A phylogenomic study quantifies competing mechanisms for pseudogenization in prokaryotes-The Mycobacterium leprae case

Eliran Avni, Dennis Montoya, David Lopez, Robert Modlin, Matteo Pellegrini, Sagi Snir

Research output: Contribution to journalArticlepeer-review


Background Pseudogenes are non-functional sequences in the genome with homologous sequences that are functional (i.e. genes). They are abundant in eukaryotes where they have been extensively investigated, while in prokaryotes they are significantly scarcer and less well studied. Here we conduct a comprehensive analysis of the evolution of orthologs of Mycobacterium leprae pseudogenes in prokaryotes. The leprosy pathogen M. leprae is of particular interest since it contains an unusually large number of pseudogenes, comprising approximately 40% of its entire genome. The analysis is conducted in both broad and narrow phylogenetic ranges. Results We have developed an informatics-based approach to characterize the evolution of pseudogenes. This approach combines tools from phylogenomics, genomics, and transcriptomics. The results we obtain are used to assess the contributions of two mechanisms for pseudogene formation: failed horizontal gene transfer events and disruption of native genes. Conclusions We conclude that, although it was reported that in most bacteria the former is most likely responsible for the majority of pseudogenization events, in mycobacteria, and in particular in M. leprae with its exceptionally high pseudogene numbers, the latter predominates. We believe that our study sheds new light on the evolution of pseudogenes in bacteria, by utilizing new methodologies that are applied to the unusually abundant M. leprae pseudogenes and their orthologs.

Original languageEnglish
Article numbere0204322
JournalPLoS ONE
Issue number11
StatePublished - Nov 2018

Bibliographical note

Publisher Copyright:
© 2018 Avni et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

ASJC Scopus subject areas

  • General Biochemistry, Genetics and Molecular Biology
  • General Agricultural and Biological Sciences
  • General


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