201
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Safian D, Wiegertjes GF, Pollux BJA. The Fish Family Poeciliidae as a Model to Study the Evolution and Diversification of Regenerative Capacity in Vertebrates. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.613157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The capacity of regenerating a new structure after losing an old one is a major challenge in the animal kingdom. Fish have emerged as an interesting model to study regeneration due to their high and diverse regenerative capacity. To date, most efforts have focused on revealing the mechanisms underlying fin regeneration, but information on why and how this capacity evolves remains incomplete. Here, we propose the livebearing fish family Poeciliidae as a promising new model system to study the evolution of fin regeneration. First, we review the current state of knowledge on the evolution of regeneration in the animal kingdom, with a special emphasis on fish fins. Second, we summarize recent advances in our understanding of the mechanisms behind fin regeneration in fish. Third, we discuss potential evolutionary pressures that may modulate the regenerative capacity of fish fins and propose three new theories for how natural and sexual selection can lead to the evolution of fin regeneration: (1) signaling-driven fin regeneration, (2) predation-driven fin regeneration, and (3) matrotrophy-suppressed fin regeneration. Finally, we argue that fish from the family Poeciliidae are an excellent model system to test these theories, because they comprise of a large variety of species in a well-defined phylogenetic framework that inhabit very different environments and display remarkable variation in reproductive traits, allowing for comparative studies of fin regeneration among closely related species, among populations within species or among individuals within populations. This new model system has the potential to shed new light on the underlying genetic and molecular mechanisms driving the evolution and diversification of regeneration in vertebrates.
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202
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Postlethwait JH, Massaquoi MS, Farnsworth DR, Yan YL, Guillemin K, Miller AC. The SARS-CoV-2 receptor and other key components of the Renin-Angiotensin-Aldosterone System related to COVID-19 are expressed in enterocytes in larval zebrafish. Biol Open 2021; 10:bio058172. [PMID: 33757938 PMCID: PMC8015242 DOI: 10.1242/bio.058172] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 01/08/2023] Open
Abstract
People with underlying conditions, including hypertension, obesity, and diabetes, are especially susceptible to negative outcomes after infection with coronavirus SARS-CoV-2, which causes COVID-19. Hypertension and respiratory inflammation are exacerbated by the Renin-Angiotensin-Aldosterone System (RAAS), which normally protects from rapidly dropping blood pressure via Angiotensin II (Ang II) produced by the enzyme Ace. The Ace paralog Ace2 degrades Ang II, counteracting its chronic effects, and serves as the SARS-CoV-2 receptor. Ace, the coronavirus, and COVID-19 comorbidities all regulate Ace2, but we do not yet understand how. To exploit zebrafish (Danio rerio) to help understand the relationship of the RAAS to COVID-19, we must identify zebrafish orthologs and co-orthologs of human RAAS genes and understand their expression patterns. To achieve these goals, we conducted genomic and phylogenetic analyses and investigated single cell transcriptomes. Results showed that most human RAAS genes have one or more zebrafish orthologs or co-orthologs. Results identified a specific type of enterocyte as the specific site of expression of zebrafish orthologs of key RAAS components, including Ace, Ace2, Slc6a19 (SARS-CoV-2 co-receptor), and the Angiotensin-related peptide cleaving enzymes Anpep (receptor for the common cold coronavirus HCoV-229E), and Dpp4 (receptor for the Middle East Respiratory Syndrome virus, MERS-CoV). Results identified specific vascular cell subtypes expressing Ang II receptors, apelin, and apelin receptor genes. These results identify genes and cell types to exploit zebrafish as a disease model for understanding mechanisms of COVID-19.
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Affiliation(s)
| | | | | | - Yi-Lin Yan
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Adam C Miller
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
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203
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Liang Y, Grauvogl M, Meyer A, Kratochwil CF. Functional conservation and divergence of color‐pattern‐related agouti family genes in teleost fishes. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:443-450. [DOI: 10.1002/jez.b.23041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/31/2021] [Accepted: 02/27/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Yipeng Liang
- Department of Biology, Chair in Zoology and Evolutionary Biology University of Konstanz Konstanz Germany
| | - Maximilian Grauvogl
- Department of Biology, Chair in Zoology and Evolutionary Biology University of Konstanz Konstanz Germany
| | - Axel Meyer
- Department of Biology, Chair in Zoology and Evolutionary Biology University of Konstanz Konstanz Germany
| | - Claudius F. Kratochwil
- Department of Biology, Chair in Zoology and Evolutionary Biology University of Konstanz Konstanz Germany
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204
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MRAP2 Interaction with Melanocortin-4 Receptor in SnakeHead ( Channa argus). Biomolecules 2021; 11:biom11030481. [PMID: 33807040 PMCID: PMC8004712 DOI: 10.3390/biom11030481] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/11/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023] Open
Abstract
The melanocortin-4 receptor (MC4R) plays an important role in the regulation of food intake and energy expenditure. Melanocortin-2 receptor accessory protein 2 (MRAP2) modulates trafficking, ligand binding, and signaling of MC4R. The Northern snakehead (Channa argus) is an economically important freshwater fish native to East Asia. To explore potential interaction between snakehead MC4R and MRAP2, herein we cloned snakehead mc4r and mrap2. The snakehead mc4r consisted of a 984 bp open reading frame encoding a protein of 327 amino acids, while snakehead mrap2 contained a 693 bp open reading frame encoding a protein of 230 amino acids. Synteny analysis indicated that mc4r was highly conserved with similar gene arrangement, while mrap2 contained two isoforms in teleost with different gene orders. Snakehead mc4r was primarily expressed in the brain, whereas mrap2 was expressed in the brain and intestine. Snakehead mc4r and mrap2 expression was modulated by fasting and refeeding. Further pharmacological experiments showed that the cloned snakehead MC4R was functional, capable of binding to peptide agonists and increasing intracellular cAMP production in a dose-dependent manner. Snakehead MC4R exhibited high constitutive activity. MRAP2 significantly decreased basal and agonist-stimulated cAMP signaling. These findings suggest that snakehead MC4R might be involved in energy balance regulation by interacting with MRAP2. Further studies are needed to elucidate MC4R in regulating diverse physiological processes in snakehead.
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205
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Lemopoulos A, Montoya-Burgos JI. From scales to armor: Scale losses and trunk bony plate gains in ray-finned fishes. Evol Lett 2021; 5:240-250. [PMID: 34136272 PMCID: PMC8190451 DOI: 10.1002/evl3.219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/04/2021] [Indexed: 11/25/2022] Open
Abstract
Actinopterygians (ray‐finned fishes) are the most diversified group of vertebrates and are characterized by a variety of protective structures covering their integument, the evolution of which has intrigued biologists for decades. Paleontological records showed that the first mineralized vertebrate skeleton was composed of dermal bony plates covering the body, including odontogenic and skeletogenic components. Later in evolution, the exoskeleton of actinopterygian's trunk was composed of scale structures. Although scales are nowadays a widespread integument cover, some contemporary lineages do not have scales but bony plates covering their trunk, whereas other lineages are devoid of any such structures. To understand the evolution of the integument coverage and particularly the transition between different structures, we investigated the pattern of scale loss events along with actinopterygian evolution and addressed the functional relationship between the scaleless phenotype and the ecology of fishes. Furthermore, we examined whether the emergence of trunk bony plates was dependent over the presence or absence of scales. To this aim, we used two recently published actinopterygian phylogenies, one including >11,600 species, and by using stochastic mapping and Bayesian methods, we inferred scale loss events and trunk bony plate acquisitions. Our results reveal that a scaled integument is the most frequent state in actinopterygians, but multiple independent scale loss events occurred along their phylogeny with essentially no scale re‐acquisition. Based on linear mixed models, we found evidence supporting that after a scale loss event, fishes tend to change their ecology and adopt a benthic lifestyle. Furthermore, we show that trunk bony plates appeared independently multiple times along the phylogeny. By using fitted likelihood models for character evolution, we show that trunk bony plate acquisitions were dependent on a previous scale loss event. Overall, our findings support the hypothesis that integument cover is a key evolutionary trait underlying actinopterygian radiation.
