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Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs
Leishmania parasites are the causative of leishmaniasis, a group of potentially fatal human diseases. Control strategies for leishmaniasis can be enhanced by genome based investigations. The publication in 2005 of the Leishmania major genome sequence, and two years later the genomes for the species...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2017
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5741766/ https://www.ncbi.nlm.nih.gov/pubmed/29273719 http://dx.doi.org/10.1038/s41598-017-18374-y |
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author | González-de la Fuente, Sandra Peiró-Pastor, Ramón Rastrojo, Alberto Moreno, Javier Carrasco-Ramiro, Fernando Requena, Jose M. Aguado, Begoña |
author_facet | González-de la Fuente, Sandra Peiró-Pastor, Ramón Rastrojo, Alberto Moreno, Javier Carrasco-Ramiro, Fernando Requena, Jose M. Aguado, Begoña |
author_sort | González-de la Fuente, Sandra |
collection | PubMed |
description | Leishmania parasites are the causative of leishmaniasis, a group of potentially fatal human diseases. Control strategies for leishmaniasis can be enhanced by genome based investigations. The publication in 2005 of the Leishmania major genome sequence, and two years later the genomes for the species Leishmania braziliensis and Leishmania infantum were major milestones. Since then, the L. infantum genome, although highly fragmented and incomplete, has been used widely as the reference genome to address whole transcriptomics and proteomics studies. Here, we report the sequencing of the L. infantum genome by two NGS methodologies and, as a result, the complete genome assembly on 36 contigs (chromosomes). Regarding the present L. infantum genome-draft, 495 new genes have been annotated, a hundred have been corrected and 75 previous annotated genes have been discontinued. These changes are not only the result of an increase in the genome size, but a significant contribution derives from the existence of a large number of incorrectly assembled regions in current chromosomal scaffolds. Furthermore, an improved assembly of tandemly repeated genes has been obtained. All these analyses support that the de novo assembled L. infantum genome represents a robust assembly and should replace the currently available in the databases. |
format | Online Article Text |
id | pubmed-5741766 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-57417662018-01-03 Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs González-de la Fuente, Sandra Peiró-Pastor, Ramón Rastrojo, Alberto Moreno, Javier Carrasco-Ramiro, Fernando Requena, Jose M. Aguado, Begoña Sci Rep Article Leishmania parasites are the causative of leishmaniasis, a group of potentially fatal human diseases. Control strategies for leishmaniasis can be enhanced by genome based investigations. The publication in 2005 of the Leishmania major genome sequence, and two years later the genomes for the species Leishmania braziliensis and Leishmania infantum were major milestones. Since then, the L. infantum genome, although highly fragmented and incomplete, has been used widely as the reference genome to address whole transcriptomics and proteomics studies. Here, we report the sequencing of the L. infantum genome by two NGS methodologies and, as a result, the complete genome assembly on 36 contigs (chromosomes). Regarding the present L. infantum genome-draft, 495 new genes have been annotated, a hundred have been corrected and 75 previous annotated genes have been discontinued. These changes are not only the result of an increase in the genome size, but a significant contribution derives from the existence of a large number of incorrectly assembled regions in current chromosomal scaffolds. Furthermore, an improved assembly of tandemly repeated genes has been obtained. All these analyses support that the de novo assembled L. infantum genome represents a robust assembly and should replace the currently available in the databases. Nature Publishing Group UK 2017-12-22 /pmc/articles/PMC5741766/ /pubmed/29273719 http://dx.doi.org/10.1038/s41598-017-18374-y Text en © The Author(s) 2017 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article González-de la Fuente, Sandra Peiró-Pastor, Ramón Rastrojo, Alberto Moreno, Javier Carrasco-Ramiro, Fernando Requena, Jose M. Aguado, Begoña Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs |
title | Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs |
title_full | Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs |
title_fullStr | Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs |
title_full_unstemmed | Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs |
title_short | Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs |
title_sort | resequencing of the leishmania infantum (strain jpcm5) genome and de novo assembly into 36 contigs |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5741766/ https://www.ncbi.nlm.nih.gov/pubmed/29273719 http://dx.doi.org/10.1038/s41598-017-18374-y |
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