The genome of the American groundhog, Marmota monax.

Daniela Puiu,Alaina Shumate,Yuchen Ge,Manoj Bhaskaran,Aleksey Zimin,Jiabin Qiu,Steven L Salzberg

doi:10.12688/f1000research.25970.1

Daniela Puiu, Alaina Shumate + Show 5 more

Open Access

https://doi.org/10.12688/f1000research.25970.1

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Abstract

We sequenced the genome of the North American groundhog, Marmota monax, also known as the woodchuck. Our sequencing strategy included a combination of short, high-quality Illumina reads plus long reads generated by both Pacific Biosciences and Oxford Nanopore instruments. Assembly of the combined data produced a genome of 2.74 Gbp in total length, with an N50 contig size of 1,094,236 bp. To annotate the genome, we mapped the genes from another M. monax genome and from the closely related Alpine marmot, Marmota marmota, onto our assembly, resulting in 20,559 annotated protein-coding genes and 28,135 transcripts. The genome assembly and annotation are available in GenBank under BioProject PRJNA587092.

Highlights

Groundhogs (Marmota monax), known as woodchucks, belong to the same family of ground squirrels as the alpine marmot, Marmota marmota
Groundhogs are found throughout the eastern United States and across much of Canada
The woodchuck is of interest to biomedical science as a model for Hepatitis B virus (HBV) infection in humans, due to endemic infections of woodchucks with woodchuck hepatitis virus (WHV), which is genetically similar to human HBV and causes a similar course of infection1

Summary

Introduction

Groundhogs (Marmota monax), known as woodchucks, belong to the same family of ground squirrels as the alpine marmot, Marmota marmota. 1. Markus Ralser , The Francis Crick Institute, London, UK Toni Gossmann, Bielefeld University, Bielefeld, Germany 2. Mihai Pop , University of Maryland, College Park, USA Introduction Groundhogs (Marmota monax), known as woodchucks, belong to the same family of ground squirrels as the alpine marmot, Marmota marmota.

Results

Conclusion