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Affiliation(s)
| | - Juan I Montoya-Burgos
- Department of Genetics and Evolution University of Geneva Geneva Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva Geneva Switzerland
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206
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Takezaki N. Resolving the Early Divergence Pattern of Teleost Fish Using Genome-Scale Data. Genome Biol Evol 2021; 13:6178791. [PMID: 33739405 PMCID: PMC8103497 DOI: 10.1093/gbe/evab052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2021] [Indexed: 12/13/2022] Open
Abstract
Regarding the phylogenetic relationship of the three primary groups of teleost fishes, Osteoglossomorpha (bonytongues and others), Elopomorpha (eels and relatives), Clupeocephala (the remaining teleost fish), early morphological studies hypothesized the first divergence of Osteoglossomorpha, whereas the recent prevailing view is the first divergence of Elopomorpha. Molecular studies supported all the possible relationships of the three primary groups. This study analyzed genome-scale data from four previous studies: 1) 412 genes from 12 species, 2) 772 genes from 15 species, 3) 1,062 genes from 30 species, and 4) 491 UCE loci from 27 species. The effects of the species, loci, and models used on the constructed tree topologies were investigated. In the analyses of the data sets (1)–(3), although the first divergence of Clupeocephala that left the other two groups in a sister relationship was supported by concatenated sequences and gene trees of all the species and genes, the first divergence of Elopomorpha among the three groups was supported using species and/or genes with low divergence of sequence and amino-acid frequencies. This result corresponded to that of the UCE data set (4), whose sequence divergence was low, which supported the first divergence of Elopomorpha with high statistical significance. The increase in accuracy of the phylogenetic construction by using species and genes with low sequence divergence was predicted by a phylogenetic informativeness approach and confirmed by computer simulation. These results supported that Elopomorpha was the first basal group of teleost fish to have diverged, consistent with the prevailing view of recent morphological studies.
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Affiliation(s)
- Naoko Takezaki
- Life Science Research Center, Kagawa University, Mikicho, Kitagun, Kagawa, Japan
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207
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Suurväli J, Whiteley AR, Zheng Y, Gharbi K, Leptin M, Wiehe T. The Laboratory Domestication of Zebrafish: From Diverse Populations to Inbred Substrains. Mol Biol Evol 2021; 37:1056-1069. [PMID: 31808937 PMCID: PMC7086173 DOI: 10.1093/molbev/msz289] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We know from human genetic studies that practically all aspects of biology are strongly influenced by the genetic background, as reflected in the advent of “personalized medicine.” Yet, with few exceptions, this is not taken into account when using laboratory populations as animal model systems for research in these fields. Laboratory strains of zebrafish (Danio rerio) are widely used for research in vertebrate developmental biology, behavior, and physiology, for modeling diseases, and for testing pharmaceutic compounds in vivo. However, all of these strains are derived from artificial bottleneck events and therefore are likely to represent only a fraction of the genetic diversity present within the species. Here, we use restriction site-associated DNA sequencing to genetically characterize wild populations of zebrafish from India, Nepal, and Bangladesh, and to compare them to previously published data on four common laboratory strains. We measured nucleotide diversity, heterozygosity, and allele frequency spectra, and find that wild zebrafish are much more diverse than laboratory strains. Further, in wild zebrafish, there is a clear signal of GC-biased gene conversion that is missing in laboratory strains. We also find that zebrafish populations in Nepal and Bangladesh are most distinct from all other strains studied, making them an attractive subject for future studies of zebrafish population genetics and molecular ecology. Finally, isolates of the same strains kept in different laboratories show a pattern of ongoing differentiation into genetically distinct substrains. Together, our findings broaden the basis for future genetic, physiological, pharmaceutic, and evolutionary studies in Danio rerio.
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Affiliation(s)
- Jaanus Suurväli
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Andrew R Whiteley
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Yichen Zheng
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom.,Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Maria Leptin
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Thomas Wiehe
- Institute for Genetics, University of Cologne, Cologne, Germany
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208
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Ritchie AM, Stark TL, Liberles DA. Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework. BMC Ecol Evol 2021; 21:39. [PMID: 33691618 PMCID: PMC7944921 DOI: 10.1186/s12862-021-01770-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/25/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Recovering the historical patterns of selection acting on a protein coding sequence is a major goal of evolutionary biology. Mutation-selection models address this problem by explicitly modelling fixation rates as a function of site-specific amino acid fitness values.However, they are restricted in their utility for investigating directional evolution because they require prior knowledge of the locations of fitness changes in the lineages of a phylogeny. RESULTS We apply a modified mutation-selection methodology that relaxes assumptions of equlibrium and time-reversibility. Our implementation allows us to identify branches where adaptive or compensatory shifts in the fitness landscape have taken place, signalled by a change in amino acid fitness profiles. Through simulation and analysis of an empirical data set of [Formula: see text]-lactamase genes, we test our ability to recover the position of adaptive events within the tree and successfully reconstruct initial codon frequencies and fitness profile parameters generated under the non-stationary model. CONCLUSION We demonstrate successful detection of selective shifts and identification of the affected branch on partitions of 300 codons or more. We successfully reconstruct fitness parameters and initial codon frequencies in simulated data and demonstrate that failing to account for non-equilibrium evolution can increase the error in fitness profile estimation. We also demonstrate reconstruction of plausible shifts in amino acid fitnesses in the bacterial [Formula: see text]-lactamase family and discuss some caveats for interpretation.
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Affiliation(s)
- Andrew M Ritchie
- Department of Biology, Temple University, 1900 North 12th Street, Philadelphia, PA, USA
| | - Tristan L Stark
- Department of Biology, Temple University, 1900 North 12th Street, Philadelphia, PA, USA
| | - David A Liberles
- Department of Biology, Temple University, 1900 North 12th Street, Philadelphia, PA, USA.
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209
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Loes AN, Hinman MN, Farnsworth DR, Miller AC, Guillemin K, Harms MJ. Identification and Characterization of Zebrafish Tlr4 Coreceptor Md-2. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 206:1046-1057. [PMID: 33472906 PMCID: PMC7889624 DOI: 10.4049/jimmunol.1901288] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/16/2020] [Indexed: 12/16/2022]
Abstract
The zebrafish (Danio rerio) is a powerful model organism for studies of the innate immune system. One apparent difference between human and zebrafish innate immunity is the cellular machinery for LPS sensing. In amniotes, the protein complex formed by TLR4 and myeloid differentiation factor 2 (Tlr4/Md-2) recognizes the bacterial molecule LPS and triggers an inflammatory response. It is believed that zebrafish have neither Md-2 nor Tlr4; Md-2 has not been identified outside of amniotes, whereas the zebrafish tlr4 genes appear to be paralogs, not orthologs, of amniote TLR4s We revisited these conclusions. We identified a zebrafish gene encoding Md-2, ly96 Using single-cell RNA sequencing, we found that ly96 is transcribed in cells that also transcribe genes diagnostic for innate immune cells, including the zebrafish tlr4-like genes. In larval zebrafish, ly96 is expressed in a small number of macrophage-like cells. In a functional assay, zebrafish Md-2 and Tlr4ba form a complex that activates NF-κB signaling in response to LPS. In larval zebrafish ly96 loss-of-function mutations perturbed LPS-induced cytokine production but gave little protection against LPS toxicity. Finally, by analyzing the genomic context of tlr4 genes in 11 jawed vertebrates, we found that tlr4 arose prior to the divergence of teleosts and tetrapods. Thus, an LPS-sensitive Tlr4/Md-2 complex is likely an ancestral feature shared by mammals and zebrafish, rather than a de novo invention on the tetrapod lineage. We hypothesize that zebrafish retain an ancestral, low-sensitivity Tlr4/Md-2 complex that confers LPS responsiveness to a specific subset of innate immune cells.
