The genome sequence of the eastern woodchuck (Marmota monax) - A preclinical animal model for chronic hepatitis B

The Eastern woodchuck (Marmota monax) has been extensively used in research of chronic hepatitis B and liver cancer because its infection with the woodchuck hepatitis virus closely resembles a human hepatitis B virus infection. Development of novel immunotherapeutic approaches requires genetic infor...

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Autores: Alioto, Tyler, Cruz, Fernando, Gómez Garrido, Jèssica, Triyatni, Miriam, Gut, Marta, Frias, Leonor, Esteve-Codina, Anna, Menne, Stephan, Kiialainen, Anna, Kumpesa, Nadine, Birzele, Fabian, Schmucki, Roland, Gut, Ivo Glynne, Spleiss, Olivia
Tipo de documento: artigo
Estado:Versão publicada
Data de publicação:2019
País:España
Recursos:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositório:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/44016
Acesso em linha:http://hdl.handle.net/10230/44016
http://dx.doi.org/10.1534/g3.119.400413
Access Level:Acceso aberto
Palavra-chave:Chronic hepatitis B
Eastern woodchuck
Genome assembly
Hepatocellular carcinoma
Immune response
Marmota monax
Whole genome sequencing
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spelling The genome sequence of the eastern woodchuck (Marmota monax) - A preclinical animal model for chronic hepatitis BAlioto, TylerCruz, FernandoGómez Garrido, JèssicaTriyatni, MiriamGut, MartaFrias, LeonorEsteve-Codina, AnnaMenne, StephanKiialainen, AnnaKumpesa, NadineBirzele, FabianSchmucki, RolandGut, Ivo GlynneSpleiss, OliviaChronic hepatitis BEastern woodchuckGenome assemblyHepatocellular carcinomaImmune responseMarmota monaxWhole genome sequencingThe Eastern woodchuck (Marmota monax) has been extensively used in research of chronic hepatitis B and liver cancer because its infection with the woodchuck hepatitis virus closely resembles a human hepatitis B virus infection. Development of novel immunotherapeutic approaches requires genetic information on immune pathway genes in this animal model. The woodchuck genome was assembled with a combination of high-coverage whole-genome shotgun sequencing of Illumina paired-end, mate-pair libraries and fosmid pool sequencing. The result is a 2.63 Gigabase (Gb) assembly with a contig N50 of 74.5 kilobases (kb), scaffold N50 of 892 kb, and genome completeness of 99.2%. RNA sequencing (RNA-seq) from seven different tissues aided in the annotation of 30,873 protein-coding genes, which in turn encode 41,826 unique protein products. More than 90% of the genes have been functionally annotated, with 82% of them containing open reading frames. This genome sequence and its annotation will enable further research in chronic hepatitis B and hepatocellular carcinoma and contribute to the understanding of immunological responses in the woodchuck.Genetics Society of America202020202019info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/44016http://dx.doi.org/10.1534/g3.119.400413reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésG3 (Bethesda). 2019; 9(12):3943-52© 2019 Alioto et al. This is an open-access article distributed 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 work is properly cited.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/440162026-05-29T05:05:01Z
dc.title.none.fl_str_mv The genome sequence of the eastern woodchuck (Marmota monax) - A preclinical animal model for chronic hepatitis B
title The genome sequence of the eastern woodchuck (Marmota monax) - A preclinical animal model for chronic hepatitis B
spellingShingle The genome sequence of the eastern woodchuck (Marmota monax) - A preclinical animal model for chronic hepatitis B
Alioto, Tyler
Chronic hepatitis B
Eastern woodchuck
Genome assembly
Hepatocellular carcinoma
Immune response
Marmota monax
Whole genome sequencing
title_short The genome sequence of the eastern woodchuck (Marmota monax) - A preclinical animal model for chronic hepatitis B
title_full The genome sequence of the eastern woodchuck (Marmota monax) - A preclinical animal model for chronic hepatitis B
title_fullStr The genome sequence of the eastern woodchuck (Marmota monax) - A preclinical animal model for chronic hepatitis B
title_full_unstemmed The genome sequence of the eastern woodchuck (Marmota monax) - A preclinical animal model for chronic hepatitis B
title_sort The genome sequence of the eastern woodchuck (Marmota monax) - A preclinical animal model for chronic hepatitis B
dc.creator.none.fl_str_mv Alioto, Tyler
Cruz, Fernando
Gómez Garrido, Jèssica
Triyatni, Miriam
Gut, Marta
Frias, Leonor
Esteve-Codina, Anna
Menne, Stephan
Kiialainen, Anna
Kumpesa, Nadine
Birzele, Fabian
Schmucki, Roland
Gut, Ivo Glynne
Spleiss, Olivia
author Alioto, Tyler
author_facet Alioto, Tyler
Cruz, Fernando
Gómez Garrido, Jèssica
Triyatni, Miriam
Gut, Marta
Frias, Leonor
Esteve-Codina, Anna
Menne, Stephan
Kiialainen, Anna
Kumpesa, Nadine
Birzele, Fabian
Schmucki, Roland
Gut, Ivo Glynne
Spleiss, Olivia
author_role author
author2 Cruz, Fernando
Gómez Garrido, Jèssica
Triyatni, Miriam
Gut, Marta
Frias, Leonor
Esteve-Codina, Anna
Menne, Stephan
Kiialainen, Anna
Kumpesa, Nadine
Birzele, Fabian
Schmucki, Roland
Gut, Ivo Glynne
Spleiss, Olivia
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Chronic hepatitis B
Eastern woodchuck
Genome assembly
Hepatocellular carcinoma
Immune response
Marmota monax
Whole genome sequencing
topic Chronic hepatitis B
Eastern woodchuck
Genome assembly
Hepatocellular carcinoma
Immune response
Marmota monax
Whole genome sequencing
description The Eastern woodchuck (Marmota monax) has been extensively used in research of chronic hepatitis B and liver cancer because its infection with the woodchuck hepatitis virus closely resembles a human hepatitis B virus infection. Development of novel immunotherapeutic approaches requires genetic information on immune pathway genes in this animal model. The woodchuck genome was assembled with a combination of high-coverage whole-genome shotgun sequencing of Illumina paired-end, mate-pair libraries and fosmid pool sequencing. The result is a 2.63 Gigabase (Gb) assembly with a contig N50 of 74.5 kilobases (kb), scaffold N50 of 892 kb, and genome completeness of 99.2%. RNA sequencing (RNA-seq) from seven different tissues aided in the annotation of 30,873 protein-coding genes, which in turn encode 41,826 unique protein products. More than 90% of the genes have been functionally annotated, with 82% of them containing open reading frames. This genome sequence and its annotation will enable further research in chronic hepatitis B and hepatocellular carcinoma and contribute to the understanding of immunological responses in the woodchuck.
publishDate 2019
dc.date.none.fl_str_mv 2019
2020
2020
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 http://hdl.handle.net/10230/44016
http://dx.doi.org/10.1534/g3.119.400413
url http://hdl.handle.net/10230/44016
http://dx.doi.org/10.1534/g3.119.400413
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv G3 (Bethesda). 2019; 9(12):3943-52
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Genetics Society of America
publisher.none.fl_str_mv Genetics Society of America
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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score 15,81155

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