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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 principales: Alioto, Tyler S., 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 G., Spleiss, Olivia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6893209/
https://www.ncbi.nlm.nih.gov/pubmed/31645421
http://dx.doi.org/10.1534/g3.119.400413
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author Alioto, Tyler S.
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 G.
Spleiss, Olivia
author_facet Alioto, Tyler S.
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 G.
Spleiss, Olivia
author_sort Alioto, Tyler S.
collection PubMed
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.
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spelling pubmed-68932092019-12-05 The Genome Sequence of the Eastern Woodchuck (Marmota monax) – A Preclinical Animal Model for Chronic Hepatitis B Alioto, Tyler S. 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 G. Spleiss, Olivia G3 (Bethesda) Genome Report 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. Genetics Society of America 2019-10-23 /pmc/articles/PMC6893209/ /pubmed/31645421 http://dx.doi.org/10.1534/g3.119.400413 Text en Copyright © 2019 Alioto et al. http://creativecommons.org/licenses/by/4.0/ 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.
spellingShingle Genome Report
Alioto, Tyler S.
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 G.
Spleiss, Olivia
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
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_short The Genome Sequence of the Eastern Woodchuck (Marmota monax) – A Preclinical Animal Model for Chronic Hepatitis B
title_sort genome sequence of the eastern woodchuck (marmota monax) – a preclinical animal model for chronic hepatitis b
topic Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6893209/
https://www.ncbi.nlm.nih.gov/pubmed/31645421
http://dx.doi.org/10.1534/g3.119.400413
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