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Affiliation(s)
- Andrea N Loes
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
| | - Melissa N Hinman
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
- Department of Biology, University of Oregon, Eugene, OR 97403
| | - Dylan R Farnsworth
- Department of Biology, University of Oregon, Eugene, OR 97403
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403; and
| | - Adam C Miller
- Department of Biology, University of Oregon, Eugene, OR 97403
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403; and
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
- Department of Biology, University of Oregon, Eugene, OR 97403
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario M5G 1Z8, Canada
| | - Michael J Harms
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403;
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
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210
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De Serrano AR, Hughes KA, Rodd FH. Paternal exposure to a common pharmaceutical (Ritalin) has transgenerational effects on the behaviour of Trinidadian guppies. Sci Rep 2021; 11:3985. [PMID: 33597600 PMCID: PMC7889922 DOI: 10.1038/s41598-021-83448-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/02/2021] [Indexed: 01/04/2023] Open
Abstract
Evidence is emerging that paternal effects, the nongenetic influence of fathers on their offspring, can be transgenerational, spanning several generations. Methylphenidate hydrochloride (MPH; e.g. Ritalin) is a dopaminergic drug that is highly prescribed to adolescent males for the treatment of Attention-deficit/hyperactivity disorder. It has been suggested that MPH could cause transgenerational effects because MPH can affect the male germline in rodents and because paternal effects have been observed in individuals taking similar drugs (e.g. cocaine). Despite these concerns, the transgenerational effects of paternal MPH exposure are unknown. Therefore, we exposed male and female Trinidadian guppies (Poecilia reticulata) to a low, chronic dose of MPH and observed that MPH affected the anxiety/exploratory behaviour of males, but not females. Because of this male-specific effect, we investigated the transgenerational effects of MPH through the paternal line. We observed behavioural effects of paternal MPH exposure on offspring and great-grandoffspring that were not directly administered the drug, making this the first study to demonstrate that paternal MPH exposure can affect descendants. These effects were not due to differential mortality or fecundity between control and MPH lines. These results highlight the transgenerational potential of MPH.
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Affiliation(s)
- Alex R De Serrano
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St, Toronto, ON, M5S 3B2, Canada.
| | - Kimberly A Hughes
- Department of Biological Science, Florida State University, 319 Stadium Dr, Tallahassee, FL, 32304, USA
| | - F Helen Rodd
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St, Toronto, ON, M5S 3B2, Canada
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211
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dos Santos RZ, Calegari RM, Silva DMZDA, Ruiz-Ruano FJ, Melo S, Oliveira C, Foresti F, Uliano-Silva M, Porto-Foresti F, Utsunomia R. A Long-Term Conserved Satellite DNA That Remains Unexpanded in Several Genomes of Characiformes Fish Is Actively Transcribed. Genome Biol Evol 2021; 13:evab002. [PMID: 33502491 PMCID: PMC8210747 DOI: 10.1093/gbe/evab002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2021] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic genomes contain large amounts of repetitive DNA sequences, such as tandemly repeated satellite DNAs (satDNAs). These sequences are highly dynamic and tend to be genus- or species-specific due to their particular evolutionary pathways, although there are few unusual cases of conserved satDNAs over long periods of time. Here, we used multiple approaches to reveal that an satDNA named CharSat01-52 originated in the last common ancestor of Characoidei fish, a superfamily within the Characiformes order, ∼140-78 Ma, whereas its nucleotide composition has remained considerably conserved in several taxa. We show that 14 distantly related species within Characoidei share the presence of this satDNA, which is highly amplified and clustered in subtelomeric regions in a single species (Characidium gomesi), while remained organized as small clusters in all the other species. Defying predictions of the molecular drive of satellite evolution, CharSat01-52 shows similar values of intra- and interspecific divergence. Although we did not provide evidence for a specific functional role of CharSat01-52, its transcriptional activity was demonstrated in different species. In addition, we identified short tandem arrays of CharSat01-52 embedded within single-molecule real-time long reads of Astyanax paranae (536 bp-3.1 kb) and A. mexicanus (501 bp-3.9 kb). Such arrays consisted of head-to-tail repeats and could be found interspersed with other sequences, inverted sequences, or neighbored by other satellites. Our results provide a detailed characterization of an old and conserved satDNA, challenging general predictions of satDNA evolution.
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Affiliation(s)
- Rodrigo Zeni dos Santos
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | - Rodrigo Milan Calegari
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | | | - Francisco J Ruiz-Ruano
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology
Centre, Uppsala University, Uppsala, Sweden
| | - Silvana Melo
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | - Fausto Foresti
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | | | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | - Ricardo Utsunomia
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, ICBS,
Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janerio,
Brazil
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212
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Kim CH, Kim EJ, Nam YK. Superoxide Dismutase Multigene Family from a Primitive Chondrostean Sturgeon, Acipenser baerii: Molecular Characterization, Evolution, and Antioxidant Defense during Development and Pathogen Infection. Antioxidants (Basel) 2021; 10:232. [PMID: 33546486 PMCID: PMC7913737 DOI: 10.3390/antiox10020232] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/16/2022] Open
Abstract
Three distinct superoxide dismutases (SODs)-copper/zinc-SOD (SOD1), manganese-SOD (SOD2), and extracellular copper/zinc-SOD (SOD3)-were identified from a primitive chondrostean fish, Acipenser baerii, enabling the comparison of their transcriptional regulation patterns during development, prelarval ontogeny, and immune stimulation. Each A. baerii SOD isoform (AbSOD) shared conserved structural features with its vertebrate orthologs; however, phylogenetic analyses hypothesized a different evolutionary history for AbSOD3 relative to AbSOD1 and AbSOD2 in the vertebrate lineage. The AbSOD isoforms showed different tissue distribution patterns; AbSOD1 was predominantly expressed in most tissues. The expression of the AbSOD isoforms showed isoform-dependent dynamic modulation according to embryonic development and prelarval ontogenic behaviors. Prelarval microinjections revealed that lipopolysaccharide only induced AbSOD3 expression, while Aeromonas hydrophila induced the expression of AbSOD2 and AbSOD3. In fingerlings, the transcriptional response of each AbSOD isoform to bacterial infection was highly tissue-specific, and the three isoforms exhibited different response patterns within a given tissue type; AbSOD3 was induced the most sensitively, and its induction was the most pronounced in the kidneys and skin. Collectively, these findings suggest isoform-dependent roles for the multigene SOD family in antioxidant defenses against the oxidative stress associated with development and immune responses in these endangered sturgeon fish.
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Affiliation(s)
| | | | - Yoon Kwon Nam
- Department of Marine Bio-Materials and Aquaculture, College of Fisheries Sciences, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan 48513, Korea; (C.-H.K.); (E.J.K.)
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213
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Tian HF, Hu QM, Li Z. A high-quality de novo genome assembly of one swamp eel (Monopterus albus) strain with PacBio and Hi-C sequencing data. G3 (BETHESDA, MD.) 2021; 11:jkaa032. [PMID: 33561235 PMCID: PMC8022708 DOI: 10.1093/g3journal/jkaa032] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/22/2020] [Indexed: 12/16/2022]
Abstract
The swamp eel (Monopterus albus) is one economically important fish in China and South-Eastern Asia and a good model species to study sex inversion. There are different genetic lineages and multiple local strains of swamp eel in China, and one local strain of M. albus with deep yellow and big spots has been selected for consecutive selective breeding due to superiority in growth rate and fecundity. A high-quality reference genome of the swamp eel would be a very useful resource for future selective breeding program. In the present study, we applied PacBio single-molecule sequencing technique (SMRT) and the high-throughput chromosome conformation capture (Hi-C) technologies to assemble the M. albus genome. A 799 Mb genome was obtained with the contig N50 length of 2.4 Mb and scaffold N50 length of 67.24 Mb, indicating 110-fold and ∼31.87-fold improvement compared to the earlier released assembly (∼22.24 Kb and 2.11 Mb, respectively). Aided with Hi-C data, a total of 750 contigs were reliably assembled into 12 chromosomes. Using 22,373 protein-coding genes annotated here, the phylogenetic relationships of the swamp eel with other teleosts showed that swamp eel separated from the common ancestor of Zig-zag eel ∼49.9 million years ago, and 769 gene families were found expanded, which are mainly enriched in the immune system, sensory system, and transport and catabolism. This highly accurate, chromosome-level reference genome of M. albus obtained in this work will be used for the development of genome-scale selective breeding.
