Transposable element-rich regions in genomes of Neocosmospora clinical isolates
Transposable elements (TEs) are repetitive DNA elements that can integrate into new genomic locations, contributing to the genome plasticity of fungi. Tes are classified into retrotransposons and DNA transposons based on their transposition intermediate. In some fungal pathogens, regions with a high...
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| Formato: | tesis de maestría |
| Estado: | Versión aceptada para publicación |
| Fecha de publicación: | 2023 |
| País: | Colombia |
| Recursos: | Universidad de los Andes |
| Repositorio: | Séneca: repositorio Uniandes |
| Idioma: | inglés |
| OAI Identifier: | oai:repositorio.uniandes.edu.co:1992/73285 |
| Acesso em linha: | https://hdl.handle.net/1992/73285 |
| Access Level: | acceso abierto |
| Palavra-chave: | Genome organization Compartmentalization Virulence Genome adaptability Microbiología |
| Resumo: | Transposable elements (TEs) are repetitive DNA elements that can integrate into new genomic locations, contributing to the genome plasticity of fungi. Tes are classified into retrotransposons and DNA transposons based on their transposition intermediate. In some fungal pathogens, regions with a high proportion of TEs are associated with putative virulence factors. Neocosmospora is a trans-kingdom pathogen that can infect plants, animals, and humans. To our knowledge, no previous study has analyzed the genomes of Neocosmospora clinical isolates. For that reason, this project aimed to characterize transposable elements in the genomes of Neocosmospora spp. clinical isolates and compare them with non-clinical isolates. To achieve this goal, we sequenced and assembled genomes of Neocosmospora clinical isolates and used contiguous assemblies of other isolates available in GenBank. We identified and classified TEs on these genomes, and identified and characterized the genes associated with TE-rich regions. To the best of our knowledge, this is the first study that has sequenced and analyzed the genome assemblies of clinical isolates of Neocosmospora and provided the first genome assemblies of N. petroliphila and N. lichenicola. We found that there is a high variance in TEs content both within and between species. Also, TE-rich regions are associated with putative genes related to biosynthesis gene clusters (BGCs), azole resistance, and the acquisition of nitrogen, iron, zinc, and copper. Based on our results, we hypothesized that 1) compartmentalization of Neocosmospora core chromosomes based on changes in TEs distribution could be more relevant than LS-chromosomes in lifestyle adaptation; and 2) TE de-repression in Neocosmospora could be mediated by nutrient starvation. |
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