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| Author(s): |
Luiz Thibério Lira Diniz Rangel
Total Authors: 1
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| Document type: | Doctoral Thesis |
| Press: | São Paulo. |
| Institution: | Universidade de São Paulo (USP). Instituto de Matemática e Estatística (IME/SBI) |
| Defense date: | 2017-08-10 |
| Examining board members: |
João Carlos Setubal;
Daniel José Galafasse Lahr;
Emanuel Maltempi de Souza;
Alessandro de Mello Varani;
Paolo Marinho de Andrade Zanotto
|
| Advisor: | João Carlos Setubal |
| Abstract | |
Horizontal Gene Transfer (HGT) is one of main mechanisms of bacterial evolution, affecting virtually all gene families. In this document we identified and assessed putative horizontal transfers of genes from two functional classes from two distinct taxonomic levels. We characterized the distribution and evolution of 45 genes important to N2 fixation among 479 Proteobacteria genomes. We identified five potential distinct acquisitions of such genes by Proteobacteria lineages. The distinct origins are consistently identified in 36 out of the 45 assessed genes. We computed possible horizontal transfers of the 45 genes among the 479 Proteobacteria genomes, and we identified enrichments of HGT, likely related to phylogenetic and ecological signals. We developed a semi-automated pipeline to identify effectors of the Type III Secretion System within Aeromonas, which reported 21 putative effector families distributed among 105 genomes. Among the 21 likely effectors 17 have been described in Aeromonas for the first time, highlighting the sensibility of our pipeline. Our colaborators performed cytotoxicity tests for the 21 likely effector families identified by in silico analysis, and only four did not inhibited Saccharomyces cerevisiae growth. Lastly, we developed a method to cluster gene families according to shared evolutionary history, without the requirement of phylogenetic tree reconstruction, increasing computational efficiency. We applied this proposed method during Aeromonas phylogenetic reconstruction, and it showed up compatible with data available on the literature. (AU) | |
| FAPESP's process: | 12/17196-2 - Phylogenomic Networks and Lateral Gene Transfer |
| Grantee: | Luiz Thibério Lira Diniz Rangel |
| Support Opportunities: | Scholarships in Brazil - Doctorate |