Fish genomics and its impact on fundamental and applied research of vertebrate biology
TL;DR: A recent overview of genomics data, address different approaches applicable to comparative genomics analyses, and illustrate these comparisons to better understand the complex mechanisms under the vertebrate genomes as mentioned in this paper, and summarize the applications in chromosomes research and cytogenomics.
Abstract: The living fishes span a unique and interesting set of animals because of their vast diversity, morphology, ecology, genetics and genomics, and higher importance to biology, economy and culture. During the past decade, the remarkable increase in fish genome sequencing has revolutionized comparative and evolutionary genomics, with the outcome of stimulating insights into vertebrate genome biology. Fish genomics has been transformed rapidly, with the availability of high-quality chromosome level genome assemblies and large collections of sequencing datasets, which are roadmaps for striking discoveries. Landmark achievements are being made; such as the accomplishment of fully assembled lungfish genome which is biggest genome ever sequenced. Here, we highlight current developments in vertebrate’s comparative genomics and discuss how fish genomes could be considered as vital resources for genomic studies. We present a recent overview of genomics data, address different approaches applicable to comparative genomics analyses, and illustrate these comparisons to better understand the complex mechanisms under the vertebrate genomes. We also summarize the applications in chromosomes research and cytogenomics.
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TL;DR: It is argued that fish provide model systems to study epigenetic drivers in human self-domestication and will 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.
Abstract: 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.
5 citations
TL;DR: Differences in the distribution and abundance of repetitive elements in chromosomes that have undergone remodeling processes during the course of evolution also suggest a possible role for simple repeat sequences in rearranged regions.
Abstract: The Pleuronectiformes order, which includes several commercially-important species, has undergone extensive chromosome evolution. One of these species is Solea senegalensis, a flatfish with 2n = 42 chromosomes. In this study, a cytogenomics approach and integration with previous maps was applied to characterize the karyotype of the species. Synteny analysis of S. senegalensis was carried out using two flatfish as a reference: Cynoglossus semilaevis and Scophthalmus maximus. Most S. senegalensis chromosomes (or chromosome arms for metacentrics and submetacentrics) showed a one-to-one macrosyntenic pattern with the other two species. In addition, we studied how repetitive sequences could have played a role in the evolution of S. senegalensis bi-armed (3, and 5–9) and acrocentric (11, 12 and 16) chromosomes, which showed the highest rearrangements compared with the reference species. A higher abundance of TEs (Transposable Elements) and other repeated elements was observed adjacent to telomeric regions on chromosomes 3, 7, 9 and 16. However, on chromosome 11, a greater abundance of DNA transposons was detected in interstitial BACs. This chromosome is syntenic with several chromosomes of the other two flatfish species, suggesting rearrangements during its evolution. A similar situation was also found on chromosome 16 (for microsatellites and low complexity sequences), but not for TEs (retroelements and DNA transposons). These differences in the distribution and abundance of repetitive elements in chromosomes that have undergone remodeling processes during the course of evolution also suggest a possible role for simple repeat sequences in rearranged regions.
3 citations
28 Feb 2022
TL;DR: In this paper , the authors compare genes that carry epigenetic changes in early domesticates of European sea bass with anatomically modern humans and neurodevelopmental cognitive disorders with abnormal self-domestication traits, i.e., schizophrenia, Williams syndrome and autism spectrum disorders.
Abstract: Abstract 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.
1 citations
TL;DR: A comprehensive overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species can be found in this article .
Abstract: 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.
1 citations
TL;DR: In this paper , the authors examined the relationship between the genome size, chromosome number and body length across all fishes and found that body length was associated with genome size whereas no relationship was noticed between the GS and the chromosome number.
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Mark Raymond Adams1, Susan E. Celniker2, Robert A. Holt1, Cheryl A. Evans1 +191 more•Institutions (23)
TL;DR: The nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome is determined using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map.
Abstract: The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.
6,180 citations
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27 Feb 2006
TL;DR: In this paper, the authors present a hierarchy of classes of the classes of Acanthodysseus: Superorder Ateleopodomorpha, Superorder Protacanthopterygii.
