Pathways to polar adaptation in fishes revealed by long‐read sequencing

Hotaling, Scott; Desvignes, Thomas; Sproul, John S.; Lins, Luana S. F.; Kelley, Joanna L.

doi:10.1111/mec.16501

Cited by 10 publications

(7 citation statements)

References 130 publications

(210 reference statements)

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“…There must be some sort of cold compensation allowing higher rates of metabolism at low temperatures [31,32]. Thus, high rates of oxygen uptake have been observed in isolated brain slices of teleost fishes, and enzymes from the brains of Antarctic teleosts are more active at very low temperatures than those from animals adapted to warmer temperatures [31,[33][34][35], suggesting that partial compensation to temperature may exist in ATP producing pathways in fish brains. A study on green sunfish (Lepomis cyanellus) demonstrates that activities of glycolytic enzymes such as glucose phosphate isomerase, glyceraldehyde phosphate dehydrogenase, and pyruvate kinase are elevated in the brain during cold exposure [15,36].…”

Section: Discussionmentioning

confidence: 99%

Tissue-Specific and Differential Cold Responses in the Domesticated Cold Tolerant Fugu

Han

Wei

Chen

et al. 2022

Fishes

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Domestication can be defined as the artificial selection in animals to achieve morphological, physiological, and developmental conformity to human needs, with the aim of improving various limitations in species under a human feeding environment. The future sustainability of aquaculture may rely partly on the availability of numerous domesticated fish species. However, the underlying adaptive mechanisms that result in the domestication of fish are still unclear. Because they are poikilothermic, temperature is a key environmental element that affects the entire life of fish, so studying the association between physiological and behavioral changes in low-temperature domesticated fish can provide a model for understanding the response mechanisms of fish under cold stress. Through 5 generations and 10 years of artificial selection at low temperatures, we used cold-tolerant fugu as a biological model to compare transcriptome changes in brain and liver tissues to study the effects of cold stress on fish. It was found that the expression of genes such as apoptosis, p53, oxidative phosphorylation, and mitochondrial β-oxidation in the brain of cold-tolerant fugu was significantly lower than the wild type due to cold stress, while excessive energy metabolism would lead to the production of reactive oxygen species (ROS) and exacerbate the brain damage, thus causing rollover and coma. Meanwhile, under cold stress, the signaling pathways involved in glycogenolysis and lipid metabolism, such as insulin signaling, adipocytokines, and mTOR signaling pathways, were significantly up-regulated in the liver of cold-tolerant fugu. Although the mitochondrial β-oxidation pathway was increased in cold-tolerant fugu liver tissues, the transcriptome was not enriched in apoptotic. These phenomena predict that in response to low-temperature conditions, cold-tolerant fugu employs a dynamic inter-organ metabolic regulation strategy to cope with cold stress and reduce damage to brain tissues.

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Section: Discussionmentioning

confidence: 99%

Tissue-Specific and Differential Cold Responses in the Domesticated Cold Tolerant Fugu

Han

Wei

Chen

et al. 2022

Fishes

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“…The authors relied on PacBio long reads to obtain a genome assembly for the Antarctic eelpout, the first representative of the family Zoarcidae of ray‐finned fish to be genome‐sequenced. This highly contiguous assembly in turn allowed the authors to focus on regions of the genome such as the haemoglobin and antifreeze gene clusters which, while representing strong candidates for cold water adaptation, are arranged in highly duplicated tandem arrays (Hotaling et al, 2023). Results were consistent with convergent as well as species‐specific mechanisms of adaptation to the extremely cold waters of the Southern Ocean.…”

Section: Adaptation Genomicsmentioning

confidence: 99%

“…Comparisons with five other poplar species provided evidence of convergent evolution during adaptation to tropical environments. Hotaling et al (2023) provide another exciting example of how long reads are fast‐tracking the study of adaptation. The authors relied on PacBio long reads to obtain a genome assembly for the Antarctic eelpout, the first representative of the family Zoarcidae of ray‐finned fish to be genome‐sequenced.…”

Section: Adaptation Genomicsmentioning

confidence: 99%

Long‐read sequencing in ecology and evolution: Understanding how complex genetic and epigenetic variants shape biodiversity

et al. 2023

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“…The power of long reads to mitigate this issue is well-documented (e.g. [6][7][8]) but not all long reads are created equal; different platforms, technologies, and chemistries yield different read length versus error profiles [9][10][11]. This difference is particularly important since some long, repeat-rich genomic regions-including many genes of phenotypic relevance (e.g., antifreeze proteins in polar fishes)-pose assembly challenges even when long read data are used [6].…”

Section: Introductionmentioning

confidence: 99%

Highly accurate long reads are crucial for realizing the potential of biodiversity genomics

et al. 2023

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Background Generating the most contiguous, accurate genome assemblies given available sequencing technologies is a long-standing challenge in genome science. With the rise of long-read sequencing, assembly challenges have shifted from merely increasing contiguity to correctly assembling complex, repetitive regions of interest, ideally in a phased manner. At present, researchers largely choose between two types of long read data: longer, but less accurate sequences, or highly accurate, but shorter reads (i.e., >Q20 or 99% accurate). To better understand how these types of long-read data as well as scale of data (i.e., mean length and sequencing depth) influence genome assembly outcomes, we compared genome assemblies for a caddisfly, Hesperophylax magnus, generated with longer, but less accurate, Oxford Nanopore (ONT) R9.4.1 and highly accurate PacBio HiFi (HiFi) data. Next, we expanded this comparison to consider the influence of highly accurate long-read sequence data on genome assemblies across 6750 plant and animal genomes. For this broader comparison, we used HiFi data as a surrogate for highly accurate long-reads broadly as we could identify when they were used from GenBank metadata. Results HiFi reads outperformed ONT reads in all assembly metrics tested for the caddisfly data set and allowed for accurate assembly of the repetitive ~ 20 Kb H-fibroin gene. Across plants and animals, genome assemblies that incorporated HiFi reads were also more contiguous. For plants, the average HiFi assembly was 501% more contiguous (mean contig N50 = 20.5 Mb) than those generated with any other long-read data (mean contig N50 = 4.1 Mb). For animals, HiFi assemblies were 226% more contiguous (mean contig N50 = 20.9 Mb) versus other long-read assemblies (mean contig N50 = 9.3 Mb). In plants, we also found limited evidence that HiFi may offer a unique solution for overcoming genomic complexity that scales with assembly size. Conclusions Highly accurate long-reads generated with HiFi or analogous technologies represent a key tool for maximizing genome assembly quality for a wide swath of plants and animals. This finding is particularly important when resources only allow for one type of sequencing data to be generated. Ultimately, to realize the promise of biodiversity genomics, we call for greater uptake of highly accurate long-reads in future studies.

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Pathways to polar adaptation in fishes revealed by long‐read sequencing

Cited by 10 publications

References 130 publications

Tissue-Specific and Differential Cold Responses in the Domesticated Cold Tolerant Fugu

Tissue-Specific and Differential Cold Responses in the Domesticated Cold Tolerant Fugu

Long‐read sequencing in ecology and evolution: Understanding how complex genetic and epigenetic variants shape biodiversity

Highly accurate long reads are crucial for realizing the potential of biodiversity genomics

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