Revision and reannotation of the Halomonas elongata DSM 2581T genoma

The genome of the Halomonas elongata type strain DSM 2581, an industrial producer, was reevaluated using the Illumina HiSeq2500 technology. To resolve duplication-associated ambiguities, PCR products were generated and sequenced. Outside of duplications, 72 sequence corrections were required, of whi...

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Autores: Pfeiffer, Friedhelm, Bagyan, Irina, Alfaro-Espinoza, Gabriela, Zamora-Lagos, Maria-A., Habermann, Bianca, Marin-Sanguino, Alberto, Oesterhelt, Dieter, Kunte, Hans Jörg
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2017
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10459.1/467725
Acceso en línea:https://doi.org/10.1002/mbo3.465
https://hdl.handle.net/10459.1/467725
Access Level:acceso abierto
Palabra clave:Frameshift
Genome annotation
Genome sequencing
Halomonas elongata
Halophilic bacteria
Sequence revision
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spelling Revision and reannotation of the Halomonas elongata DSM 2581T genomaPfeiffer, FriedhelmBagyan, IrinaAlfaro-Espinoza, GabrielaZamora-Lagos, Maria-A.Habermann, BiancaMarin-Sanguino, AlbertoOesterhelt, DieterKunte, Hans JörgFrameshiftGenome annotationGenome sequencingHalomonas elongataHalophilic bacteriaSequence revisionThe genome of the Halomonas elongata type strain DSM 2581, an industrial producer, was reevaluated using the Illumina HiSeq2500 technology. To resolve duplication-associated ambiguities, PCR products were generated and sequenced. Outside of duplications, 72 sequence corrections were required, of which 24 were point mutations and 48 were indels of one or few bases. Most of these were associated with polynucleotidestretches (poly-T stretch overestimated in 19 cases, poly-Cunderestimated in 15 cases). These problems may be attributed to using 454 technology for original genoma sequencing. On average, the original genome sequence had only one error in 56 kb. There 10:01 24/3/2025were 23 frameshift error corrections in the 29 protein-coding genes affected by sequence revision. The genome has been subjected to major reannotation in order to substantially increase the annotation quality.John Wiley & Sons2017info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://doi.org/10.1002/mbo3.465https://hdl.handle.net/10459.1/467725reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésReproducció del document publicat a: https://doi.org/10.1002/mbo3.465Microbiology Open, 2017, vol. 6, núm. 4cc-by (c)The Authors, 2017Attribution 4.0 Internationalinfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by/4.0/oai:recercat.cat:10459.1/4677252026-05-29T05:05:01Z
dc.title.none.fl_str_mv Revision and reannotation of the Halomonas elongata DSM 2581T genoma
title Revision and reannotation of the Halomonas elongata DSM 2581T genoma
spellingShingle Revision and reannotation of the Halomonas elongata DSM 2581T genoma
Pfeiffer, Friedhelm
Frameshift
Genome annotation
Genome sequencing
Halomonas elongata
Halophilic bacteria
Sequence revision
title_short Revision and reannotation of the Halomonas elongata DSM 2581T genoma
title_full Revision and reannotation of the Halomonas elongata DSM 2581T genoma
title_fullStr Revision and reannotation of the Halomonas elongata DSM 2581T genoma
title_full_unstemmed Revision and reannotation of the Halomonas elongata DSM 2581T genoma
title_sort Revision and reannotation of the Halomonas elongata DSM 2581T genoma
dc.creator.none.fl_str_mv Pfeiffer, Friedhelm
Bagyan, Irina
Alfaro-Espinoza, Gabriela
Zamora-Lagos, Maria-A.
Habermann, Bianca
Marin-Sanguino, Alberto
Oesterhelt, Dieter
Kunte, Hans Jörg
author Pfeiffer, Friedhelm
author_facet Pfeiffer, Friedhelm
Bagyan, Irina
Alfaro-Espinoza, Gabriela
Zamora-Lagos, Maria-A.
Habermann, Bianca
Marin-Sanguino, Alberto
Oesterhelt, Dieter
Kunte, Hans Jörg
author_role author
author2 Bagyan, Irina
Alfaro-Espinoza, Gabriela
Zamora-Lagos, Maria-A.
Habermann, Bianca
Marin-Sanguino, Alberto
Oesterhelt, Dieter
Kunte, Hans Jörg
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Frameshift
Genome annotation
Genome sequencing
Halomonas elongata
Halophilic bacteria
Sequence revision
topic Frameshift
Genome annotation
Genome sequencing
Halomonas elongata
Halophilic bacteria
Sequence revision
description The genome of the Halomonas elongata type strain DSM 2581, an industrial producer, was reevaluated using the Illumina HiSeq2500 technology. To resolve duplication-associated ambiguities, PCR products were generated and sequenced. Outside of duplications, 72 sequence corrections were required, of which 24 were point mutations and 48 were indels of one or few bases. Most of these were associated with polynucleotidestretches (poly-T stretch overestimated in 19 cases, poly-Cunderestimated in 15 cases). These problems may be attributed to using 454 technology for original genoma sequencing. On average, the original genome sequence had only one error in 56 kb. There 10:01 24/3/2025were 23 frameshift error corrections in the 29 protein-coding genes affected by sequence revision. The genome has been subjected to major reannotation in order to substantially increase the annotation quality.
publishDate 2017
dc.date.none.fl_str_mv 2017
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://doi.org/10.1002/mbo3.465
https://hdl.handle.net/10459.1/467725
url https://doi.org/10.1002/mbo3.465
https://hdl.handle.net/10459.1/467725
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: https://doi.org/10.1002/mbo3.465
Microbiology Open, 2017, vol. 6, núm. 4
dc.rights.none.fl_str_mv cc-by (c)The Authors, 2017
Attribution 4.0 International
info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by/4.0/
rights_invalid_str_mv cc-by (c)The Authors, 2017
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv John Wiley & Sons
publisher.none.fl_str_mv John Wiley & Sons
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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