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Affiliation(s)
- Hai-Feng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Qiao-Mu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Zhong Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
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214
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Mehta TK, Koch C, Nash W, Knaack SA, Sudhakar P, Olbei M, Bastkowski S, Penso-Dolfin L, Korcsmaros T, Haerty W, Roy S, Di-Palma F. Evolution of regulatory networks associated with traits under selection in cichlids. Genome Biol 2021; 22:25. [PMID: 33419455 PMCID: PMC7791837 DOI: 10.1186/s13059-020-02208-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is known about gene regulatory network (GRN) evolution associated with phenotypic effect across ecologically diverse species. Here we use a novel approach for comparative GRN analysis in vertebrate species to study GRN evolution in representative species of the most striking examples of adaptive radiations, the East African cichlids. We previously demonstrated how the explosive phenotypic diversification of East African cichlids can be attributed to diverse molecular mechanisms, including accelerated regulatory sequence evolution and gene expression divergence. RESULTS To investigate these mechanisms across species at a genome-wide scale, we develop a novel computational pipeline that predicts regulators for co-extant and ancestral co-expression modules along a phylogeny, and candidate regulatory regions associated with traits under selection in cichlids. As a case study, we apply our approach to a well-studied adaptive trait-the visual system-for which we report striking cases of network rewiring for visual opsin genes, identify discrete regulatory variants, and investigate their association with cichlid visual system evolution. In regulatory regions of visual opsin genes, in vitro assays confirm that transcription factor binding site mutations disrupt regulatory edges across species and segregate according to lake species phylogeny and ecology, suggesting GRN rewiring in radiating cichlids. CONCLUSIONS Our approach reveals numerous novel potential candidate regulators and regulatory regions across cichlid genomes, including some novel and some previously reported associations to known adaptive evolutionary traits.
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Affiliation(s)
| | - Christopher Koch
- Department of Biostatistics and Medical Informatics, UW Madison, Madison, USA
| | | | - Sara A Knaack
- Wisconsin Institute for Discovery (WID), Madison, USA
| | | | - Marton Olbei
- Earlham Institute (EI), Norwich, UK
- Quadram Institute, Norwich, UK
| | - Sarah Bastkowski
- Earlham Institute (EI), Norwich, UK
- Quadram Institute, Norwich, UK
| | | | - Tamas Korcsmaros
- Earlham Institute (EI), Norwich, UK
- Quadram Institute, Norwich, UK
| | | | - Sushmita Roy
- Department of Biostatistics and Medical Informatics, UW Madison, Madison, USA.
- Wisconsin Institute for Discovery (WID), Madison, USA.
- Department of Computer Sciences, UW Madison, Madison, USA.
| | - Federica Di-Palma
- Earlham Institute (EI), Norwich, UK.
- Norwich Medical School, University of East Anglia, Norwich, UK.
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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215
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Costa VA, Mifsud JCO, Gilligan D, Williamson JE, Holmes EC, Geoghegan JL. Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray-Darling Basin, Australia. Virus Evol 2021; 7:veab034. [PMID: 34017611 PMCID: PMC8121191 DOI: 10.1093/ve/veab034] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Biological invasions are among the biggest threats to freshwater biodiversity. This is increasingly relevant in the Murray-Darling Basin, Australia, particularly since the introduction of the common carp (Cyprinus carpio). This invasive species now occupies up to ninety per cent of fish biomass, with hugely detrimental impacts on native fauna and flora. To address the ongoing impacts of carp, cyprinid herpesvirus 3 (CyHV-3) has been proposed as a potentially effective biological control agent. Crucially, however, it is unknown whether CyHV-3 and other cyprinid herpesviruses already exist in the Murray-Darling. Further, little is known about those viruses that naturally occur in wild freshwater fauna, and the frequency with which these viruses jump species boundaries. To document the evolution and diversity of freshwater fish viromes and better understand the ecological context to the proposed introduction of CyHV-3, we performed a meta-transcriptomic viral survey of invasive and native fish across the Murray-Darling Basin, covering over 2,200 km of the river system. Across a total of thirty-six RNA libraries representing ten species, we failed to detect CyHV-3 nor any closely related viruses. Rather, meta-transcriptomic analysis identified eighteen vertebrate-associated viruses that could be assigned to the Arenaviridae, Astroviridae, Bornaviridae, Caliciviridae, Coronaviridae, Chuviridae, Flaviviridae, Hantaviridae, Hepeviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae and Rhabdoviridae families, and a further twenty-seven that were deemed to be associated with non-vertebrate hosts. Notably, we revealed a marked lack of viruses that are shared among invasive and native fish sampled here, suggesting that there is little virus transmission from common carp to native fish species, despite co-existing for over fifty years. Overall, this study provides the first data on the viruses naturally circulating in a major river system and supports the notion that fish harbour a large diversity of viruses with often deep evolutionary histories.
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Affiliation(s)
- Vincenzo A Costa
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Jonathon C O Mifsud
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Dean Gilligan
- NSW Department of Primary Industries, Batemans Bay Fisheries Office, Batemans Bay 2536, Australia
| | - Jane E Williamson
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
- Institute of Environmental Science and Research, Wellington, Porirua 5022, New Zealand
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216
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Lv X, Hu J, Hu Y, Li Y, Xu D, Ryder OA, Irwin DM, Yu L. Diverse phylogenomic datasets uncover a concordant scenario of laurasiatherian interordinal relationships. Mol Phylogenet Evol 2020; 157:107065. [PMID: 33387649 DOI: 10.1016/j.ympev.2020.107065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 10/22/2022]
Abstract
Resolving the interordinal relationships in the mammalian superorder Laurasiatheria has been among the most intractable problems in higher-level mammalian systematics, with many conflicting hypotheses having been proposed. The present study collected three different sources of genome-scale data with comprehensive taxon sampling of laurasiatherian species, including two protein-coding datasets (4,186 protein-coding genes for an amino acid dataset comprising 2,761,247 amino acid residues and a nucleotide dataset comprising 5,516,340 nucleotides from 1st and 2nd codon positions), an intronic dataset (1,210 introns comprising 1,162,723 nucleotides) and an ultraconserved elements (UCEs) dataset (1,246 UCEs comprising 1,946,472 nucleotides) from 40 species representing all six laurasiatherian orders and 7 non-laurasiatherian outgroups. Remarkably, phylogenetic trees reconstructed with the four datasets using different tree-building methods (RAxML, FastTree, ASTRAL and MP-EST) all supported the relationship (Eulipotyphla, (Chiroptera, ((Carnivora, Pholidota), (Cetartiodactyla, Perissodactyla)))). We find a resolution of interordinal relationships of Laurasiatheria among all types of markers used in the present study, and the likelihood ratio tests for tree comparisons confirmed that the present tree topology is the optimal hypothesis compared to other examined hypotheses. Jackknifing subsampling analyses demonstrate that the results of laurasiatherian tree reconstruction varied with the number of loci and ordinal representatives used, which are likely the two main contributors to phylogenetic disagreements of Laurasiatheria seen in previous studies. Our study provides significant insight into laurasiatherian evolution, and moreover, an important methodological strategy and reference for resolving phylogenies of adaptive radiation, which have been a long-standing challenge in the field of phylogenetics.
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Affiliation(s)
- Xue Lv
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yiwen Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Yitian Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Dongming Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China
| | - Oliver A Ryder
- Institute for Conservation Research, San Diego Zoo Global, Escondido, CA, USA
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.
