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

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Keane, Michael, Craig, Thomas, Alföldi, Jessica, Berlin, Aaron M., Johnson, Jeremy, Seluanov, Andrei, Gorbunova, Vera, Di Palma, Federica, Lindblad-Toh, Kerstin, Church, George M., de Magalhães, João Pedro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Discovery Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253829/
https://www.ncbi.nlm.nih.gov/pubmed/25172923
http://dx.doi.org/10.1093/bioinformatics/btu579
_version_ 1782347295147163648
author Keane, Michael
Craig, Thomas
Alföldi, Jessica
Berlin, Aaron M.
Johnson, Jeremy
Seluanov, Andrei
Gorbunova, Vera
Di Palma, Federica
Lindblad-Toh, Kerstin
Church, George M.
de Magalhães, João Pedro
author_facet Keane, Michael
Craig, Thomas
Alföldi, Jessica
Berlin, Aaron M.
Johnson, Jeremy
Seluanov, Andrei
Gorbunova, Vera
Di Palma, Federica
Lindblad-Toh, Kerstin
Church, George M.
de Magalhães, João Pedro
author_sort Keane, Michael
collection PubMed
description 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. Availability and implementation: The Naked Mole Rat Genome Resource is freely available online at http://www.naked-mole-rat.org. This resource is open source and the source code is available at https://github.com/maglab/naked-mole-rat-portal. Contact: jp@senescence.info
format Online
Article
Text
id pubmed-4253829
institution National Center for Biotechnology Information
language English
publishDate 2014
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-42538292014-12-04 The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations Keane, Michael Craig, Thomas Alföldi, Jessica Berlin, Aaron M. Johnson, Jeremy Seluanov, Andrei Gorbunova, Vera Di Palma, Federica Lindblad-Toh, Kerstin Church, George M. de Magalhães, João Pedro Bioinformatics Discovery Notes 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. Availability and implementation: The Naked Mole Rat Genome Resource is freely available online at http://www.naked-mole-rat.org. This resource is open source and the source code is available at https://github.com/maglab/naked-mole-rat-portal. Contact: jp@senescence.info Oxford University Press 2014-12-15 2014-08-28 /pmc/articles/PMC4253829/ /pubmed/25172923 http://dx.doi.org/10.1093/bioinformatics/btu579 Text en © The Author 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Discovery Notes
Keane, Michael
Craig, Thomas
Alföldi, Jessica
Berlin, Aaron M.
Johnson, Jeremy
Seluanov, Andrei
Gorbunova, Vera
Di Palma, Federica
Lindblad-Toh, Kerstin
Church, George M.
de Magalhães, João Pedro
The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations
title The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations
title_full The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations
title_fullStr The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations
title_full_unstemmed The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations
title_short The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations
title_sort naked mole rat genome resource: facilitating analyses of cancer and longevity-related adaptations
topic Discovery Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253829/
https://www.ncbi.nlm.nih.gov/pubmed/25172923
http://dx.doi.org/10.1093/bioinformatics/btu579
work_keys_str_mv AT keanemichael thenakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT craigthomas thenakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT alfoldijessica thenakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT berlinaaronm thenakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT johnsonjeremy thenakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT seluanovandrei thenakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT gorbunovavera thenakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT dipalmafederica thenakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT lindbladtohkerstin thenakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT churchgeorgem thenakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT demagalhaesjoaopedro thenakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT keanemichael nakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT craigthomas nakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT alfoldijessica nakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT berlinaaronm nakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT johnsonjeremy nakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT seluanovandrei nakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT gorbunovavera nakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT dipalmafederica nakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT lindbladtohkerstin nakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT churchgeorgem nakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations
AT demagalhaesjoaopedro nakedmoleratgenomeresourcefacilitatinganalysesofcancerandlongevityrelatedadaptations

Ejemplares similares