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Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi
Although the genome of Trypanosoma cruzi, the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (the abundance of repetitive sequences and genes organized in tandem) has traditionally hindered...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Microbiology Society
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5994713/ https://www.ncbi.nlm.nih.gov/pubmed/29708484 http://dx.doi.org/10.1099/mgen.0.000177 |
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author | Berná, Luisa Rodriguez, Matias Chiribao, María Laura Parodi-Talice, Adriana Pita, Sebastián Rijo, Gastón Alvarez-Valin, Fernando Robello, Carlos |
author_facet | Berná, Luisa Rodriguez, Matias Chiribao, María Laura Parodi-Talice, Adriana Pita, Sebastián Rijo, Gastón Alvarez-Valin, Fernando Robello, Carlos |
author_sort | Berná, Luisa |
collection | PubMed |
description | Although the genome of Trypanosoma cruzi, the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (the abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This also limits diverse types of analyses that require high degrees of precision. Long reads generated by third-generation sequencing technologies are particularly suitable to address the challenges associated with T. cruzi’s genome since they permit direct determination of the full sequence of large clusters of repetitive sequences without collapsing them. This, in turn, not only allows accurate estimation of gene copy numbers but also circumvents assembly fragmentation. Here, we present the analysis of the genome sequences of two T. cruzi clones: the hybrid TCC (TcVI) and the non-hybrid Dm28c (TcI), determined by PacBio Single Molecular Real-Time (SMRT) technology. The improved assemblies herein obtained permitted us to accurately estimate gene copy numbers, abundance and distribution of repetitive sequences (including satellites and retroelements). We found that the genome of T. cruzi is composed of a ‘core compartment’ and a ‘disruptive compartment’ which exhibit opposite GC content and gene composition. Novel tandem and dispersed repetitive sequences were identified, including some located inside coding sequences. Additionally, homologous chromosomes were separately assembled, allowing us to retrieve haplotypes as separate contigs instead of a unique mosaic sequence. Finally, manual annotation of surface multigene families, mucins and trans-sialidases allows now a better overview of these complex groups of genes. |
format | Online Article Text |
id | pubmed-5994713 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Microbiology Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-59947132018-06-12 Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi Berná, Luisa Rodriguez, Matias Chiribao, María Laura Parodi-Talice, Adriana Pita, Sebastián Rijo, Gastón Alvarez-Valin, Fernando Robello, Carlos Microb Genom Research Article Although the genome of Trypanosoma cruzi, the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (the abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This also limits diverse types of analyses that require high degrees of precision. Long reads generated by third-generation sequencing technologies are particularly suitable to address the challenges associated with T. cruzi’s genome since they permit direct determination of the full sequence of large clusters of repetitive sequences without collapsing them. This, in turn, not only allows accurate estimation of gene copy numbers but also circumvents assembly fragmentation. Here, we present the analysis of the genome sequences of two T. cruzi clones: the hybrid TCC (TcVI) and the non-hybrid Dm28c (TcI), determined by PacBio Single Molecular Real-Time (SMRT) technology. The improved assemblies herein obtained permitted us to accurately estimate gene copy numbers, abundance and distribution of repetitive sequences (including satellites and retroelements). We found that the genome of T. cruzi is composed of a ‘core compartment’ and a ‘disruptive compartment’ which exhibit opposite GC content and gene composition. Novel tandem and dispersed repetitive sequences were identified, including some located inside coding sequences. Additionally, homologous chromosomes were separately assembled, allowing us to retrieve haplotypes as separate contigs instead of a unique mosaic sequence. Finally, manual annotation of surface multigene families, mucins and trans-sialidases allows now a better overview of these complex groups of genes. Microbiology Society 2018-04-30 /pmc/articles/PMC5994713/ /pubmed/29708484 http://dx.doi.org/10.1099/mgen.0.000177 Text en © 2018 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open access article under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Berná, Luisa Rodriguez, Matias Chiribao, María Laura Parodi-Talice, Adriana Pita, Sebastián Rijo, Gastón Alvarez-Valin, Fernando Robello, Carlos Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi |
title | Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi |
title_full | Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi |
title_fullStr | Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi |
title_full_unstemmed | Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi |
title_short | Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi |
title_sort | expanding an expanded genome: long-read sequencing of trypanosoma cruzi |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5994713/ https://www.ncbi.nlm.nih.gov/pubmed/29708484 http://dx.doi.org/10.1099/mgen.0.000177 |
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