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SANTIAGO, Caio Rafael do Nascimento. GTACG: A computational framework focused on comparative genomics of bacteria from the same evolutionary branch. 2019. 105 p. Thesis (Doctor of Science) – Bioinformatics Graduate Program, University of São Paulo, São Paulo, 2019. Research in the field of genomics produces a large amount of data. However, genetic knowledge about certain phenotypes is limited. Besides, a considerable part of the studied genomes has coding sequences (CDSs) with unknown functions, representing an additional challenge for researchers. Organisms from the same evolutionary branch share many of their CDSs, and certain phenotypes specific to a group of these individuals may be the result of a unique set of unique genes. In this work the GTACG computational framework is presented, a user-friendly tool to help researches to identify unique genetic characteristics in subgroups of bacterial genomes that have a common phenotype, finding data that differentiate them from other organisms in a simple way. GTACG analysis is based on the formation of homologous CDS groups based on local alignments. The front end is simple to use, and the package installation is designed to allow users with little knowledge of computer science can do complex analysis using this tool. The validation of the GTACG results was based on two case studies involving a set of 161 genomes of the Xanthomonadaceae family and 45 Streptococcus pyogenes genomes. In the first case study, we attempted to find out why some Xanthomonadaceae are associated with plants and others not, and, in fact, 19 families of orthologous proteins unique to plant-associated genomes were found (representing over 90% of these genomes), allowing the identification of proteins potentially associated with the adaptation and virulence of these bacteria in plant tissues. In the second study, we attempted to find phylogenetic markers for the protein emm of Streptococcus pyogenes, and found 15 families of orthologous proteins that would play this role. In addition, some combined families were also found that could explain some of the diseases caused by Streptococcus pyogenes in humans. The results show the potential use of GTACG to find new research objects for molecular studies of bacterial comparative genomics.

GTACG: um arcabouço computacional focado em genômica comparativa de bactérias de um mesmo ramo evolutivo