De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome
Abstract Background Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above...
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ftdoajarticles:oai:doaj.org/article:892aecc46edd4c31b7e55775c1e42a53 2024-09-15T17:48:21+00:00 De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome David Ryder David Stone Diana Minardi Ainsley Riley Justin Avant Lisa Cross Marta Soeffker Deborah Davidson Andrew Newman Peter Thomson Chris Darby Ronny van Aerle 2024-03-01T00:00:00Z https://doi.org/10.1186/s12864-024-10141-4 https://doaj.org/article/892aecc46edd4c31b7e55775c1e42a53 EN eng BMC https://doi.org/10.1186/s12864-024-10141-4 https://doaj.org/toc/1471-2164 doi:10.1186/s12864-024-10141-4 1471-2164 https://doaj.org/article/892aecc46edd4c31b7e55775c1e42a53 BMC Genomics, Vol 25, Iss 1, Pp 1-15 (2024) Dissostichus eleginoides Nototheniidae Illumina sequencing PacBio sequencing Anti-freeze glycoprotein Biotechnology TP248.13-248.65 Genetics QH426-470 article 2024 ftdoajarticles https://doi.org/10.1186/s12864-024-10141-4 2024-08-05T17:49:53Z Abstract Background Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. As apex predators, they are a key part of the food web, feeding on a variety of prey, including krill, squid, and other fish. Despite its importance, genomic sequence data, which could be used for more accurate dating of the divergence between Patagonian and Antarctic toothfish, or establish whether it shares adaptations to temperature with fish living in more polar or equatorial climes, has so far been limited. Results A high-quality D. eleginoides genome was generated using a combination of Illumina, PacBio and Omni-C sequencing technologies. To aid the genome annotation, the transcriptome derived from a variety of toothfish tissues was also generated using both short and long read sequencing methods. The final genome assembly was 797.8 Mb with a N50 scaffold length of 3.5 Mb. Approximately 31.7% of the genome consisted of repetitive elements. A total of 35,543 putative protein-coding regions were identified, of which 50% have been functionally annotated. Transcriptomics analysis showed that approximately 64% of the predicted genes (22,617 genes) were found to be expressed in the tissues sampled. Comparative genomics analysis revealed that the anti-freeze glycoprotein (AFGP) locus of D. eleginoides does not contain any AFGP proteins compared to the same locus in the Antarctic toothfish (Dissostichus mawsoni). This is in agreement with previously published results looking at hybridization signals and confirms that Patagonian toothfish do not possess AFGP coding sequences in their genome. Conclusions We have assembled and annotated the Patagonian toothfish genome, which will provide a valuable genetic resource for ecological and ... Article in Journal/Newspaper Antarc* Antarctic Antarctic Toothfish Patagonian Toothfish Southern Ocean Directory of Open Access Journals: DOAJ Articles BMC Genomics 25 1 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Dissostichus eleginoides Nototheniidae Illumina sequencing PacBio sequencing Anti-freeze glycoprotein Biotechnology TP248.13-248.65 Genetics QH426-470 |
spellingShingle |
Dissostichus eleginoides Nototheniidae Illumina sequencing PacBio sequencing Anti-freeze glycoprotein Biotechnology TP248.13-248.65 Genetics QH426-470 David Ryder David Stone Diana Minardi Ainsley Riley Justin Avant Lisa Cross Marta Soeffker Deborah Davidson Andrew Newman Peter Thomson Chris Darby Ronny van Aerle De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome |
topic_facet |
Dissostichus eleginoides Nototheniidae Illumina sequencing PacBio sequencing Anti-freeze glycoprotein Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
Abstract Background Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. As apex predators, they are a key part of the food web, feeding on a variety of prey, including krill, squid, and other fish. Despite its importance, genomic sequence data, which could be used for more accurate dating of the divergence between Patagonian and Antarctic toothfish, or establish whether it shares adaptations to temperature with fish living in more polar or equatorial climes, has so far been limited. Results A high-quality D. eleginoides genome was generated using a combination of Illumina, PacBio and Omni-C sequencing technologies. To aid the genome annotation, the transcriptome derived from a variety of toothfish tissues was also generated using both short and long read sequencing methods. The final genome assembly was 797.8 Mb with a N50 scaffold length of 3.5 Mb. Approximately 31.7% of the genome consisted of repetitive elements. A total of 35,543 putative protein-coding regions were identified, of which 50% have been functionally annotated. Transcriptomics analysis showed that approximately 64% of the predicted genes (22,617 genes) were found to be expressed in the tissues sampled. Comparative genomics analysis revealed that the anti-freeze glycoprotein (AFGP) locus of D. eleginoides does not contain any AFGP proteins compared to the same locus in the Antarctic toothfish (Dissostichus mawsoni). This is in agreement with previously published results looking at hybridization signals and confirms that Patagonian toothfish do not possess AFGP coding sequences in their genome. Conclusions We have assembled and annotated the Patagonian toothfish genome, which will provide a valuable genetic resource for ecological and ... |
format |
Article in Journal/Newspaper |
author |
David Ryder David Stone Diana Minardi Ainsley Riley Justin Avant Lisa Cross Marta Soeffker Deborah Davidson Andrew Newman Peter Thomson Chris Darby Ronny van Aerle |
author_facet |
David Ryder David Stone Diana Minardi Ainsley Riley Justin Avant Lisa Cross Marta Soeffker Deborah Davidson Andrew Newman Peter Thomson Chris Darby Ronny van Aerle |
author_sort |
David Ryder |
title |
De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome |
title_short |
De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome |
title_full |
De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome |
title_fullStr |
De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome |
title_full_unstemmed |
De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome |
title_sort |
de novo assembly and annotation of the patagonian toothfish (dissostichus eleginoides) genome |
publisher |
BMC |
publishDate |
2024 |
url |
https://doi.org/10.1186/s12864-024-10141-4 https://doaj.org/article/892aecc46edd4c31b7e55775c1e42a53 |
genre |
Antarc* Antarctic Antarctic Toothfish Patagonian Toothfish Southern Ocean |
genre_facet |
Antarc* Antarctic Antarctic Toothfish Patagonian Toothfish Southern Ocean |
op_source |
BMC Genomics, Vol 25, Iss 1, Pp 1-15 (2024) |
op_relation |
https://doi.org/10.1186/s12864-024-10141-4 https://doaj.org/toc/1471-2164 doi:10.1186/s12864-024-10141-4 1471-2164 https://doaj.org/article/892aecc46edd4c31b7e55775c1e42a53 |
op_doi |
https://doi.org/10.1186/s12864-024-10141-4 |
container_title |
BMC Genomics |
container_volume |
25 |
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1 |
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1810289492763869184 |