The genome of the American groundhog, Marmota monax

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 da...

Descripción completa

Detalles Bibliográficos
Autores principales: Puiu, Daniela, Zimin, Aleksey, Shumate, Alaina, Ge, Yuchen, Qiu, Jiabin, Bhaskaran, Manoj, Salzberg, Steven L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2020
Materias:
Data Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7682491/
https://www.ncbi.nlm.nih.gov/pubmed/33274050
http://dx.doi.org/10.12688/f1000research.25970.1
_version_ 1783612697674252288
author Puiu, Daniela
Zimin, Aleksey
Shumate, Alaina
Ge, Yuchen
Qiu, Jiabin
Bhaskaran, Manoj
Salzberg, Steven L.
author_facet Puiu, Daniela
Zimin, Aleksey
Shumate, Alaina
Ge, Yuchen
Qiu, Jiabin
Bhaskaran, Manoj
Salzberg, Steven L.
author_sort Puiu, Daniela
collection PubMed
description 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.
format Online
Article
Text
id pubmed-7682491
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher F1000 Research Limited
record_format MEDLINE/PubMed
spelling pubmed-76824912020-12-02 The genome of the American groundhog, Marmota monax Puiu, Daniela Zimin, Aleksey Shumate, Alaina Ge, Yuchen Qiu, Jiabin Bhaskaran, Manoj Salzberg, Steven L. F1000Res Data Note 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. F1000 Research Limited 2020-09-16 /pmc/articles/PMC7682491/ /pubmed/33274050 http://dx.doi.org/10.12688/f1000research.25970.1 Text en Copyright: © 2020 Puiu D et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Data Note
Puiu, Daniela
Zimin, Aleksey
Shumate, Alaina
Ge, Yuchen
Qiu, Jiabin
Bhaskaran, Manoj
Salzberg, Steven L.
The genome of the American groundhog, Marmota monax
title The genome of the American groundhog, Marmota monax
title_full The genome of the American groundhog, Marmota monax
title_fullStr The genome of the American groundhog, Marmota monax
title_full_unstemmed The genome of the American groundhog, Marmota monax
title_short The genome of the American groundhog, Marmota monax
title_sort genome of the american groundhog, marmota monax
topic Data Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7682491/
https://www.ncbi.nlm.nih.gov/pubmed/33274050
http://dx.doi.org/10.12688/f1000research.25970.1
work_keys_str_mv AT puiudaniela thegenomeoftheamericangroundhogmarmotamonax
AT ziminaleksey thegenomeoftheamericangroundhogmarmotamonax
AT shumatealaina thegenomeoftheamericangroundhogmarmotamonax
AT geyuchen thegenomeoftheamericangroundhogmarmotamonax
AT qiujiabin thegenomeoftheamericangroundhogmarmotamonax
AT bhaskaranmanoj thegenomeoftheamericangroundhogmarmotamonax
AT salzbergstevenl thegenomeoftheamericangroundhogmarmotamonax
AT puiudaniela genomeoftheamericangroundhogmarmotamonax
AT ziminaleksey genomeoftheamericangroundhogmarmotamonax
AT shumatealaina genomeoftheamericangroundhogmarmotamonax
AT geyuchen genomeoftheamericangroundhogmarmotamonax
AT qiujiabin genomeoftheamericangroundhogmarmotamonax
AT bhaskaranmanoj genomeoftheamericangroundhogmarmotamonax
AT salzbergstevenl genomeoftheamericangroundhogmarmotamonax

Ejemplares similares