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...
Main Authors: | , , , , , , , , , , , , , , |
---|---|
Format: | Article in Journal/Newspaper |
Language: | unknown |
Published: |
eScholarship, University of California
2022
|
Subjects: | |
Online Access: | https://escholarship.org/uc/item/5b78m5sm |
id |
ftcdlib:oai:escholarship.org:ark:/13030/qt5b78m5sm |
---|---|
record_format |
openpolar |
spelling |
ftcdlib:oai:escholarship.org:ark:/13030/qt5b78m5sm 2023-09-05T13:12:24+02:00 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 Hückstädt, 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 140 2022-01-01 application/pdf https://escholarship.org/uc/item/5b78m5sm unknown eScholarship, University of California qt5b78m5sm https://escholarship.org/uc/item/5b78m5sm public Communications Biology, vol 5, iss 1 Human Genome Biotechnology Genetics Animals Antarctic Regions Gene Expression Regulation Genome Genome-Wide Association Study Lipid Metabolism Oxygen Phylogeny Seals Earless Species Specificity article 2022 ftcdlib 2023-08-21T18:07:59Z 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. Article in Journal/Newspaper Antarc* Antarctic harbor seal Weddell Seal Weddell Seals University of California: eScholarship Antarctic The Antarctic Weddell |
institution |
Open Polar |
collection |
University of California: eScholarship |
op_collection_id |
ftcdlib |
language |
unknown |
topic |
Human Genome Biotechnology Genetics Animals Antarctic Regions Gene Expression Regulation Genome Genome-Wide Association Study Lipid Metabolism Oxygen Phylogeny Seals Earless Species Specificity |
spellingShingle |
Human Genome Biotechnology Genetics Animals Antarctic Regions Gene Expression Regulation Genome Genome-Wide Association Study Lipid Metabolism Oxygen Phylogeny Seals Earless Species Specificity Noh, Hyun Ji Turner-Maier, Jason Schulberg, S Anne Fitzgerald, Michael L Johnson, Jeremy Allen, Kaitlin N Hückstädt, 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 |
Human Genome Biotechnology Genetics Animals Antarctic Regions Gene Expression Regulation Genome Genome-Wide Association Study Lipid Metabolism Oxygen Phylogeny Seals Earless Species Specificity |
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. |
format |
Article in Journal/Newspaper |
author |
Noh, Hyun Ji Turner-Maier, Jason Schulberg, S Anne Fitzgerald, Michael L Johnson, Jeremy Allen, Kaitlin N Hückstädt, 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 Hückstädt, 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 |
eScholarship, University of California |
publishDate |
2022 |
url |
https://escholarship.org/uc/item/5b78m5sm |
op_coverage |
140 |
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_source |
Communications Biology, vol 5, iss 1 |
op_relation |
qt5b78m5sm https://escholarship.org/uc/item/5b78m5sm |
op_rights |
public |
_version_ |
1776200140129828864 |