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Accessing the Variability of Multicopy Genes in Complex Genomes using Unassembled Next-Generation Sequencing Reads: The Case of Trypanosoma cruzi Multigene Families
Repetitive elements cause assembly fragmentation in complex eukaryotic genomes, limiting the study of their variability. The genome of Trypanosoma cruzi, the parasite that causes Chagas disease, has a high repetitive content, including multigene families. Although many T. cruzi multigene families en...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society for Microbiology
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9765020/ https://www.ncbi.nlm.nih.gov/pubmed/36264102 http://dx.doi.org/10.1128/mbio.02319-22 |
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author | Reis-Cunha, João Luís Coqueiro-dos-Santos, Anderson Pimenta-Carvalho, Samuel Alexandre Marques, Larissa Pinheiro Rodrigues-Luiz, Gabriela F. Baptista, Rodrigo P. de Almeida, Laila Viana Honorato, Nathan Ravi Medeiros Lobo, Francisco Pereira Fraga, Vanessa Gomes Galvão, Lucia Maria da Cunha Bueno, Lilian Lacerda Fujiwara, Ricardo Toshio Cardoso, Mariana Santos Cerqueira, Gustavo Coutinho Bartholomeu, Daniella C. |
author_facet | Reis-Cunha, João Luís Coqueiro-dos-Santos, Anderson Pimenta-Carvalho, Samuel Alexandre Marques, Larissa Pinheiro Rodrigues-Luiz, Gabriela F. Baptista, Rodrigo P. de Almeida, Laila Viana Honorato, Nathan Ravi Medeiros Lobo, Francisco Pereira Fraga, Vanessa Gomes Galvão, Lucia Maria da Cunha Bueno, Lilian Lacerda Fujiwara, Ricardo Toshio Cardoso, Mariana Santos Cerqueira, Gustavo Coutinho Bartholomeu, Daniella C. |
author_sort | Reis-Cunha, João Luís |
collection | PubMed |
description | Repetitive elements cause assembly fragmentation in complex eukaryotic genomes, limiting the study of their variability. The genome of Trypanosoma cruzi, the parasite that causes Chagas disease, has a high repetitive content, including multigene families. Although many T. cruzi multigene families encode surface proteins that play pivotal roles in host-parasite interactions, their variability is currently underestimated, as their high repetitive content results in collapsed gene variants. To estimate sequence variability and copy number variation of multigene families, we developed a read-based approach that is independent of gene-specific read mapping and de novo assembly. This methodology was used to estimate the copy number and variability of MASP, TcMUC, and Trans-Sialidase (TS), the three largest T. cruzi multigene families, in 36 strains, including members of all six parasite discrete typing units (DTUs). We found that these three families present a specific pattern of variability and copy number among the distinct parasite DTUs. Inter-DTU hybrid strains presented a higher variability of these families, suggesting that maintaining a larger content of their members could be advantageous. In addition, in a chronic murine model and chronic Chagasic human patients, the immune response was focused on TS antigens, suggesting that targeting TS conserved sequences could be a potential avenue to improve diagnosis and vaccine design against Chagas disease. Finally, the proposed approach can be applied to study multicopy genes in any organism, opening new avenues to access sequence variability in complex genomes. |
format | Online Article Text |
id | pubmed-9765020 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Society for Microbiology |
record_format | MEDLINE/PubMed |
spelling | pubmed-97650202022-12-21 Accessing the Variability of Multicopy Genes in Complex Genomes using Unassembled Next-Generation Sequencing Reads: The Case of Trypanosoma cruzi Multigene Families Reis-Cunha, João Luís Coqueiro-dos-Santos, Anderson Pimenta-Carvalho, Samuel Alexandre Marques, Larissa Pinheiro Rodrigues-Luiz, Gabriela F. Baptista, Rodrigo P. de Almeida, Laila Viana Honorato, Nathan Ravi Medeiros Lobo, Francisco Pereira Fraga, Vanessa Gomes Galvão, Lucia Maria da Cunha Bueno, Lilian Lacerda Fujiwara, Ricardo Toshio Cardoso, Mariana Santos Cerqueira, Gustavo Coutinho Bartholomeu, Daniella C. mBio Research Article Repetitive elements cause assembly fragmentation in complex eukaryotic genomes, limiting the study of their variability. The genome of Trypanosoma cruzi, the parasite that causes Chagas disease, has a high repetitive content, including multigene families. Although many T. cruzi multigene families encode surface proteins that play pivotal roles in host-parasite interactions, their variability is currently underestimated, as their high repetitive content results in collapsed gene variants. To estimate sequence variability and copy number variation of multigene families, we developed a read-based approach that is independent of gene-specific read mapping and de novo assembly. This methodology was used to estimate the copy number and variability of MASP, TcMUC, and Trans-Sialidase (TS), the three largest T. cruzi multigene families, in 36 strains, including members of all six parasite discrete typing units (DTUs). We found that these three families present a specific pattern of variability and copy number among the distinct parasite DTUs. Inter-DTU hybrid strains presented a higher variability of these families, suggesting that maintaining a larger content of their members could be advantageous. In addition, in a chronic murine model and chronic Chagasic human patients, the immune response was focused on TS antigens, suggesting that targeting TS conserved sequences could be a potential avenue to improve diagnosis and vaccine design against Chagas disease. Finally, the proposed approach can be applied to study multicopy genes in any organism, opening new avenues to access sequence variability in complex genomes. American Society for Microbiology 2022-10-20 /pmc/articles/PMC9765020/ /pubmed/36264102 http://dx.doi.org/10.1128/mbio.02319-22 Text en Copyright © 2022 Reis-Cunha et al. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Research Article Reis-Cunha, João Luís Coqueiro-dos-Santos, Anderson Pimenta-Carvalho, Samuel Alexandre Marques, Larissa Pinheiro Rodrigues-Luiz, Gabriela F. Baptista, Rodrigo P. de Almeida, Laila Viana Honorato, Nathan Ravi Medeiros Lobo, Francisco Pereira Fraga, Vanessa Gomes Galvão, Lucia Maria da Cunha Bueno, Lilian Lacerda Fujiwara, Ricardo Toshio Cardoso, Mariana Santos Cerqueira, Gustavo Coutinho Bartholomeu, Daniella C. Accessing the Variability of Multicopy Genes in Complex Genomes using Unassembled Next-Generation Sequencing Reads: The Case of Trypanosoma cruzi Multigene Families |
title | Accessing the Variability of Multicopy Genes in Complex Genomes using Unassembled Next-Generation Sequencing Reads: The Case of Trypanosoma cruzi Multigene Families |
title_full | Accessing the Variability of Multicopy Genes in Complex Genomes using Unassembled Next-Generation Sequencing Reads: The Case of Trypanosoma cruzi Multigene Families |
title_fullStr | Accessing the Variability of Multicopy Genes in Complex Genomes using Unassembled Next-Generation Sequencing Reads: The Case of Trypanosoma cruzi Multigene Families |
title_full_unstemmed | Accessing the Variability of Multicopy Genes in Complex Genomes using Unassembled Next-Generation Sequencing Reads: The Case of Trypanosoma cruzi Multigene Families |
title_short | Accessing the Variability of Multicopy Genes in Complex Genomes using Unassembled Next-Generation Sequencing Reads: The Case of Trypanosoma cruzi Multigene Families |
title_sort | accessing the variability of multicopy genes in complex genomes using unassembled next-generation sequencing reads: the case of trypanosoma cruzi multigene families |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9765020/ https://www.ncbi.nlm.nih.gov/pubmed/36264102 http://dx.doi.org/10.1128/mbio.02319-22 |
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