A de novo transcriptome assembly of the annelid worm Hediste diversicolor

The development of Next-Generation Sequencing (NGS) technologies has revolutionized multiple fields of Biology. The ability to sequence DNA and RNA in an automated, parallel and low-cost approach, was key to boost the applicability and acquisition efficiency of omics resources. In this context, the...

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Autores: Samico, Rodrigo, Machado, André M., Domingues, Marcos, Hagemann, Andreas, Valente, Luisa M. P., Malzahn, Arne M., Gomes-dos-Santos, André, Ruivo, Raquel, Monroig, Óscar, Castro, L. Filipe C.
Tipo de recurso: artículo
Estado:Versión enviada para evaluación y publicación
Fecha de publicación:2022
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/305077
Acceso en línea:http://hdl.handle.net/10261/305077
Access Level:acceso abierto
Palabra clave:Transcriptomes
Ecology
Ragworm
Annelida
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spelling A de novo transcriptome assembly of the annelid worm Hediste diversicolorSamico, RodrigoMachado, André M.Domingues, MarcosHagemann, AndreasValente, Luisa M. P.Malzahn, Arne M.Gomes-dos-Santos, AndréRuivo, RaquelMonroig, ÓscarCastro, L. Filipe C.TranscriptomesEcologyRagwormAnnelidaThe development of Next-Generation Sequencing (NGS) technologies has revolutionized multiple fields of Biology. The ability to sequence DNA and RNA in an automated, parallel and low-cost approach, was key to boost the applicability and acquisition efficiency of omics resources. In this context, the availability of these tools has become indispensable towards our understanding of biodiversity, deepening our knowledge on the distinct complexity levels, from cells to ecosystems. In this study we comprehensively characterised and annotated a whole-body transcriptome of Hediste diversicolor. This annelid worm species belongs to the family Nereididae and inhabits estuarine and lagoon areas on the Atlantic coasts of Europe and North America. Ecologically, this species plays an important role in benthic food webs. The ability of rework sediments through bioturbation activity makes this species essential to the estuarine mechanisms. Here, we used Illumina next-generation sequencing technology, to sequence a total 105 million (M) paired-end (PE) raw reads and produce the first multi-tissue transcriptome assembly of an adult of H. diversicolor. This transcriptome contains 69,335 transcripts with a N50 transcript length of 2,313 bp and a BUSCO gene completeness of 97.7% and 96% (S: 88.2%; D: 7.8%) in Eukaryota and Metazoa lineage-specific profile libraries. Our findings offer a valuable resource for multiple biological studies using this species.This research was partially supported by the ERA-NET BlueBio COFUND Project SIDESTREAM [Grant ID 68], co-funded through national funds provided by FCT [BLUEBIO/0005/2019]; Agencia Estatal de Investigación [PCI2020-111960], NRC – Norwegian Research Council [#311701]. A.G.S. was funded by the Portuguese Foundation for Science and Technology (FCT) under the Grant [SFRH/BD/137935/2018]. Additional strategic funding was provided by FCT [UIDP/04423/2020].NoBioRxivFundação para a Ciência e a Tecnologia (Portugal)Ministerio de Ciencia, Innovación y Universidades (España)Agencia Estatal de Investigación (España)Norwegian Research CouncilConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202320232022info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Preprintinfo:eu-repo/semantics/submittedVersionapplication/pdfhttp://hdl.handle.net/10261/305077reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PCI2020-111960https://doi.org/10.1101/2022.07.20.500767Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3050772026-05-22T06:33:51Z
dc.title.none.fl_str_mv A de novo transcriptome assembly of the annelid worm Hediste diversicolor
title A de novo transcriptome assembly of the annelid worm Hediste diversicolor
spellingShingle A de novo transcriptome assembly of the annelid worm Hediste diversicolor
Samico, Rodrigo
Transcriptomes
Ecology
Ragworm
Annelida
title_short A de novo transcriptome assembly of the annelid worm Hediste diversicolor
title_full A de novo transcriptome assembly of the annelid worm Hediste diversicolor
title_fullStr A de novo transcriptome assembly of the annelid worm Hediste diversicolor
title_full_unstemmed A de novo transcriptome assembly of the annelid worm Hediste diversicolor
title_sort A de novo transcriptome assembly of the annelid worm Hediste diversicolor
dc.creator.none.fl_str_mv Samico, Rodrigo
Machado, André M.
Domingues, Marcos
Hagemann, Andreas
Valente, Luisa M. P.
Malzahn, Arne M.
Gomes-dos-Santos, André
Ruivo, Raquel
Monroig, Óscar
Castro, L. Filipe C.
author Samico, Rodrigo
author_facet Samico, Rodrigo
Machado, André M.
Domingues, Marcos
Hagemann, Andreas
Valente, Luisa M. P.
Malzahn, Arne M.
Gomes-dos-Santos, André
Ruivo, Raquel
Monroig, Óscar
Castro, L. Filipe C.
author_role author
author2 Machado, André M.
Domingues, Marcos
Hagemann, Andreas
Valente, Luisa M. P.
Malzahn, Arne M.
Gomes-dos-Santos, André
Ruivo, Raquel
Monroig, Óscar
Castro, L. Filipe C.
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Fundação para a Ciência e a Tecnologia (Portugal)
Ministerio de Ciencia, Innovación y Universidades (España)
Agencia Estatal de Investigación (España)
Norwegian Research Council
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Transcriptomes
Ecology
Ragworm
Annelida
topic Transcriptomes
Ecology
Ragworm
Annelida
description The development of Next-Generation Sequencing (NGS) technologies has revolutionized multiple fields of Biology. The ability to sequence DNA and RNA in an automated, parallel and low-cost approach, was key to boost the applicability and acquisition efficiency of omics resources. In this context, the availability of these tools has become indispensable towards our understanding of biodiversity, deepening our knowledge on the distinct complexity levels, from cells to ecosystems. In this study we comprehensively characterised and annotated a whole-body transcriptome of Hediste diversicolor. This annelid worm species belongs to the family Nereididae and inhabits estuarine and lagoon areas on the Atlantic coasts of Europe and North America. Ecologically, this species plays an important role in benthic food webs. The ability of rework sediments through bioturbation activity makes this species essential to the estuarine mechanisms. Here, we used Illumina next-generation sequencing technology, to sequence a total 105 million (M) paired-end (PE) raw reads and produce the first multi-tissue transcriptome assembly of an adult of H. diversicolor. This transcriptome contains 69,335 transcripts with a N50 transcript length of 2,313 bp and a BUSCO gene completeness of 97.7% and 96% (S: 88.2%; D: 7.8%) in Eukaryota and Metazoa lineage-specific profile libraries. Our findings offer a valuable resource for multiple biological studies using this species.
publishDate 2022
dc.date.none.fl_str_mv 2022
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Preprint
info:eu-repo/semantics/submittedVersion
format article
status_str submittedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/305077
url http://hdl.handle.net/10261/305077
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PCI2020-111960
https://doi.org/10.1101/2022.07.20.500767
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv BioRxiv
publisher.none.fl_str_mv BioRxiv
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,812429

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