Fish genomics and its impact on fundamental and applied research of vertebrate biology

Ahmad, Syed Farhan; Jehangir, Maryam; Srikulnath, Kornsorn; Martins, Cesar

doi:10.1007/s11160-021-09691-7

Cited by 10 publications

(11 citation statements)

References 304 publications

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“…First, they consist of a phylogenetically diverse group with species that have evolved phenotypes naturally mimicking human diseases, called “evolutionary mutant models” [ 90 , 91 , 92 ]. Cross-species comparisons allow for the identification of the best models to study a specific physiological pathway [ 43 ]. Furthermore, in model species like zebrafish, genetic mutants for specific genes can be easily generated.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, sequencing of fish genomes has revolutionized vertebrate comparative genomics and has greatly contributed to our understanding of selection targets, evolutionary changes and speciation. Subsequently, fish have been suggested to serve as suitable models for human biomedical research [ 42 , 43 ]. Recently, epigenetic patterns emerging during the first stages of domestication, in the absence of genetic differences, have been studied in salmonids [ 44 , 45 ], European sea bass ( Dicentrarchus labrax ) [ 39 ], Nile tilapia ( Oreochromis niloticus ) [ 46 , 47 ] and grass carp ( Ctenopharyngodon idellus ) [ 48 ].…”

Section: Introductionmentioning

confidence: 99%

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Fish as Model Systems to Study Epigenetic Drivers in Human Self-Domestication and Neurodevelopmental Cognitive Disorders

Anastasiadi

Piferrer

Wellenreuther

et al. 2022

Genes

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Modern humans exhibit phenotypic traits and molecular events shared with other domesticates that are thought to be by-products of selection for reduced aggression. This is the human self-domestication hypothesis. As one of the first types of responses to a novel environment, epigenetic changes may have also facilitated early self-domestication in humans. Here, we argue that fish species, which have been recently domesticated, can provide model systems to study epigenetic drivers in human self-domestication. To test this, we used in silico approaches to compare genes with epigenetic changes in early domesticates of European sea bass with genes exhibiting methylation changes in anatomically modern humans (comparison 1), and neurodevelopmental cognitive disorders considered to exhibit abnormal self-domestication traits, i.e., schizophrenia, Williams syndrome, and autism spectrum disorders (comparison 2). Overlapping genes in comparison 1 were involved in processes like limb morphogenesis and phenotypes like abnormal jaw morphology and hypopigmentation. Overlapping genes in comparison 2 affected paralogue genes involved in processes such as neural crest differentiation and ectoderm differentiation. These findings pave the way for future studies using fish species as models to investigate epigenetic changes as drivers of human-self domestication and as triggers of cognitive disorders.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Fish as Model Systems to Study Epigenetic Drivers in Human Self-Domestication and Neurodevelopmental Cognitive Disorders

Anastasiadi

Piferrer

Wellenreuther

et al. 2022

Genes

View full text Add to dashboard Cite

show abstract

“…First, they consist of a phylogenetically diverse group with species that have evolved phenotypes naturally mimicking human diseases, called "evolutionary mutant models" [89][90][91]. Cross-species comparisons allow to identify the best models to study a specific physiological pathway [39]. Furthermore, in model species like zebrafish, genetic mutants for specific genes can be easily generated.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, sequencing of fish genomes has revolutionized vertebrate comparative genomics and has greatly contributed to our understanding of selection targets, evolutionary changes and speciation. Subsequently, fish have been suggested to serve as suitable models for human biomedical research [38,39]. Recently, epigenetic patterns emerging during the first stages of domestication, in the absence of genetic differences, have been studied in salmonids [40,41], European sea bass ( Dicentrarchus labrax ) [35], Nile tilapia ( Oreochromis niloticus ) [42,43] and grass carp ( Ctenopharyngodon idellus ) [44].…”

Section: Introductionmentioning

confidence: 99%

Fish as model systems to study epigenetic drivers in human self-domestication and neurodevelopmental cognitive disorders

Anastasiadi

Piferrer

Wellenreuther

et al. 2022

Preprint

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Modern humans exhibit phenotypic traits that are shared across independent domestication events, suggesting the human self-domestication hypothesis. Epigenetic changes may facilitate early self-domestication in humans, since they can be the first layer of response to a novel environment. Here, we argue that fish provide model systems to study epigenetic drivers in human self-domestication. To do this, we compare genes that carry epigenetic changes in early domesticates of European sea bass with 1) anatomically modern humans and 2) neurodevelopmental cognitive disorders with abnormal self-domestication traits, i.e., schizophrenia, Williams syndrome and autism spectrum disorders. We found that genes with epigenetic changes in fish and in modern vs ancient humans were shared and were involved in processes like limb morphogenesis and phenotypes like abnormal snout morphology and hypopigmentation. Moreover, early domestication in fish and neurodevelopmental cognitive impairment in humans affected paralogue genes involved in processes such as neural crest differentiation and ectoderm differentiation. We conclude that parallel epigenetic changes may occur at the initial steps of domestication in absence of deliberate selection in phylogenetically distant vertebrates. These findings pave the way for future studies using fish as models to investigate epigenetic changes as drivers of human-self domestication and as triggers of cognitive disorders.

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“…It is widely believed that WGD promotes evolutionary diversification through mechanisms that are still not fully understood [ 63 ]. Some authors have suggested that WGD, which is salmonid-specific, is followed by radiation exposure [ 64 , 65 ]. Autotetraploidization involves the spontaneous doubling of all chromosomes distinct from the other major WGD classes, allotetraploidization, which involves hybridization between different species.…”

Section: Characterization Of the Salmon Genomementioning

confidence: 99%

Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics

Dysin

Shcherbakov

Николаева

et al. 2022

Genes

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The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.

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Fish genomics and its impact on fundamental and applied research of vertebrate biology

Cited by 10 publications

References 304 publications

Fish as Model Systems to Study Epigenetic Drivers in Human Self-Domestication and Neurodevelopmental Cognitive Disorders

Fish as Model Systems to Study Epigenetic Drivers in Human Self-Domestication and Neurodevelopmental Cognitive Disorders

Fish as model systems to study epigenetic drivers in human self-domestication and neurodevelopmental cognitive disorders

Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics

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