The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling
The Weddell seal (Leptonychotes weddellii) thrives in its extreme Antarctic environment. We generated the Weddell seal genome assembly and a high-quality annotation to investigate genome-wide evolutionary pressures that underlie its phenotype and to study genes implicated in hypoxia tolerance and a...
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Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi
2022
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Online Access: | http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-470460 https://doi.org/10.1038/s42003-022-03089-2 |
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ftuppsalauniv:oai:DiVA.org:uu-470460 2024-02-11T09:58:01+01:00 The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling Noh, Hyun Ji Turner-Maier, Jason Schulberg, S. Anne Fitzgerald, Michael L. Johnson, Jeremy Allen, Kaitlin N. Huckstadt, Luis A. Batten, Annabelle J. Alfoldi, Jessica Costa, Daniel P. Karlsson, Elinor K. Zapol, Warren M. Buys, Emmanuel S. Lindblad-Toh, Kerstin Hindle, Allyson G. 2022 application/pdf http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-470460 https://doi.org/10.1038/s42003-022-03089-2 eng eng Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi Uppsala universitet, Science for Life Laboratory, SciLifeLab Broad Inst MIT & Harvard, 7 Cambridge Ctr, Cambridge, MA 02142 USA. Harvard Med Sch, Anesthesia Ctr Crit Care Res, Massachusetts Gen Hosp, Dept Anesthesia Crit Care & Pain Med, 55 Fruit St, Boston, MA 02114 USA. Harvard Med Sch, Ctr Computat & Integrat Biol, Massachusetts Gen Hosp, Lipid Metab Unit, 55 Fruit St, Boston, MA 02114 USA. Univ Calif Santa Cruz, Inst Marine Sci, Dept Ecol & Evolutionary Biol, 130 McAllister Way, Santa Cruz, CA 95060 USA. Broad Inst MIT & Harvard, 7 Cambridge Ctr, Cambridge, MA 02142 USA.;Univ Massachusetts, Program Bioinformat & Integrat Biol, Med Sch, Worcester, MA 01655 USA. Broad Inst MIT & Harvard, 7 Cambridge Ctr, Cambridge, MA 02142 USA.;Harvard Med Sch, Anesthesia Ctr Crit Care Res, Massachusetts Gen Hosp, Dept Anesthesia Crit Care & Pain Med, 55 Fruit St, Boston, MA 02114 USA. Broad Inst MIT & Harvard, 7 Cambridge Ctr, Cambridge, MA 02142 USA Broad Inst MIT & Harvard, 7 Cambridge Ctr, Cambridge, MA 02142 USA.;Harvard Med Sch, Anesthesia Ctr Crit Care Res, Massachusetts Gen Hosp, Dept Anesthesia Crit Care & Pain Med, 55 Fruit St, Boston, MA 02114 USA.;Univ Nevada, Sch Life Sci, 4505S Maryland Pkwy, Las Vegas, NV 89154 USA. Springer Nature Communications Biology, 2022, 5:1, orcid:0000-0001-8338-0253 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-470460 doi:10.1038/s42003-022-03089-2 PMID 35177770 ISI:000757506400003 info:eu-repo/semantics/openAccess Genetics Genetik Article in journal info:eu-repo/semantics/article text 2022 ftuppsalauniv https://doi.org/10.1038/s42003-022-03089-2 2024-01-17T23:33:17Z The Weddell seal (Leptonychotes weddellii) thrives in its extreme Antarctic environment. We generated the Weddell seal genome assembly and a high-quality annotation to investigate genome-wide evolutionary pressures that underlie its phenotype and to study genes implicated in hypoxia tolerance and a lipid-based metabolism. Genome-wide analyses included gene family expansion/contraction, positive selection, and diverged sequence (acceleration) compared to other placental mammals, identifying selection in coding and non-coding sequence in five pathways that may shape cardiovascular phenotype. Lipid metabolism as well as hypoxia genes contained more accelerated regions in the Weddell seal compared to genomic background. Top-significant genes were SUMO2 and EP300; both regulate hypoxia inducible factor signaling. Liver expression of four genes with the strongest acceleration signals differ between Weddell seals and a terrestrial mammal, sheep. We also report a high-density lipoprotein-like particle in Weddell seal serum not present in other mammals, including the shallow-diving harbor seal. The Antarctic Weddell inhabits one of the most extreme environments on Earth. Comparative genomics with close relatives reveals the specific genetic adaptations for cardiovascular and fat metabolism that enable it to thrive. Article in Journal/Newspaper Antarc* Antarctic harbor seal Weddell Seal Weddell Seals Uppsala University: Publications (DiVA) Antarctic The Antarctic Weddell Communications Biology 5 1 |
