The genome of the American groundhog, Marmota monax

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

doi:10.12688/f1000research.25970.1

The genome of the American groundhog, Marmota monax

F1000Res. 2020 Sep 16:9:1137. doi: 10.12688/f1000research.25970.1. eCollection 2020.

Authors

Daniela Puiu^{1

2}, Aleksey Zimin^{1

2}, Alaina Shumate^{1

2}, Yuchen Ge¹, Jiabin Qiu³, Manoj Bhaskaran³, Steven L Salzberg^{1

2

4}

Affiliations

¹ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21211, USA.
² Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21211, USA.
³ Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA.
⁴ Departments of Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD, USA.

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.

Keywords: genome annotation; genome assembly; groundhog; woodchuck.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Base Sequence
Genome
High-Throughput Nucleotide Sequencing
Marmota* / genetics
Nanopores*
United States

Grants and funding

R01 HG006677/HG/NHGRI NIH HHS/United States