currently, there is a number of Plasmodium genomes available on the CoGe database. You can obtain more about them by following these steps:

1. Go to: [[4]]

2. Create an account/ login into CoGe

3. On the main CoGe page, find the Tools tile and click on to Organism View ([5])

4. Organism View allows the researcher to find all publicly available genomes uploaded into CoGe and browse any corresponding information. You can find any published genome by typing a scientific name into the Search box. For each organism uploaded to CoGe you will find the following information:

Organisms: In the case of Plasmodium spp., the different parasitic strains currently uploaded. Any organelle genomes independently uploaded (mitochondrial and apicoplast) can also be found here.

Organism Information: provides an outline of organisms’ taxonomy (following that published on NCBI), quick links to some of the main CoGe analysis tools, and the search engines were information can be found.

Genomes: All the genome versions for this species. Selecting different genome versions modifies al other output observed in this page; in addition, it allows the user to access to previous versions of a published genome (e.g. access scaffolds from a previous genome version currently under the chromosome assemble level).

Genome information: Shows the genome IDs, type of sequences uploaded and length of the whole genome. In addition, this tab allows the user to directly perform analyses using the CoGe platform.

Datasets: This section will show the number of datasets included for this genome. In the case of completely sequenced Plasmodium genomes, this will indicate the code numbers for the datasets of each individual chromosome.

Dataset information: Provides specific information for each individually selected dataset including. Information includes the accession numbers (if available), source of the upload, chromosome length and GC%.

Chromosomes: Shows the number of available chromosome for the selected genome. However, depending of the methodology used to upload the data into CoGe and the nature of the dataset itself, the count and length of chromosomes shown will be larger than expected (e.g. will show the number of contigs in lieu of the number of chromosomes). For whole sequenced genomes, specific IDs under the Dataset section will showcase the chromosome number and length.

Chromosome information: Shows the chromosome ID and the number of base pairs for that chromosome.

5. Under Genome Information, clicking on the Genome Info section permits the user to access to a more detailed genome description. It also allows access to other quick links to comparative analysis tools available on CoGe.

1.2 Uploading Plasmodium spp. genomes into CoGe

While data can be uploaded into CoGe using a variety of methods, we will focus on the two most relevant for the incorporation of Plasmodium spp. genomes. We will follow each method with an example. For additional information, please check the following link: [[6]]