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217
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Rincon-Sandoval M, Duarte-Ribeiro E, Davis AM, Santaquiteria A, Hughes LC, Baldwin CC, Soto-Torres L, Acero P A, Walker HJ, Carpenter KE, Sheaves M, Ortí G, Arcila D, Betancur-R R. Evolutionary determinism and convergence associated with water-column transitions in marine fishes. Proc Natl Acad Sci U S A 2020; 117:33396-33403. [PMID: 33328271 PMCID: PMC7777220 DOI: 10.1073/pnas.2006511117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Repeatable, convergent outcomes are prima facie evidence for determinism in evolutionary processes. Among fishes, well-known examples include microevolutionary habitat transitions into the water column, where freshwater populations (e.g., sticklebacks, cichlids, and whitefishes) recurrently diverge toward slender-bodied pelagic forms and deep-bodied benthic forms. However, the consequences of such processes at deeper macroevolutionary scales in the marine environment are less clear. We applied a phylogenomics-based integrative, comparative approach to test hypotheses about the scope and strength of convergence in a marine fish clade with a worldwide distribution (snappers and fusiliers, family Lutjanidae) featuring multiple water-column transitions over the past 45 million years. We collected genome-wide exon data for 110 (∼80%) species in the group and aggregated data layers for body shape, habitat occupancy, geographic distribution, and paleontological and geological information. We also implemented approaches using genomic subsets to account for phylogenetic uncertainty in comparative analyses. Our results show independent incursions into the water column by ancestral benthic lineages in all major oceanic basins. These evolutionary transitions are persistently associated with convergent phenotypes, where deep-bodied benthic forms with truncate caudal fins repeatedly evolve into slender midwater species with furcate caudal fins. Lineage diversification and transition dynamics vary asymmetrically between habitats, with benthic lineages diversifying faster and colonizing midwater habitats more often than the reverse. Convergent ecological and functional phenotypes along the benthic-pelagic axis are pervasive among different lineages and across vastly different evolutionary scales, achieving predictable high-fitness solutions for similar environmental challenges, ultimately demonstrating strong determinism in fish body-shape evolution.
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Affiliation(s)
- Melissa Rincon-Sandoval
- Department of Biology, The University of Oklahoma, Norman, OK 73019
- Universidad Nacional de Colombia sede Caribe, Centro de Estudios en Ciencias del Mar (CECIMAR), Santa Marta, Magdalena, Colombia
| | | | - Aaron M Davis
- Centre for Tropical Water and Aquatic Ecosystem Research, School of Marine and Tropical Biology, James Cook University, Townsville, QLD 4811, Australia
| | | | - Lily C Hughes
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Luisángely Soto-Torres
- Department of Biology, Universidad de Puerto Rico-Rio Piedras, San Juan Puerto Rico, 00931
| | - Arturo Acero P
- Universidad Nacional de Colombia sede Caribe, Centro de Estudios en Ciencias del Mar (CECIMAR), Santa Marta, Magdalena, Colombia
| | - H J Walker
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0244
| | | | - Marcus Sheaves
- Marine Data Technology Hub, James Cook University, Townsville, QLD 4811, Australia
| | - Guillermo Ortí
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Dahiana Arcila
- Department of Biology, The University of Oklahoma, Norman, OK 73019
- Department of Ichthyology, Sam Noble Oklahoma Museum of Natural History, Norman, OK
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218
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Marisaldi L, Basili D, Gioacchini G, Canapa A, Carnevali O. De novo transcriptome assembly, functional annotation and characterization of the Atlantic bluefin tuna (Thunnus thynnus) larval stage. Mar Genomics 2020; 58:100834. [PMID: 33371994 DOI: 10.1016/j.margen.2020.100834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 10/22/2022]
Abstract
In the present work, we assembled and characterized a de novo larval transcriptome of the Atlantic bluefin tuna Thunnus thynnus by taking advantage of publicly available databases with the goal of better understanding its larval development. The assembled transcriptome comprised 37,117 protein-coding transcripts, of which 13,633 full-length (>80% coverage), with an Ex90N50 of 3061 bp and 76% of complete and single-copy core vertebrate genes orthologues. Of these transcripts, 34,980 had a hit against the EggNOG database and 14,983 with the KEGG database. Codon usage bias was identified in processes such as translation and muscle development. By comparing our data with a set of representative fish species, 87.1% of tuna transcripts were included in orthogroups with other species and 5.1% in assembly-specific orthogroups, which were enriched in terms related to muscle and bone development, visual system and ion transport. Following this comparative approach, protein families related to myosin, extracellular matrix and immune system resulted significantly expanded in the Atlantic bluefin tuna. Altogether, these results provide a glimpse of how the Atlantic bluefin tuna might have achieved early physical advantages over competing species in the pelagic environment. The information generated lays the foundation for future research on the more detailed exploration of physiological responses at the molecular level in different larval stages and paves the way to evolutionary studies on the Atlantic bluefin tuna.
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Affiliation(s)
- Luca Marisaldi
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona 60131, Italy
| | - Danilo Basili
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona 60131, Italy; Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Giorgia Gioacchini
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona 60131, Italy
| | - Adriana Canapa
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona 60131, Italy
| | - Oliana Carnevali
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona 60131, Italy.
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219
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Abstract
Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.
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Affiliation(s)
- M. Lisette Delgado
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Daniel E. Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
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220
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Scholz T, Waeschenbach A, Oros M, Brabec J, Littlewood DTJ. Phylogenetic reconstruction of early diverging tapeworms (Cestoda: Caryophyllidea) reveals ancient radiations in vertebrate hosts and biogeographic regions. Int J Parasitol 2020; 51:263-277. [PMID: 33275944 DOI: 10.1016/j.ijpara.2020.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/16/2020] [Accepted: 09/22/2020] [Indexed: 12/19/2022]
Abstract
Tapeworms of the order Caryophyllidea are the earliest diverging 'true' tapeworms (Eucestoda) and parasitise cypriniform and siluriform fishes almost exclusively. They are typified by a monozoic (non-proglottised) body plan, which is a characteristic shared with early diverging 'cestodarians' Gyrocotylidea and Amphilinidea. Here we present the most comprehensive multi-gene molecular phylogeny of this group, to date. Specimens of 63 species from 32 genera (~50% and ~75% of known species and genus diversity, respectively) were gathered during an intense and targeted 15-year collecting effort. Phylogenetic reconstructions provide high nodal support for three major lineages, which only partly correspond to currently recognised families. The three well-supported clades were as follows: Clade A was in an unsupported position at the base of the tree and was almost exclusively comprised of parasites of catfishes (Siluriformes) from the Afrotropical and Indomalayan regions, including the type genus of the Lytocestidae (Lytocestus). Clade B formed the sister group to the remaining taxa (Clade C) and was composed of species that parasitise cyprinids and loaches (Cypriniformes: Cyprinoidei and Cobitoidei) from the Palaearctic Region. This clade included the type genus of the Caryophyllaeidae (Caryophyllaeus). Clade C comprised Nearctic species from suckers and minnows (Cypriniformes: Catostomidae and Cyprinoidei), which were previously accommodated in two families, i.e. Capingentidae and Caryophyllaeidae. This clade included the type genus of the Capingentidae (Capingens). In addition to Clades A-C, Balanotaenia bancrofti from the monotypic Balanotaeniidae, which parasitises plotosid catfishes in Australia, and Lytocestoides tanganyikae, which parasitises African cichlids, formed a poorly supported clade at the base of the tree. Whereas morphological characteristics traditionally used to differentiate caryophyllidean families do not characterise molecular lineages, host association and biogeographical distribution play a key role in the circumscription of the three well-supported clades revealed by molecular data. Thus, the taxonomic rearrangement proposed herein was guided by the molecular clades. The names of all four extant families were preserved and family affinity was determined by topological clustering with the type genera of the families. The family diagnoses of the Lytocestidae, Caryophyllaeidae and Capingentidae are amended. Biogeographic patterns are indicative of separate Gondwanan and Laurasian radiations having taken place. Regarding the Gondwanan radiation in the Siluriformes, the topology in Clade A indicates an Asian origin with a subsequent African colonisation. Concerning Laurasia, separate radiations appear to have taken place in the Cypriniformes in the temperate zones of North America and Eurasia. Complete absence of caryophyllideans in the Neotropical Region, where numerous catfishes occur, may be due to the Gondwanan radiation having taken place after the continental separation of Africa and South America.
