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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Autores: González-de la Fuente, Sandra, Peiró-Pastor, Ramón, Rastrojo Lastras, Alberto, Moreno, Javier, Carrasco-Ramiro, Fernando, Requena Rolania, José María, Aguado, Begoña
Tipo de recurso: artículo
Fecha de publicación:2017
País:España
Institución:Universidad Autónoma de Madrid
Repositorio:Biblos-e Archivo. Repositorio Institucional de la UAM
Idioma:inglés
OAI Identifier:oai:repositorio.uam.es:10486/681317
Acceso en línea:http://hdl.handle.net/10486/681317
https://dx.doi.org/10.1038/s41598-017-18374-y
Access Level:acceso abierto
Palabra clave:Leishmania parasites
Infantum
36 contigs
Robust assembly
Biología y Biomedicina / Biología
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spelling Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigsGonzález-de la Fuente, SandraPeiró-Pastor, RamónRastrojo Lastras, AlbertoMoreno, JavierCarrasco-Ramiro, FernandoRequena Rolania, José MaríaAguado, BegoñaLeishmania parasitesInfantum36 contigsRobust assemblyBiología y Biomedicina / BiologíaLeishmania 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 databasesThis work was supported by grants from Proyecto del Ministerio de Economía y Competitividad (SAF2013-47556-R, co-financed with FEDER funds), and the Fondo de Investigaciones Sanitarias (ISCIII-RETIC RD16/0027/0008-FEDER). The CBMSO receives institutional grants from the Fundación Ramón Areces and from the Fundación Banco de SantanderNature Publishing GroupDepartamento de Biología MolecularFacultad de CienciasCentro de Biología Molecular Severo Ochoa (CBM)20172017-12-22research articlehttp://purl.org/coar/resource_type/c_2df8fbb1VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10486/681317https://dx.doi.org/10.1038/s41598-017-18374-yreponame:Biblos-e Archivo. Repositorio Institucional de la UAMinstname:Universidad Autónoma de MadridInglésengopen accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:repositorio.uam.es:10486/6813172026-06-23T12:46:27Z
dc.title.none.fl_str_mv 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
spellingShingle Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs
González-de la Fuente, Sandra
Leishmania parasites
Infantum
36 contigs
Robust assembly
Biología y Biomedicina / Biología
title_short 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_sort Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs
dc.creator.none.fl_str_mv González-de la Fuente, Sandra
Peiró-Pastor, Ramón
Rastrojo Lastras, Alberto
Moreno, Javier
Carrasco-Ramiro, Fernando
Requena Rolania, José María
Aguado, Begoña
author González-de la Fuente, Sandra
author_facet González-de la Fuente, Sandra
Peiró-Pastor, Ramón
Rastrojo Lastras, Alberto
Moreno, Javier
Carrasco-Ramiro, Fernando
Requena Rolania, José María
Aguado, Begoña
author_role author
author2 Peiró-Pastor, Ramón
Rastrojo Lastras, Alberto
Moreno, Javier
Carrasco-Ramiro, Fernando
Requena Rolania, José María
Aguado, Begoña
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Departamento de Biología Molecular
Facultad de Ciencias
Centro de Biología Molecular Severo Ochoa (CBM)
dc.subject.none.fl_str_mv Leishmania parasites
Infantum
36 contigs
Robust assembly
Biología y Biomedicina / Biología
topic Leishmania parasites
Infantum
36 contigs
Robust assembly
Biología y Biomedicina / Biología
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
publishDate 2017
dc.date.none.fl_str_mv 2017
2017-12-22
dc.type.none.fl_str_mv research article
http://purl.org/coar/resource_type/c_2df8fbb1
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/10486/681317
https://dx.doi.org/10.1038/s41598-017-18374-y
url http://hdl.handle.net/10486/681317
https://dx.doi.org/10.1038/s41598-017-18374-y
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Nature Publishing Group
publisher.none.fl_str_mv Nature Publishing Group
dc.source.none.fl_str_mv reponame:Biblos-e Archivo. Repositorio Institucional de la UAM
instname:Universidad Autónoma de Madrid
instname_str Universidad Autónoma de Madrid
reponame_str Biblos-e Archivo. Repositorio Institucional de la UAM
collection Biblos-e Archivo. Repositorio Institucional de la UAM
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.300719

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