Contrasting life-history traits of two toothfish (Dissostichus spp.) species at their range edge around the South Sandwich Islands

Soeffker, Marta; Hollyman, Philip R.; Collins, Martin A.; Hogg, Oliver T.; Riley, Ainsley; Laptikhovsky, Vladimir; Earl, Timothy; Roberts, Jim; MacLeod, Eleanor; Belchier, Mark; Darby, Chris

doi:10.1016/j.dsr2.2022.105098

Cited by 12 publications

(7 citation statements)

References 40 publications

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“…Patagonian toothfish support fisheries around the sub-Antarctic regions and understanding spatial stock structure is an important component in precautionary and sustainable management. Multiple studies have been carried out to identify stock structure of both toothfish species, including analysis of tagged fish movements [ 4 , 47 ], mineral deposits within otoliths [ 48 ], microsatellites [ 49 ], and SNP/RAD-Seq phylogenetic markers [ 50 ]. The Patagonian toothfish genome sequences provided by this study will further strengthen the resources available for population genetics, allowing identification of the most suitable restriction enzymes to use for RAD-Seq analysis [ 51 , 52 ], guiding the choice of neutral markers or restriction enzymes based on proximity to gene coding regions [ 53 ] and allowing a scan of the genome to identify regions showing higher levels of adaptive or balancing selection [ 54 , 55 ].…”

Section: Discussionmentioning

confidence: 99%

De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome

Ryder,

Stone,

Minardi

et al. 2024

BMC Genomics

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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 evolutionary studies on this and other closely related species.

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Section: Discussionmentioning

confidence: 99%

De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome

Ryder,

Stone,

Minardi

et al. 2024

BMC Genomics

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“…It is crucial to understand the spatial stock structure of the species to enable precautionary, sustainable management. Multiple studies have been carried out to identify stock structure of both toothfish species, including analysis of tagged fish movements (Soeffker et. al.…”

Section: Discussionmentioning

confidence: 99%

“…Patagonian toothfish ( Dissostichus eleginoides ) are found at depths between 70 and 2,500 m, on the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean (Collins et al ., 2010; Canales-Aguirre et al ., 2018a). D. eleginoides and its closely related sister species, the Antarctic toothfish ( Dissostichus mawsoni ), are both within the Nototheniidae clade, and their geographical distributions, for the most part, do not appear to overlap (Soeffker et al ., 2022, Roberts, Xavier and Agnew, 2011).…”

Section: Introductionmentioning

confidence: 99%

De novoassembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome

Ryder

Stone

Minardi

et al. 2022

Preprint

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Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae, found at depths between 70 and 2,500 meters on the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. Genomic sequence data for this species is limited. Here, we report a high-quality assembly and annotation of the D. eleginoides genome, 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. The high-quality genome assembly of the Patagonian toothfish will provide a valuable genetic resource for ecological and evolutionary studies on this and other closely related species.

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“…Oceanic fronts exemplify this: temperature abruptly decreases southwards of the Antarctic Polar Front, and where the Weddell Front cross the South Sandwich Islands. Consequently, communities in the northern part of the archipelago are typically composed by subantarctic species while those in the south are typically Antarctic species [23][24][25][26]. Conditions at border regions are less favourable for the survival and proliferation of species, with individuals inhabiting these areas being more susceptible to environmental change [27,28].…”

Section: Introductionmentioning

confidence: 99%

Southern Ocean food-webs and climate change: A short review and future directions

Queirós,

Borras-Chavez,

Friscourt

et al. 2024

PLOS Clim

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Food-webs are a critical feature of ecosystems and help us understand how communities will respond to climate change. The Southern Ocean is facing rapid and accelerating changes due to climate change. Though having evolved in an isolated and somewhat extreme environment, Southern Ocean biodiversity and food-webs are among the most vulnerable. Here, we review 1) current knowledge on Southern Ocean food-webs; 2) methods to study food-webs; 3) assessment of current and future impacts of climate change on Southern Ocean food-webs; 4) knowledge gaps; and 5) the role of Early Career Researchers (ECRs) in future studies. Most knowledge on Southern Ocean food-webs come from the pelagic environment, both at macro- and microbial levels. Modelling and diet studies of individual species are major contributors to the food-web knowledge. These studies revealed a short food-web, predominantly sustained by Antarctic Krill (Euphausia superba). Additionally, alternative pathways exist, involving other krill species, fish, and squid, which play equally important roles in connecting primary producers with top predators. Advantages and disadvantages of several techniques used to study Southern Ocean food-webs were identified, from the classical analyses of stomach contents, scats, or boluses to the most recent approaches such as metabarcoding and trophic-biomarkers. Observations show that climate change can impact the food-web in different ways. As an example, changes to smaller phytoplankton species can lengthen the food-web, increasing assimilation losses and/or changing nutrient cycles. Future studies need to focus on the benthic-dominated food-webs and the benthopelagic coupling. Furthermore, research during the winter season and below the ice-shelves is needed as these areas may play a crucial role in the functioning of this ecosystem. ECRs can play a significant role in advancing the study of Southern Ocean food-webs due to their willingness for interdisciplinary collaboration and proficiency in employing various methodologies, contributing to the construction of high-resolution food-webs.

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Contrasting life-history traits of two toothfish (Dissostichus spp.) species at their range edge around the South Sandwich Islands

Cited by 12 publications

References 40 publications

De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome

De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome

De novoassembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome

Southern Ocean food-webs and climate change: A short review and future directions

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