A phylogenomic study quantifies competing mechanisms for pseudogenization in prokaryotes—The Mycobacterium leprae case
| العنوان: | A phylogenomic study quantifies competing mechanisms for pseudogenization in prokaryotes—The Mycobacterium leprae case |
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| المؤلفون: | Matteo Pellegrini, Sagi Snir, Dennis Montoya, Eliran Avni, Robert L. Modlin, David Lopez |
| المساهمون: | Robinson-Rechavi, Marc |
| المصدر: | Avni, Eliran; Montoya, Dennis; Lopez, David; Modlin, Robert; Pellegrini, Matteo; & Snir, Sagi. (2018). A phylogenomic study quantifies competing mechanisms for pseudogenization in prokaryotes-The Mycobacterium leprae case.. PloS one, 13(11), e0204322. doi: 10.1371/journal.pone.0204322. UCLA: Retrieved from: http://www.escholarship.org/uc/item/0p15g5s3 PloS one, vol 13, iss 11 PLoS ONE, Vol 13, Iss 11, p e0204322 (2018) PLoS ONE |
| بيانات النشر: | Public Library of Science (PLoS), 2018. |
| سنة النشر: | 2018 |
| مصطلحات موضوعية: | Evolutionary Genetics, 0301 basic medicine, Gene Transfer, lcsh:Medicine, Genome, 0302 clinical medicine, Phylogenomics, Fungal Evolution, 2.2 Factors relating to the physical environment, Aetiology, lcsh:Science, Mycobacterium leprae, Phylogeny, Data Management, Horizontal Gene Transfer, Multidisciplinary, biology, Bacterial, Phylogenetic Analysis, Genomics, Mycobacterium Leprae, Phylogenetics, Actinobacteria, Horizontal gene transfer, Pseudogenes, Research Article, Computer and Information Sciences, Evolutionary Processes, Gene Transfer, Horizontal, Evolution, General Science & Technology, Pseudogene, Mycology, Genome Complexity, Horizontal, Evolution, Molecular, 03 medical and health sciences, Gene Types, Leprosy, MD Multidisciplinary, Genetics, Humans, Evolutionary Systematics, Gene, Taxonomy, Evolutionary Biology, Bacteria, lcsh:R, Organisms, Biology and Life Sciences, Computational Biology, Molecular, biology.organism_classification, Good Health and Well Being, 030104 developmental biology, Evolutionary biology, lcsh:Q, Mycobacterium Tuberculosis, Genome, Bacterial, 030217 neurology & neurosurgery |
| الوصف: | Author(s): Avni, Eliran; Montoya, Dennis; Lopez, David; Modlin, Robert; Pellegrini, Matteo; Snir, Sagi | Abstract: BackgroundPseudogenes 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.ResultsWe 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.ConclusionsWe 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. |
| وصف الملف: | application/pdf |
| تدمد: | 1932-6203 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::38c09238f6df9bd72bdc785f6d56c289 https://doi.org/10.1371/journal.pone.0204322 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....38c09238f6df9bd72bdc785f6d56c289 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 19326203 |
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