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Affiliation(s)
- Tomáš Scholz
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic.
| | - Andrea Waeschenbach
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Mikuláš Oros
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 040 10 Košice, Slovak Republic
| | - Jan Brabec
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - D Timothy J Littlewood
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
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221
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Wee NQX, Cutmore SC, Pérez-del-Olmo A, Cribb TH. First steps to restructuring the problematic genus Lasiotocus Looss, 1907 (Digenea: Monorchiidae) with the proposal of four new genera. Parasitol Int 2020; 79:102164. [DOI: 10.1016/j.parint.2020.102164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 10/24/2022]
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222
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Hughes LC, Ortí G, Saad H, Li C, White WT, Baldwin CC, Crandall KA, Arcila D, Betancur-R R. Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics. Mol Ecol Resour 2020; 21:816-833. [PMID: 33084200 DOI: 10.1111/1755-0998.13287] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 10/09/2020] [Indexed: 11/28/2022]
Abstract
Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon-capture sequence data into an existing data matrix of 1,104 exons and 300 ray-finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target-capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR-generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR-based exon and mitochondrial data.
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Affiliation(s)
- Lily C Hughes
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Computational Biology Institute, Milken Institute of Public Health, George Washington University, Washington, DC, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Guillermo Ortí
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Hadeel Saad
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Chenhong Li
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - William T White
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Keith A Crandall
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Computational Biology Institute, Milken Institute of Public Health, George Washington University, Washington, DC, USA
| | - Dahiana Arcila
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Sam Noble Oklahoma Museum of Natural History, Norman, OK, USA.,Department of Biology, University of Oklahoma, Norman, OK, USA
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223
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Matschiner M, Böhne A, Ronco F, Salzburger W. The genomic timeline of cichlid fish diversification across continents. Nat Commun 2020; 11:5895. [PMID: 33208747 PMCID: PMC7674422 DOI: 10.1038/s41467-020-17827-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/15/2020] [Indexed: 11/23/2022] Open
Abstract
Cichlid fishes are celebrated for their vast taxonomic, phenotypic, and ecological diversity; however, a central aspect of their evolution - the timeline of their diversification - remains contentious. Here, we generate draft genome assemblies of 14 species representing the global cichlid diversity and integrate these into a new phylogenomic hypothesis of cichlid and teleost evolution that we time-calibrate with 58 re-evaluated fossil constraints and a new Bayesian model accounting for fossil-assignment uncertainty. Our results support cichlid diversification long after the breakup of the supercontinent Gondwana and lay the foundation for precise temporal reconstructions of the exceptional continental cichlid adaptive radiations.
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Affiliation(s)
- Michael Matschiner
- Zoological Institute, University of Basel, Basel, Switzerland.
- Department of Palaeontology and Museum, University of Zurich, Zurich, Switzerland.
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Astrid Böhne
- Zoological Institute, University of Basel, Basel, Switzerland
- Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Fabrizia Ronco
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Walter Salzburger
- Zoological Institute, University of Basel, Basel, Switzerland.
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
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224
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Delgado ML, Manosalva A, Urbina MA, Habit E, Link O, Ruzzante DE. Genomic basis of the loss of diadromy in Galaxias maculatus: Insights from reciprocal transplant experiments. Mol Ecol 2020; 29:4857-4870. [PMID: 33048403 DOI: 10.1111/mec.15686] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/18/2022]
Abstract
Diadromy is known for having major effects on the distribution and richness of aquatic species, and so does its loss. The loss of diadromy has led to the diversification of many species, yet research focusing on understanding its molecular basis and consequences are limited. This is particularly true for amphidromous species despite being the most abundant group of diadromous species. Galaxias maculatus, an amphidromous species and one of the most widely distributed fishes in the Southern Hemisphere, exhibits many instances of nonmigratory or resident populations. The existence of naturally replicated resident populations in Patagonia can serve as an ideal system for the study of the mechanisms that lead to the loss of the diadromy and its ecological and evolutionary consequences. Here, we studied two adjacent river systems in which resident populations are genetically differentiated yet derived from the same diadromous population. By combining a reciprocal transplant experiment with genomic data, we showed that the two resident populations followed different evolutionary pathways by exhibiting a differential response in their capacity to survive in salt water. While one resident population was able to survive salt water, the other was not. Genomic analyses provided insights into the genes that distinguished (a) migratory from nonmigratory populations; (b) populations that can vs those that cannot survive a saltwater environment; and (c) between these resident populations. This study demonstrates that the loss of diadromy can be achieved by different pathways and that environmental (selection) and random (genetic drift) forces shape this dynamic evolutionary process.
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Affiliation(s)
| | - Aliro Manosalva
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA, Universidad de Concepción, Concepción, Chile
| | - Mauricio A Urbina
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Instituto Milenio de Oceanografía (IMO), Universidad de Concepción, Concepción, Chile
| | - Evelyn Habit
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA, Universidad de Concepción, Concepción, Chile
| | - Oscar Link
- Departamento de Ingeniería Civil, Facultad de Ingeniería, Universidad de Concepción, Concepción, Chile
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225
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Thieme P, Vallainc D, Moritz T. Postcranial skeletal development of Mugil cephalus (Teleostei: Mugiliformes): morphological and life-history implications for Mugiliformes. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Within the fish taxon Mugiliformes, the larval development of Mugil cephalus has been studied most intensively, because it has the widest range of distribution among all mugilids and is of interest to aquaculture all over the world. Although numerous studies have dealt with larval rearing, growth and development, the osteological development of M. cephalus and mugiliforms in general has largely been neglected. Herein, we describe the skeletal development of mullets for the first time. Cleared and double-stained specimens of aquaculture-reared M. cephalus and wild-caught mugilid larvae were examined to describe the early development of the pectoral and pelvic girdle, the vertebral column and the caudal and median fins. The description of four embryonic and six larval developmental steps within the embryonic and larval period enables us to compare larval sizes of reared and wild-caught larvae. Ontogenetic fusions of ural centra 1 and 2 into a compound centrum, in addition to the fusion of two pterygiophores in the anal fin, have implications for the perception of the adult morphology. Moreover, comparison of mugilid development with that of other ovalentarian taxa shows that recent phylogenetic hypotheses need further morphological investigation.
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Affiliation(s)
- Philipp Thieme
- Deutsches Meeresmuseum, Stralsund, Germany
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Dario Vallainc
- International Marine Centre IMC, Loc. Sa Mardini, Torregrande, (OR), Italy
| | - Timo Moritz
- Deutsches Meeresmuseum, Stralsund, Germany
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, Jena, Germany
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226
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Marín I. Tumor Necrosis Factor Superfamily: Ancestral Functions and Remodeling in Early Vertebrate Evolution. Genome Biol Evol 2020; 12:2074-2092. [PMID: 33210144 PMCID: PMC7674686 DOI: 10.1093/gbe/evaa140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2020] [Indexed: 01/01/2023] Open
Abstract
The evolution of the tumor necrosis factor superfamily (TNFSF) in early vertebrates is inferred by comparing the TNFSF genes found in humans and nine fishes: three agnathans, two chondrichthyans, three actinopterygians, and the sarcopterygian Latimeria chalumnae. By combining phylogenetic and synteny analyses, the TNFSF sequences detected are classified into five clusters of genes and 24 orthology groups. A model for their evolution since the origin of vertebrates is proposed. Fifteen TNFSF genes emerged from just three progenitors due to the whole-genome duplications (WGDs) that occurred before the agnathan/gnathostome split. Later, gnathostomes not only kept most of the genes emerged in the WGDs but soon added several tandem duplicates. More recently, complex, lineage-specific patterns of duplications and losses occurred in different gnathostome lineages. In agnathan species only seven to eight TNFSF genes are detected, because this lineage soon lost six of the genes emerged in the ancestral WGDs and additional losses in both hagfishes and lampreys later occurred. The orthologs of many of these lost genes are, in mammals, ligands of death-domain-containing TNFSF receptors, indicating that the extrinsic apoptotic pathway became simplified in the agnathan lineage. From the patterns of emergence of these genes, it is deduced that both the regulation of apoptosis and the control of the NF-κB pathway that depends in modern mammals on TNFSF members emerged before the ancestral vertebrate WGDs.
