Using ACT to find pseudogenes in two Mycobacterial species

Please note: Our previous course “Bacterial Genomes: accessing and analysing microbial genome data” is a recommended pre-requisite for this part of the course. It is open for joining and access during the 3 week, live presentation of this course, and then closes until the next live presentation

In the previous course, we explored the genome of two the Mycobacterial species, Mycobacterium leprae and Mycobacterium tuberculosis. Despite being from the same genus these two bacterial species had very different genomes. We looked at the genes in both species for evidence of reductive evolution that M. leprae had undergone resulting in the accumulation of pseudogenes. Pseudogenes are non-functional genes characterised by and identified by the presence of premature stop codons. The only accurate way to determine if the genes are non-functional, is to use another similar genome to determine if they are indeed pseudogenes. In this instance we used M. tuberculosis.

In this step, we will be using ACT to compare the to M. tuberculosis and M. leprae and see if can identify the pseudogenes you found in the previous course. If you do not have these written down, do not worry; you can use the scroll buttons and the synteny colours to identify potential pseudogenes in M.leprae compared to their functional counterparts in M. tuberculosis.

To refresh your knowledge on the types of genes that have undergone reductive evolution in M. leprae, you can find the article here: Mycobacterium leprae: genes, pseudogenes and genetic diversity. Singh, P. and S. T. Cole (2011).

Be sure to concentrate on the following sections in the article :

  • Introduction
  • Genome Biology
  • Physiology & Biochemistry
  • Reductive evolution
  • Pseudogenes and Transcription of pseudogenes.

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This article is from the free online course:

Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT)

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