The Genome Sequence of the Eastern Woodchuck (Marmota monax) - A Preclinical Animal Model for Chronic Hepatitis B

被引：12

作者：

Alioto, Tyler S. ^{[1
,2
]}

Cruz, Fernando ^{[1
]}

Gomez-Garrido, Jessica ^{[1
]}

Triyatni, Miriam ^{[3
]}

Gut, Marta ^{[1
,2
]}

Frias, Leonor ^{[1
,2
]}

Esteve-Codina, Anna ^{[1
]}

Menne, Stephan ^{[4
]}

Kiialainen, Anna ^{[3
]}

Kumpesa, Nadine ^{[3
]}

Birzele, Fabian ^{[3
]}

Schmucki, Roland ^{[3
]}

Gut, Ivo G. ^{[1
,2
]}

Spleiss, Olivia ^{[3
]}

机构：

[1] BIST, CRG, CNAG, Baldiri & Reixac 4, Barcelona 08028, Spain

[2] UPF, Barcelona, Spain

[3] F Hoffmann La Roche Ltd, Roche Innovat Ctr Basel, Basel, Switzerland

[4] Georgetown Univ, Med Ctr, Dept Microbiol & Immunol, Washington, DC 20007 USA

来源：

G3-GENES GENOMES GENETICS | 2019年 / 9卷 / 12期

关键词：

Eastern Woodchuck; Marmota monax; Chronic Hepatitis B; Hepatocellular Carcinoma; Immune Response; Whole Genome Sequencing; Genome Assembly; ALIGNMENT; GENES; TOOL;

D O I：

10.1534/g3.119.400413

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页码：3943 / 3952

页数：10

共 56 条

[1] Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx [J].

Abascal, Federico ;

Corvelo, Andre ;

Cruz, Fernando ;

Villanueva-Canas, Jose L. ;

Vlasova, Anna ;

Marcet-Houben, Marina ;

Martinez-Cruz, Begona ;

Cheng, Jade Yu ;

Prieto, Pablo ;

Quesada, Victor ;

Quilez, Javier ;

Li, Gang ;

Garcia, Francisca ;

Rubio-Camarillo, Miriam ;

Frias, Leonor ;

Ribeca, Paolo ;

Capella-Gutierrez, Salvador ;

Rodriguez, Jose M. ;

Camara, Francisco ;

Lowy, Ernesto ;

Cozzuto, Luca ;

Erb, Ionas ;

Tress, Michael L. ;

Rodriguez-Ales, Jose L. ;

Ruiz-Orera, Jorge ;

Reverter, Ferran ;

Casas-Marce, Mireia ;

Soriano, Laura ;

Arango, Javier R. ;

Derdak, Sophia ;

Galan, Beatriz ;

Blanc, Julie ;

Gut, Marta ;

Lorente-Galdos, Belen ;

Andres-Nieto, Marta ;

Lopez-Otin, Carlos ;

Valencia, Alfonso ;

Gut, Ivo ;

Garcia, Jose L. ;

Guigo, Roderic ;

Murphy, William J. ;

Ruiz-Herrera, Aurora ;

Marques-Bonet, Tomas ;

Roma, Guglielmo ;

Notredame, Cedric ;

Mailund, Thomas ;

Mar Alba, M. ;

Gabaldon, Toni ;

Alioto, Tyler ;

Godoy, Jose A. .

GENOME BIOLOGY, 2016, 17

[2] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[3]

[Anonymous], 2017 GLOB HEP REP

[4] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[5] Safety and efficacy of anti-PD-L1 therapy in the woodchuck model of HBV infection [J].

Balsitis, Scott ;

Gali, Volodymyr ;

Mason, Pamela J. ;

Chaniewski, Susan ;

Levine, Steven M. ;

Wichroski, Michael J. ;

Feulner, Michael ;

Song, Yunling ;

Granaldi, Karen ;

Loy, James K. ;

Thompson, Chris M. ;

Lesniak, Jacob A. ;

Brockus, Catherine ;

Kishnani, Narendra ;

Menne, Stephan ;

Cockett, Mark I. ;

Iyer, Renuka ;

Mason, Stephen W. ;

Tenney, Daniel J. .

PLOS ONE, 2018, 13 (02)

[6] SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing [J].

Bankevich, Anton ;

Nurk, Sergey ;

Antipov, Dmitry ;

Gurevich, Alexey A. ;

Dvorkin, Mikhail ;

Kulikov, Alexander S. ;

Lesin, Valery M. ;

Nikolenko, Sergey I. ;

Son Pham ;

Prjibelski, Andrey D. ;

Pyshkin, Alexey V. ;

Sirotkin, Alexander V. ;

Vyahhi, Nikolay ;

Tesler, Glenn ;

Alekseyev, Max A. ;

Pevzner, Pavel A. .

JOURNAL OF COMPUTATIONAL BIOLOGY, 2012, 19 (05) :455-477

[7]

Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkr1065, 10.1093/nar/gkp985, 10.1093/nar/gkh121]

[8] Toward almost closed genomes with GapFiller [J].

Boetzer, Marten ;

Pirovano, Walter .

GENOME BIOLOGY, 2012, 13 (06)

[9] Scaffolding pre-assembled contigs using SSPACE [J].

Boetzer, Marten ;

Henkel, Christiaan V. ;

Jansen, Hans J. ;

Butler, Derek ;

Pirovano, Walter .

BIOINFORMATICS, 2011, 27 (04) :578-579

[10] A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors [J].

Bryant, Donald M. ;

Johnson, Kimberly ;

DiTommaso, Tia ;

Tickle, Timothy ;

Couger, Matthew Brian ;

Payzin-Dogru, Duygu ;

Lee, Tae J. ;

Leigh, Nicholas D. ;

Kuo, Tzu-Hsing ;

Davis, Francis G. ;

Bateman, Joel ;

Bryant, Sevara ;

Guzikowski, Anna R. ;

Tsai, Stephanie L. ;

Coyne, Steven ;

Ye, William W. ;

Freeman, Robert M., Jr. ;

Peshkin, Leonid ;

Tabin, Clifford J. ;

Regev, Aviv ;

Haas, Brian J. ;

Whited, Jessica L. .

CELL REPORTS, 2017, 18 (03) :762-776

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