Abstract: PREFACE. ACKNOWLEDGMENTS. INTRODUCTION. PHYLUM CHORDATA. Subphylum Craniata. Superclass Myxinomorphi to Osteostracomorphi. Superclass Gnathostomata. +Class Placodermi. Class Chondrichthyes. Subclass Holocephali. Order Chimaeriformes. Subclass Elasmobranchii. Order Heterodontiformes. Order Orectolobiformes. Order Lamniformes. Order Carcharhiniformes. Order Hexanchiformes. Order Echinorhiniformes. Order Squaliformes. Order Squatiniformes. Order Pristiophoriformes. Order Torpediniformes. Order Pristiformes. Order Rajiformes. Order Myliobatiformes. +Class Acanthodii. Class Actinopterygii. Subclass Cladistia. Order Polypteriformes. Subclass Chrondrostei. Order Acipenseriformes. Subclass Neopterygii. Order Lepisosteiformes. Order Amiiformes. Division Teleostei. Subdivision Osteoglossomorpha. Order Hiodontiformes. Order Osteoglossiformes. Subdivision Elopomorpha. Order Elopiformes. Order Albuliformes. Order Anguilliformes. Order Saccopharyngiformes. Subdivision Ostarioclupeomorpha (= Otocephala). Superorder Clupeomorpha. Order Clupeiformes. Superorder Ostariophysi. Order Gonorynchiformes. Order Cypriniformes. Order Characiformes. Order Siluriformes. Order Gymnotiformes. Subdivision Euteleostei. Superorder Protacanthopterygii. Order Argentiniformes. Order Osmeriformes. Order Salmoniformes. Order Esociformes. Superorder Stenopterygii. Order Stomiiformes. Superorder Ateleopodomorpha. Order Ateleopodiformes. Superorder Cyclosquamata. Order Aulopiformes. Superorder Scopelomorpha. Order Myctophiformes. Superorder Lampriomorpha. Order Lampriformes. Superorder Polymixiomorpha. Order Polymixiiformes. Superorder Paracanthopterygii. Order Percopsiformes. Order Gadiformes. Order Ophidiiformes. Order Batrachoidiformes. Order Lophiiformes. Superorder Acanthopterygii. Series Mugilomorpha. Order Mugiliformes. Series Atherinomorpha. Order Atheriniformes. Order Beloniformes. Order Cyprinodontiformes. Series Percomorpha. Order Stephanoberyciformes. Order Beryciformes. Order Zeiformes. Order Gasterosteiformes. Order Synbranchiformes. Order Scorpaeniformes. Order Perciformes. Order Pleuronectiformes. Order Tetraodontiformes. Class Sarcopterygii. Subclass Coelacanthimorpha. Order Coelacanthiformes. Subclass Dipnotetrapodomorpha. Order Ceratodontiformes. Unranked Tetrapodomorpha. Infraclass Tetrapoda. APPENDIX. BIBLIOGRAPHY. INDEX.
5,681 citations
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Université catholique de Louvain1, McGill University2, Stanford University3, Pierre-and-Marie-Curie University4, Ludwig Maximilian University of Munich5, Centre national de la recherche scientifique6, École Normale Supérieure7, Washington University in St. Louis8, John Radcliffe Hospital9, Max Planck Society10, University of Basel11, University of Manchester12
TL;DR: The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration and provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history.
Abstract: The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275 transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent genetic redundancy, and one of the major problems to be tackled during the next stage of the yeast genome project is to elucidate the biological functions of all of these genes.
4,254 citations
TL;DR: The current version of iTOL v4 introduces four new dataset types, together with numerous new features, and is the first tool which supports direct visualization of Qiime 2 trees and associated annotations.
Abstract: The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. The current version introduces four new dataset types, together with numerous new features. Annotation options have been expanded and new control options added for many display elements. An interactive spreadsheet-like editor has been implemented, providing dataset creation and editing directly in the web interface. Font support has been rewritten with full support for UTF-8 character encoding throughout the user interface. Google Web Fonts are now fully supported in the tree text labels. iTOL v4 is the first tool which supports direct visualization of Qiime 2 trees and associated annotations. The user account system has been streamlined and expanded with new navigation options, and currently handles >700 000 trees from more than 40 000 individual users. Full batch access has been implemented allowing programmatic upload and export of trees and annotations.
4,233 citations