Accessing the Variability of Multicopy Genes in Complex Genomes using Unassembled Next-Generation Sequencing Reads: The Case of Trypanosoma cruzi Multigene Families
João Luís Reis-Cunha, Anderson Coqueiro dos Santos, Samuel Alexandre Pimenta Carvalho, Larissa Pinheiro Marques, Gabriela F Rodrigues-Luiz, Rodrigo P. Baptista, Laila Viana de Almeida, Nathan Ravi Medeiros Honorato, Francisco Pereira Lobo, Vanêssa Gomes Fraga, Lúcia Maria da Cunha Galvão, Lilian Lacerda Bueno, Ricardo Toshio Fujiwara, Mariana Santos Cardoso, Gustavo Cerqueira, Daniella Castanheira Bartholomeu
Abstract
Sequences that have several copies in a genome, such as multicopy-gene families, mobile elements, and microsatellites, are among the most challenging genomic segments to study. They are frequently underestimated in genome assemblies, hampering the correct assessment of these important players in genome evolution and adaptation. Here, we developed a new methodology to estimate variability and copy numbers of repetitive genomic regions and employed it to characterize the T. cruzi multigene families MASP, TcMUC, and transsialidase (TS), which are important virulence factors in this parasite. We showed that multigene families vary in sequence and content among the parasite's lineages, whereas hybrid strains have a higher sequence variability that could be advantageous to the parasite's survivability. By identifying conserved sequences within multigene families, we showed that the mammalian host immune response toward these multigene families is usually focused on the TS multigene family. These TS conserved and immunogenic peptides can be explored in future works as diagnostic targets or vaccine candidates for Chagas disease. Finally, this methodology can be easily applied to any organism of interest, which will aid in our understanding of complex genomic regions.