Genomics and Bioinformatics of Pathogens

We use bioinformatic tools and specialized databases to study rare diseases in humans, using the rat as a model (in collaboration with the lab Genetics and Genomics of Human Hereditary Diseases) and the amoeboid protist Dictyostelium discoideum (in collaboration with the lab Development and Morphogenesis in Dictyostelium discoideum). In these projects, information derived from complete genomes is used to determine the degree of conservation of genes involved in different rare diseases with respect to these laboratory models, as well as to identify sequences that play a role in gene regulation.

The integration of DNA sequence and gene expression analyses with existing medical information allows us to more precisely identify the genetic determinants of these diseases. In addition, to generate new multi-omics data, we are incorporating third-generation sequencing technologies (Oxford Nanopore).

Massively parallel sequencing, also known as next-generation sequencing (NGS), has enabled a leap of several orders of magnitude in the number of genes that can be studied simultaneously. This methodology allows the analysis of an organism’s entire genome, its coding regions (exome), or a selected set of genes of interest (gene panels or targeted sequencing). It is also possible to analyze all genes being expressed in a given cell type or condition (transcriptomics), as well as to study microbial communities in biological samples (metagenomics) and their expression (metatranscriptomics) without the need for isolation or cultivation.

Currently, several platforms and technological developments are available for these large-scale studies. The Oxford Nanopore Sequencing Platform at iB3 is based on nanopores that detect the passage of DNA or RNA molecules. This technology enables the “native” sequencing of DNA or RNA molecules without prior amplification or the need for intermediate sequencing steps, and allows the generation of long reads (10,000 to 50,000 nucleotides).

The production of longer sequences facilitates efficient assembly of genomes, metagenomes, and transcriptomes, reducing computational time and simplifying assembly algorithms. It also enables the resolution of regions containing repetitive sequence motifs, which are difficult to assemble using short-read sequencing technologies. Additionally, it allows real-time sequencing and the detection of methylation patterns.

Our platform supports genomic, metagenomic, transcriptomic, and metatranscriptomic studies using third-generation massively parallel sequencing. Our research lines apply this technology to studies in human, animal, and environmental health, following a One Health approach.

The platform is equipped with advanced instrumentation and staffed by professionals from multiple disciplines, fostering synergy among research groups and promoting the development of biotechnological tools.