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Affiliation(s)
- Ignacio Marín
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
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227
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Presti P, Johnson GD, Datovo A. Anatomy and evolution of the pectoral filaments of threadfins (Polynemidae). Sci Rep 2020; 10:17751. [PMID: 33082461 PMCID: PMC7575576 DOI: 10.1038/s41598-020-74896-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/05/2020] [Indexed: 11/23/2022] Open
Abstract
The most remarkable anatomical specialization of threadfins (Percomorphacea: Polynemidae) is the division of their pectoral fin into an upper, unmodified fin and a lower portion with rays highly modified into specialized filaments. Such filaments are usually elongate, free from interradial membrane, and move independently from the unmodified fin to explore the environment. The evolution of the pectoral filaments involved several morphological modifications herein detailed for the first time. The posterior articular facet of the coracoid greatly expands anteroventrally during development. Similar expansions occur in pectoral radials 3 and 4, with the former usually acquiring indentations with the surrounding bones and losing association with both rays and filaments. Whereas most percomorphs typically have four or five muscles serving the pectoral fin, adult polynemids have up to 11 independent divisions in the intrinsic pectoral musculature. The main adductor and abductor muscles masses of the pectoral system are completely divided into two muscle segments, each independently serving the pectoral-fin rays (dorsally) and the pectoral filaments (ventrally). Based on the innervation pattern and the discovery of terminal buds in the external surface of the filaments, we demonstrate for the first time that the pectoral filaments of threadfins have both tactile and gustatory functions.
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Affiliation(s)
- Paulo Presti
- Museu de Zoologia da Universidade de São Paulo, Avenida Nazaré, 481, Ipiranga, São Paulo, SP, 04263-000, Brazil.
| | - G David Johnson
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Aléssio Datovo
- Museu de Zoologia da Universidade de São Paulo, Avenida Nazaré, 481, Ipiranga, São Paulo, SP, 04263-000, Brazil
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228
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Sun C, Li J, Dong J, Niu Y, Hu J, Lian J, Li W, Li J, Tian Y, Shi Q, Ye X. Chromosome-level genome assembly for the largemouth bass Micropterus salmoides provides insights into adaptation to fresh and brackish water. Mol Ecol Resour 2020; 21:301-315. [PMID: 32985096 DOI: 10.1111/1755-0998.13256] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022]
Abstract
Largemouth bass (LMB; Micropterus salmoides) has been an economically important fish in North America, Europe, and China. This study obtained a chromosome-level genome assembly of LMB using PacBio and Hi-C sequencing. The final assembled genome is 964 Mb, with contig N50 and scaffold N50 values of 1.23 Mb and 36.48 Mb, respectively. Combining with RNA sequencing data, we annotated a total of 23,701 genes. Chromosomal assembly and syntenic analysis proved that, unlike most Perciformes with the popular haploid chromosome number of 24, LMB has only 23 chromosomes (Chr), among which the Chr1 seems to be resulted from a chromosomal fusion event. LMB is phylogenetically closely related to European seabass and spotted seabass, diverging 64.1 million years ago (mya) from the two seabass species. Eight gene families comprising 294 genes associated with ionic regulation were identified through positive selection, transcriptome and genome comparisons. These genes involved in iron facilitated diffusion (such as claudin, aquaporins, sodium channel protein and so on) and others related to ion active transport (such as sodium/potassium-transporting ATPase and sodium/calcium exchanger). The claudin gene family, which is critical for regulating cell tight junctions and osmotic homeostasis, showed a significant expansion in LMB with 27 family members and 68 copies for salinity adaptation. In summary, we reported the first high-quality LMB genome, and provided insights into the molecular mechanisms of LMB adaptation to fresh and brackish water. The chromosome-level LMB genome will also be a valuable genomic resource for in-depth biological and evolutionary studies, germplasm conservation and genetic breeding of LMB.
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Affiliation(s)
- Chengfei Sun
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jia Li
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Junjian Dong
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | | | - Jie Hu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | | | - Wuhui Li
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jiang Li
- Biozeron Shenzhen Inc., Shenzhen, China
| | - Yuanyuan Tian
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Qiong Shi
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Xing Ye
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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229
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Galbraith JD, Ludington AJ, Suh A, Sanders KL, Adelson DL. New Environment, New Invaders-Repeated Horizontal Transfer of LINEs to Sea Snakes. Genome Biol Evol 2020; 12:2370-2383. [PMID: 33022046 PMCID: PMC7846101 DOI: 10.1093/gbe/evaa208] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2020] [Indexed: 12/12/2022] Open
Abstract
Although numerous studies have found horizontal transposon transfer (HTT) to be widespread across metazoans, few have focused on HTT in marine ecosystems. To investigate potential recent HTTs into marine species, we searched for novel repetitive elements in sea snakes, a group of elapids which transitioned to a marine habitat at most 18 Ma. Our analysis uncovered repeated HTTs into sea snakes following their marine transition. The seven subfamilies of horizontally transferred LINE retrotransposons we identified in the olive sea snake (Aipysurus laevis) are transcribed, and hence are likely still active and expanding across the genome. A search of 600 metazoan genomes found all seven were absent from other amniotes, including terrestrial elapids, with the most similar LINEs present in fish and marine invertebrates. The one exception was a similar LINE found in sea kraits, a lineage of amphibious elapids which independently transitioned to a marine environment 25 Ma. Our finding of repeated horizontal transfer events into marine snakes greatly expands past findings that the marine environment promotes the transfer of transposons. Transposons are drivers of evolution as sources of genomic sequence and hence genomic novelty. We identified 13 candidate genes for HTT-induced adaptive change based on internal or neighboring HTT LINE insertions. One of these, ADCY4, is of particular interest as a part of the KEGG adaptation pathway “Circadian Entrainment.” This provides evidence of the ecological interactions between species influencing evolution of metazoans not only through specific selection pressures, but also by contributing novel genomic material.
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Affiliation(s)
| | | | - Alexander Suh
- Department of Ecology and Genetics-Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden.,Department of Organismal Biology-Systematic Biology, Evolutionary Biology Centre, Uppsala University, Sweden.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Kate L Sanders
- School of Biological Sciences, University of Adelaide, Australia
| | - David L Adelson
- School of Biological Sciences, University of Adelaide, Australia
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230
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McCraney WT, Thacker CE, Alfaro ME. Supermatrix phylogeny resolves goby lineages and reveals unstable root of Gobiaria. Mol Phylogenet Evol 2020; 151:106862. [DOI: 10.1016/j.ympev.2020.106862] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 05/06/2020] [Accepted: 05/21/2020] [Indexed: 01/04/2023]
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231
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Carducci F, Barucca M, Canapa A, Carotti E, Biscotti MA. Mobile Elements in Ray-Finned Fish Genomes. Life (Basel) 2020; 10:E221. [PMID: 32992841 PMCID: PMC7599744 DOI: 10.3390/life10100221] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
Ray-finned fishes (Actinopterygii) are a very diverse group of vertebrates, encompassing species adapted to live in freshwater and marine environments, from the deep sea to high mountain streams. Genome sequencing offers a genetic resource for investigating the molecular bases of this phenotypic diversity and these adaptations to various habitats. The wide range of genome sizes observed in fishes is due to the role of transposable elements (TEs), which are powerful drivers of species diversity. Analyses performed to date provide evidence that class II DNA transposons are the most abundant component in most fish genomes and that compared to other vertebrate genomes, many TE superfamilies are present in actinopterygians. Moreover, specific TEs have been reported in ray-finned fishes as a possible result of an intricate relationship between TE evolution and the environment. The data summarized here underline the biological interest in Actinopterygii as a model group to investigate the mechanisms responsible for the high biodiversity observed in this taxon.
