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http://hdl.handle.net/10609/99306
Title: Estudio de la estructura poblacional de los géneros Escherichia y Shigella
Author: Chacón Vargas, Lucía
Director: Villanueva Cañas, José Luis
Tutor: Ventura Royo, Carles  
Keywords: comparative genomics
microbiology
phylogeny
Escherichia
Shigella
Issue Date: 5-Jun-2019
Publisher: Universitat Oberta de Catalunya (UOC)
Abstract: Escherichia and Shigella have been deemed as two distinct bacterial genus. However, with the advances in microbiology it has been seen that they are strongly related. A study of the phylogenetic and pangenomic relationships of 14,078 sequences of Escherichia and 1,781 of Shigella has been carried out. Genomic and amino acid sequences from both genus were downloaded of the RefSeq database. Redundant genomic sequences were eliminated and the distance matrix was calculated with MASH. Shigella and Escherichia strains were classified according to the Clermont laboratory algorithm. The corresponding clusters were obtained by genus and by phylogenetic group with UMAP (in R) and with Gephi. Mmseqs2 was used for clustering protein sequences. The pangenome, coregenome and accessory genome were calculated and the corresponding graphs obtained in R. It could be observed very related clusters, suggesting the genomic proximity of both genus. Shigella strains classified as B1 phylogroup (more than 90 % of the total) were located in clusters very close to Escherichia phylogroup B1. The pangenome of both genus together and of each genus separately follows an open distribution. The size of the coregenome decreases as the number of genomes increases. By lowering the threshold to 95% of shared genes, the size of the coregenome remains virtually constant in about 3,000 genes.
Language: Spanish
URI: http://hdl.handle.net/10609/99306
Appears in Collections:Bachelor thesis, research projects, etc.

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