The Genome Sequence of the Eastern Woodchuck (Marmota monax) - A Preclinical Animal Model for Chronic Hepatitis B
The Genome Sequence of the Eastern Woodchuck (Marmota monax) - A Preclinical Animal Model for Chronic Hepatitis B
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DOI：
10.1534/g3.119.400413
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发表时间：
2019-12-01
影响因子：
2.6
通讯作者：
Spleiss, Olivia
中科院分区：
文献类型：
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作者：
Alioto, Tyler S.;Cruz, Fernando;Spleiss, Olivia
东方土拨鼠（Marmota monax）已被广泛用于慢性B型肝炎和肝癌的研究，因为其感染土拨鼠肝炎病毒与人类B型肝炎病毒感染非常相似。新的免疫途径的发展需要在这种动物模型中的免疫途径基因的遗传信息。土拨鼠基因组与Illumina配对末端、配偶对文库的高覆盖全基因组鸟枪测序和fosmid池测序的组合组装。结果是2.63千兆字节（Gb）的组装，其中重叠群N50为74.5个碱基（kb），支架N50为892 kb，基因组完整性为99.2%。来自七种不同组织的RNA测序（RNA-seq）有助于注释30，873个蛋白质编码基因，这些基因又编码41，826种独特的蛋白质产物。超过90%的基因已被功能注释，其中82%包含开放阅读框架。这一基因组序列及其注释将使慢性B型肝炎和肝细胞癌的进一步研究，并有助于了解土拨鼠的免疫反应。
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.