Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness
The Antarctic fur seal (Arctocephalus gazella) is an important top predator and indicator of the health of the Southern Ocean ecosystem. Although abundant, this species narrowly escaped extinction due to historical sealing and is currently declining as a consequence of climate change. Genomic tools...
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Oxford University Press on behalf of Genetics Society of America
2024
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Online Access: | http://nora.nerc.ac.uk/id/eprint/537678/ https://nora.nerc.ac.uk/id/eprint/537678/1/jkae179.pdf https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkae179/7724771 |
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ftnerc:oai:nora.nerc.ac.uk:537678 2024-10-13T14:02:41+00:00 Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness Hench, Kosmas Vendrami, David L.J. Forcada, Jaume Hoffman, Joseph I. 2024-07-31 text http://nora.nerc.ac.uk/id/eprint/537678/ https://nora.nerc.ac.uk/id/eprint/537678/1/jkae179.pdf https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkae179/7724771 en eng Oxford University Press on behalf of Genetics Society of America https://nora.nerc.ac.uk/id/eprint/537678/1/jkae179.pdf Hench, Kosmas; Vendrami, David L.J.; Forcada, Jaume orcid:0000-0002-2115-0150 Hoffman, Joseph I. orcid:0000-0001-5895-8949 . 2024 Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness. G3 Genes%7CGenomes%7CGenetics, jkae179. 12, pp. https://doi.org/10.1093/g3journal/jkae179 <https://doi.org/10.1093/g3journal/jkae179> cc_by_4 Publication - Article PeerReviewed 2024 ftnerc https://doi.org/10.1093/g3journal/jkae179 2024-09-18T00:05:58Z The Antarctic fur seal (Arctocephalus gazella) is an important top predator and indicator of the health of the Southern Ocean ecosystem. Although abundant, this species narrowly escaped extinction due to historical sealing and is currently declining as a consequence of climate change. Genomic tools are essential for understanding these anthropogenic impacts and for predicting long-term viability. However, the current reference genome (“arcGaz3”) shows considerable room for improvement in terms of both completeness and contiguity. We therefore combined PacBio sequencing, haplotype-aware HiRise assembly and scaffolding based on Hi-C information to generate a refined assembly of the Antarctic fur seal reference genome (“arcGaz4_h1”). The new assembly is 2.53Gb long, has a scaffold N50 of 55.6Mb and includes 18 chromosome-sized scaffolds, which correspond to the 18 chromosomes expected in otariids. Genome completeness is greatly improved, with 23,408 annotated genes and a Benchmarking Universal Single-Copy Orthologs (BUSCO) score raised from 84.7% to 95.2%. We furthermore included the new genome in a reference-free alignment of the genomes of eleven pinniped species to characterize evolutionary conservation across the Pinnipedia using genome-wide Genomic Evolutionary Rate Profiling (GERP). We then implemented Gene Ontology (GO) enrichment analyses to identify biological processes associated with those genes showing the highest levels of either conservation or differentiation between the two major pinniped families, the Otariidae and Phocidae. We show that processes linked to neuronal development, the circulatory system and osmoregulation are overrepresented both in conserved as well as in differentiated regions of the genome. Article in Journal/Newspaper Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella Southern Ocean Natural Environment Research Council: NERC Open Research Archive Antarctic Southern Ocean The Antarctic G3: Genes, Genomes, Genetics |
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Open Polar |
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Natural Environment Research Council: NERC Open Research Archive |
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ftnerc |
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English |
description |
The Antarctic fur seal (Arctocephalus gazella) is an important top predator and indicator of the health of the Southern Ocean ecosystem. Although abundant, this species narrowly escaped extinction due to historical sealing and is currently declining as a consequence of climate change. Genomic tools are essential for understanding these anthropogenic impacts and for predicting long-term viability. However, the current reference genome (“arcGaz3”) shows considerable room for improvement in terms of both completeness and contiguity. We therefore combined PacBio sequencing, haplotype-aware HiRise assembly and scaffolding based on Hi-C information to generate a refined assembly of the Antarctic fur seal reference genome (“arcGaz4_h1”). The new assembly is 2.53Gb long, has a scaffold N50 of 55.6Mb and includes 18 chromosome-sized scaffolds, which correspond to the 18 chromosomes expected in otariids. Genome completeness is greatly improved, with 23,408 annotated genes and a Benchmarking Universal Single-Copy Orthologs (BUSCO) score raised from 84.7% to 95.2%. We furthermore included the new genome in a reference-free alignment of the genomes of eleven pinniped species to characterize evolutionary conservation across the Pinnipedia using genome-wide Genomic Evolutionary Rate Profiling (GERP). We then implemented Gene Ontology (GO) enrichment analyses to identify biological processes associated with those genes showing the highest levels of either conservation or differentiation between the two major pinniped families, the Otariidae and Phocidae. We show that processes linked to neuronal development, the circulatory system and osmoregulation are overrepresented both in conserved as well as in differentiated regions of the genome. |
format |
Article in Journal/Newspaper |
author |
Hench, Kosmas Vendrami, David L.J. Forcada, Jaume Hoffman, Joseph I. |
spellingShingle |
Hench, Kosmas Vendrami, David L.J. Forcada, Jaume Hoffman, Joseph I. Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness |
author_facet |
Hench, Kosmas Vendrami, David L.J. Forcada, Jaume Hoffman, Joseph I. |
author_sort |
Hench, Kosmas |
title |
Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness |
title_short |
Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness |
title_full |
Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness |
title_fullStr |
Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness |
title_full_unstemmed |
Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness |
title_sort |
refinement of the antarctic fur seal (arctocephalus gazella) reference genome increases continuity and completeness |
publisher |
Oxford University Press on behalf of Genetics Society of America |
publishDate |
2024 |
url |
http://nora.nerc.ac.uk/id/eprint/537678/ https://nora.nerc.ac.uk/id/eprint/537678/1/jkae179.pdf https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkae179/7724771 |
geographic |
Antarctic Southern Ocean The Antarctic |
geographic_facet |
Antarctic Southern Ocean The Antarctic |
genre |
Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella Southern Ocean |
genre_facet |
Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella Southern Ocean |
op_relation |
https://nora.nerc.ac.uk/id/eprint/537678/1/jkae179.pdf Hench, Kosmas; Vendrami, David L.J.; Forcada, Jaume orcid:0000-0002-2115-0150 Hoffman, Joseph I. orcid:0000-0001-5895-8949 . 2024 Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness. G3 Genes%7CGenomes%7CGenetics, jkae179. 12, pp. https://doi.org/10.1093/g3journal/jkae179 <https://doi.org/10.1093/g3journal/jkae179> |
op_rights |
cc_by_4 |
op_doi |
https://doi.org/10.1093/g3journal/jkae179 |
container_title |
G3: Genes, Genomes, Genetics |
_version_ |
1812819155399737344 |