The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations

Affiliations

¹ Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Department of Biology, University of Rochester, NY, USA, Vertebrate and Health Genomics, The Genome Analysis Center, Norwich, UK, Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden and Department of Genetics, Harvard Medical School, Boston, MA, USA.
² Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Department of Biology, University of Rochester, NY, USA, Vertebrate and Health Genomics, The Genome Analysis Center, Norwich, UK, Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden and Department of Genetics, Harvard Medical School, Boston, MA, USA Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Department of Biology, University of Rochester, NY, USA, Vertebrate and Health Genomics, The Genome Analysis Center, Norwich, UK, Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden and Department of Genetics, Harvard Medical School, Boston, MA, USA.

PMID: 25172923
PMCID: PMC4253829
DOI: 10.1093/bioinformatics/btu579

The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations

Michael Keane et al. Bioinformatics. 2014.

. 2014 Dec 15;30(24):3558-60.

doi: 10.1093/bioinformatics/btu579. Epub 2014 Aug 28.

Affiliations

¹ Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Department of Biology, University of Rochester, NY, USA, Vertebrate and Health Genomics, The Genome Analysis Center, Norwich, UK, Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden and Department of Genetics, Harvard Medical School, Boston, MA, USA.
² Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Department of Biology, University of Rochester, NY, USA, Vertebrate and Health Genomics, The Genome Analysis Center, Norwich, UK, Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden and Department of Genetics, Harvard Medical School, Boston, MA, USA Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Department of Biology, University of Rochester, NY, USA, Vertebrate and Health Genomics, The Genome Analysis Center, Norwich, UK, Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden and Department of Genetics, Harvard Medical School, Boston, MA, USA.

PMID: 25172923
PMCID: PMC4253829
DOI: 10.1093/bioinformatics/btu579

Abstract

Motivation: The naked mole rat (Heterocephalus glaber) is an exceptionally long-lived and cancer-resistant rodent native to East Africa. Although its genome was previously sequenced, here we report a new assembly sequenced by us with substantially higher N50 values for scaffolds and contigs.

Results: We analyzed the annotation of this new improved assembly and identified candidate genomic adaptations which may have contributed to the evolution of the naked mole rat's extraordinary traits, including in regions of p53, and the hyaluronan receptors CD44 and HMMR (RHAMM). Furthermore, we developed a freely available web portal, the Naked Mole Rat Genome Resource (http://www.naked-mole-rat.org), featuring the data and results of our analysis, to assist researchers interested in the genome and genes of the naked mole rat, and also to facilitate further studies on this fascinating species.

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Figures

**Fig. 1.**
Alignment of p53 sequences from NMR, guinea pig, rat, mouse and human. The TADII is in green, the PRD in yellow and PXXP motifs are boxed

**Fig. 2.**
Alignment of p16 sequences from guinea pig, mouse and NMR using both the Broad and BGI assemblies

See this image and copyright information in PMC

References

1. Ashur-Fabian O, et al. Evolution of p53 in hypoxia-stressed Spalax mimics human tumor mutation. Proc. Natl Acad. Sci. USA. 2004;101:12236–12241. - PMC - PubMed
1. Buffenstein R. Negligible senescence in the longest living rodent, the naked mole-rat: insights from a successfully aging species. J. Comp. Physiol. B. 2008;178:439–445. - PubMed
1. Gnerre S, et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl Acad. Sci. USA. 2011;108:1513–1518. - PMC - PubMed
1. Huang DW, et al. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009;4:44–57. - PubMed
1. Kim EB, et al. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature. 2011;479:223–227. - PMC - PubMed

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The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations

Affiliations

The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations

Authors

Affiliations

Abstract

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Molecular Biology Databases

Research Materials

Miscellaneous