institution |
Open Polar |
collection |
Uppsala University: Publications (DiVA) |
op_collection_id |
ftuppsalauniv |
language |
English |
topic |
Genetics Genetik |
spellingShingle |
Genetics Genetik Noh, Hyun Ji Turner-Maier, Jason Schulberg, S. Anne Fitzgerald, Michael L. Johnson, Jeremy Allen, Kaitlin N. Huckstadt, Luis A. Batten, Annabelle J. Alfoldi, Jessica Costa, Daniel P. Karlsson, Elinor K. Zapol, Warren M. Buys, Emmanuel S. Lindblad-Toh, Kerstin Hindle, Allyson G. The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling |
topic_facet |
Genetics Genetik |
description |
The Weddell seal (Leptonychotes weddellii) thrives in its extreme Antarctic environment. We generated the Weddell seal genome assembly and a high-quality annotation to investigate genome-wide evolutionary pressures that underlie its phenotype and to study genes implicated in hypoxia tolerance and a lipid-based metabolism. Genome-wide analyses included gene family expansion/contraction, positive selection, and diverged sequence (acceleration) compared to other placental mammals, identifying selection in coding and non-coding sequence in five pathways that may shape cardiovascular phenotype. Lipid metabolism as well as hypoxia genes contained more accelerated regions in the Weddell seal compared to genomic background. Top-significant genes were SUMO2 and EP300; both regulate hypoxia inducible factor signaling. Liver expression of four genes with the strongest acceleration signals differ between Weddell seals and a terrestrial mammal, sheep. We also report a high-density lipoprotein-like particle in Weddell seal serum not present in other mammals, including the shallow-diving harbor seal. The Antarctic Weddell inhabits one of the most extreme environments on Earth. Comparative genomics with close relatives reveals the specific genetic adaptations for cardiovascular and fat metabolism that enable it to thrive. |
format |
Article in Journal/Newspaper |
author |
Noh, Hyun Ji Turner-Maier, Jason Schulberg, S. Anne Fitzgerald, Michael L. Johnson, Jeremy Allen, Kaitlin N. Huckstadt, Luis A. Batten, Annabelle J. Alfoldi, Jessica Costa, Daniel P. Karlsson, Elinor K. Zapol, Warren M. Buys, Emmanuel S. Lindblad-Toh, Kerstin Hindle, Allyson G. |
author_facet |
Noh, Hyun Ji Turner-Maier, Jason Schulberg, S. Anne Fitzgerald, Michael L. Johnson, Jeremy Allen, Kaitlin N. Huckstadt, Luis A. Batten, Annabelle J. Alfoldi, Jessica Costa, Daniel P. Karlsson, Elinor K. Zapol, Warren M. Buys, Emmanuel S. Lindblad-Toh, Kerstin Hindle, Allyson G. |
author_sort |
Noh, Hyun Ji |
title |
The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling |
title_short |
The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling |
title_full |
The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling |
title_fullStr |
The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling |
title_full_unstemmed |
The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling |
title_sort |
antarctic weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling |
publisher |
Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi |
publishDate |
2022 |
url |
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-470460 https://doi.org/10.1038/s42003-022-03089-2 |
geographic |
Antarctic The Antarctic Weddell |
geographic_facet |
Antarctic The Antarctic Weddell |
genre |
Antarc* Antarctic harbor seal Weddell Seal Weddell Seals |
genre_facet |
Antarc* Antarctic harbor seal Weddell Seal Weddell Seals |
op_relation |
Communications Biology, 2022, 5:1, orcid:0000-0001-8338-0253 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-470460 doi:10.1038/s42003-022-03089-2 PMID 35177770 ISI:000757506400003 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1038/s42003-022-03089-2 |
container_title |
Communications Biology |
container_volume |
5 |
container_issue |
1 |
_version_ |
1790593591773495296 |