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Ensembl Protists: Comparative genomics data in Ensembl Protists

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Ensembl Protists: Comparative genomics data in Ensembl Protists

The protist species L. panamensis is the main causative agent of tegumentary leishmaniasis in Panama and Colombia. In Panama, there are about 3,000 new cases per year, 5% of which progress to the mucocutaneous presentation. The condition occurs when parasites may occasionally migrate to nasopharyngeal tissues leading to highly disfiguring lesions (Llanes et al., 2015; https://doi.org/10.1038/srep08550) We will use the LPMP_140880 gene, a glutathione synthetase in Leishmania panamensis str. MHOM/PA/94/PSC-1 (GCA_000755165.1) as a reference to find the following information:

  1. Find the Ensembl gene tree ID. How many speciation and duplication nodes does it have?
  2. How many orthologues does Leishmania panamensis have? What type of orthologues are they?
  3. Does this species have an orthologue in Leishmania major? If so, what is the gene ID and coordinates in Leishmania major?
  4. View the protein alignment of the Leishmania major orthologue.
  5. What are the peptide IDs for the translations in Leishmania panamensis str. MHOM/PA/94/PSC-1 (GCA_000755165.1) and Leishmania major?

  1. Go to Ensembl Protists, search for LPMP_140880 gene in Leishmania panamensis str. MHOM/PA/94/PSC-1 (GCA_000755165.1).

  2. Click on orthologues on the left hand side of the gene tab.

  3. Filter for Leishmania major in the second table.

  4. Click on Ensembl stable ID for Leishmania major and select view protein alignment.

  5. The peptide ID’s are given in the summary table above the protein alignments.