Bioinformatics applied to the genomic study of Cnidarian parasites of the subphylum Myxozoa

• Grant number: 23/12298-6
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: November 01, 2023
• End date: October 31, 2025
• Field of knowledge: Agronomical Sciences - Fishery Resources and Fishery Engineering - Inland Water Fishery Resources
• Principal Investigator: Edson Aparecido Adriano
• Grantee: Amr Galal Abdelraheem Ibrahim
• Host Institution: Instituto de Ciências Ambientais, Químicas e Farmacêuticas (ICAQF). Universidade Federal de São Paulo (UNIFESP). Campus Diadema. Diadema , SP, Brazil
• Associated research grant: 18/24980-8 - Myxozoa - cnidarians adapted to parasitismo: integrating different tools to investigate diversity, evolutionary history, development, and host-parasite interactions, AP.BTA.TEM

Abstract

Currently, much molecular data available for evolutionary analysis within Myxozoa is based on the sequencing of the small subunit ribosomal DNA (SSU-rDNA). This restriction of molecular markers available for the study of this group has made comparisons and corroborations of phylogenetic inferences difficult and is still an important challenge for this area of research. Thus, with the aim of producing genomic data for the phylogenetic hypotheses of Myxozoa, we propose the use of Next Generation Sequencing (NGS), in an approach still unpublished in fish parasites in Brazil, but widely used in several other groups of organisms. To this end, with the objective of taxonomic and evolutionary studies, focusing on different levels of classification and on the analysis of intraspecific genetic variability, two different NGS approaches are proposed: (1) sequence capture of Ultraconserved Elements (Ultraconserved Elements-UCEs, in English); and (2) DNA sequencing associated with the restriction site (Restriction site Associated DNA sequencing-RadSeq, in English). The ECUs, due to their universality and low cost, when compared to the amount of data available, have become an important means of obtaining data for evolutionary analyses. This method allows many homologous markers to be sequenced in a set of species with little genomic resources available. As it is obtained from DNA, it enables the efficient sequencing of hundreds of loci, with great efficiency in evolutionary analyses, being a tool with strong potential for reconstructing the evolutionary history of myxozoans, allowing comparison and validation, or not, of hypotheses phylogenetics of the different Myxozoa lineages supported so far by analysis based on SSU-rDNA sequences. The Restriction Site Associated DNA sequencing (RadSeq) method, on the other hand, uses restriction enzymes to digest the entire genome and then sequence from the cut sites of each fragment, a large number of markers are also produced, usually in the thousands, which reflect the evolutionary history of the entire genome, making genetic studies of populations possible in depth and complexity, being feasible for genomes of non-model organisms, with genomes of any size and without the need for a reference genome. Thus, the method allows for studies of wild populations in sophisticated analyses, such as quantitative genetics and phylogeographical studies. Another advantage of RadSeq is that, due to the high number of SNPs produced, genetic parameters and population structure may require a relatively small number of individuals, making it particularly relevant for rare or difficult-to-access species, as is the case with many parasites. This method will also be of great importance in evaluating the existence of genetic variability within Myxozoa populations from different regions and/or hosts, facilitating the identification of parasite lineages. (AU)