marcusnizalvarez/PhD-Thesis

Abstract: Development of a user-friendly computational tool for analyzing low-coverage genomic sequencing data and application in population genetics studies Advances in genomic sequencing technologies in recent years have significantly reduced the cost of this technique. However, large-scale projects still present high costs, often impractical. An alternative strategy is low-coverage whole-genome sequencing (lcWGS). This study aimed to evaluate the genotyping performance in various scenarios using a specific program for lcWGS data that was developed with a complete workflow optimized for low- coverage sequencing genotyping. Parameters such as sequencing depth and sample size were tested to evaluate the performance of this tool. The results demonstrated that properly processed lcWGS data have satisfactory genotyping reliability and great potential for large- scale genotyping studies. Subsequently, the developed tool, entitled LCSeqTools, was applied in a second study, in which samples of Nyssorhynchus darlingi collected in the municipality of Mâncio Lima, Acre state, were used to detect chromosome inversions. The objective was to test the capacity and accuracy of detecting chromosome inversions using lcWGS data, as well as to contribute to a better understanding of the inversions in the genome of Ny. darlingi, as well as the structure and dynamics of this species genome. Ten chromosome inversions were detected in the genome of Ny. darlingi, and comparative genomic analysis revealed no inversions in synteny with known inversions of Anopheles gambiae.