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Affiliation(s)
| | | | | | | | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy; (F.C.); (M.B.); (A.C.); (E.C.)
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232
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Emlaw JR, Burkett KM, daCosta CJB. Contingency between Historical Substitutions in the Acetylcholine Receptor Pore. ACS Chem Neurosci 2020; 11:2861-2868. [PMID: 32786311 DOI: 10.1021/acschemneuro.0c00410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Human adult muscle-type acetylcholine receptors incorporating a reconstructed ancestral β-subunit exhibit reduced single-channel conductance when compared to wild-type. The ancestral and wild-type β-subunits differ by 132 amino acids, including substitution of residues that line the lumen of the channel pore, near its narrowest constriction. Here we show that a single historical substitution in this region of the ancestral β-subunit accounts for the difference in conductance. Furthermore, the contribution of the substituted residue to conductance is dependent upon its ancestral or wild-type background, and it can be modulated by a neighboring residue that has also evolved throughout the β-subunit history. Using an expanded molecular phylogeny, we track the order in which these two mutations occurred and then show that the order in which they are installed upon the ancestral, but not the human, background determines their individual contribution to conductance. Our results show how the contribution of amino acids to acetylcholine receptor conductance is contingent upon their evolutionary history and that the order in which substitutions occurred was important for shaping conductance in the modern-day receptor.
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233
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Smith SA, Walker-Hale N, Walker JF. Intragenic Conflict in Phylogenomic Data Sets. Mol Biol Evol 2020; 37:3380-3388. [DOI: 10.1093/molbev/msaa170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Abstract
Most phylogenetic analyses assume that a single evolutionary history underlies one gene. However, both biological processes and errors can cause intragenic conflict. The extent to which this conflict is present in empirical data sets is not well documented, but if common, could have far-reaching implications for phylogenetic analyses. We examined several large phylogenomic data sets from diverse taxa using a fast and simple method to identify well-supported intragenic conflict. We found conflict to be highly variable between data sets, from 1% to >92% of genes investigated. We analyzed four exemplar genes in detail and analyzed simulated data under several scenarios. Our results suggest that alignment error may be one major source of conflict, but other conflicts remain unexplained and may represent biological signal or other errors. Whether as part of data analysis pipelines or to explore biologically processes, analyses of within-gene phylogenetic signal should become common.
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Affiliation(s)
- Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | | | - Joseph F Walker
- The Sainsbury Laboratory (SLCU), University of Cambridge, Cambridge, United Kingdom
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234
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Development of the ventricular myocardial trabeculae in Scyliorhinus canicula (Chondrichthyes): evolutionary implications. Sci Rep 2020; 10:14434. [PMID: 32879349 PMCID: PMC7468296 DOI: 10.1038/s41598-020-71318-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/05/2020] [Indexed: 12/16/2022] Open
Abstract
The development of the ventricular myocardial trabeculae occurs in three steps: emergence, trabeculation and remodeling. The whole process has been described in vertebrates with two different myocardial structural types, spongy (zebrafish) and compact (chicken and mouse). In this context, two alternative mechanisms of myocardial trabeculae emergence have been identified: (1) in chicken and mouse, the endocardial cells invade the two-layered myocardium; (2) in zebrafish, cardiomyocytes from the monolayered myocardium invaginate towards the endocardium. Currently, the process has not been studied in detail in vertebrates having a mixed type of ventricular myocardium, with an inner trabecular and an outer compact layer, which is presumptively the most primitive morphology in gnathostomes. We studied the formation of the mixed ventricular myocardium in the lesser spotted dogfish (Scyliorhinus canicula, Elasmobranchii), using light, scanning and transmission electron microscopy. Our results show that early formation of the mixed ventricular myocardium, specifically the emergence and the trabeculation steps, is driven by an endocardial invasion of the myocardium. The mechanism of trabeculation of the mixed ventricular myocardium in chondrichthyans is the one that best reproduces how this developmental process has been established from the beginning of the gnathostome radiation. The process has been apparently preserved throughout the entire group of sarcopterygians, including birds and mammals. In contrast, teleosts, at least those possessing a mostly spongy ventricular myocardium, seem to have introduced notable changes in their myocardial trabeculae development.
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235
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Postlethwait JH, Farnsworth DR, Miller AC. An intestinal cell type in zebrafish is the nexus for the SARS-CoV-2 receptor and the Renin-Angiotensin-Aldosterone System that contributes to COVID-19 comorbidities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32908984 DOI: 10.1101/2020.09.01.278366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
People with underlying conditions, including hypertension, obesity, and diabetes, are especially susceptible to negative outcomes after infection with the coronavirus SARS-CoV-2. These COVID-19 comorbidities are exacerbated by the Renin-Angiotensin-Aldosterone System (RAAS), which normally protects from rapidly dropping blood pressure or dehydration via the peptide Angiotensin II (Ang II) produced by the enzyme Ace. The Ace paralog Ace2 degrades Ang II, thus counteracting its chronic effects. Ace2 is also the SARS-CoV-2 receptor. Ace , the coronavirus, and COVID-19 comorbidities all regulate Ace2 , but we don't yet understand how. To exploit zebrafish ( Danio rerio ) as a disease model to understand mechanisms regulating the RAAS and its relationship to COVID-19 comorbidities, we must first identify zebrafish orthologs and co-orthologs of human RAAS genes, and second, understand where and when these genes are expressed in specific cells in zebrafish development. To achieve these goals, we conducted genomic analyses and investigated single cell transcriptomes. Results showed that most human RAAS genes have an ortholog in zebrafish and some have two or more co-orthologs. Results further identified a specific intestinal cell type in zebrafish larvae as the site of expression for key RAAS components, including Ace, Ace2, the coronavirus co-receptor Slc6a19, and the Angiotensin-related peptide cleaving enzymes Anpep and Enpep. Results also identified specific vascular cell subtypes as expressing Ang II receptors, apelin , and apelin receptor genes. These results identify specific genes and cell types to exploit zebrafish as a disease model for understanding the mechanisms leading to COVID-19 comorbidities. SUMMARY STATEMENT Genomic analyses identify zebrafish orthologs of the Renin-Angiotensin-Aldosterone System that contribute to COVID-19 comorbidities and single-cell transcriptomics show that they act in a specialized intestinal cell type.
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236
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Stundl J, Pospisilova A, Matějková T, Psenicka M, Bronner ME, Cerny R. Migratory patterns and evolutionary plasticity of cranial neural crest cells in ray-finned fishes. Dev Biol 2020; 467:14-29. [PMID: 32835652 DOI: 10.1016/j.ydbio.2020.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
The cranial neural crest (CNC) arises within the developing central nervous system, but then migrates away from the neural tube in three consecutive streams termed mandibular, hyoid and branchial, respectively, according to the order along the anteroposterior axis. While the process of neural crest emigration generally follows a conserved anterior to posterior sequence across vertebrates, we find that ray-finned fishes (bichir, sterlet, gar, and pike) exhibit several heterochronies in the timing and order of CNC emergence that influences their subsequent migratory patterns. First, emigration of the cranial neural crest in these fishes occurs prematurely compared to other vertebrates, already initiating during early neurulation and well before neural tube closure. Second, delamination of the hyoid stream occurs prior to the more anterior mandibular stream; this is associated with early morphogenesis of key hyoid structures like external gills (bichir), a large opercular flap (gar) or first forming cartilage (pike). In sterlet, the hyoid and branchial CNC cells form a single hyobranchial sheet, which later segregates in concert with second pharyngeal pouch morphogenesis. Taken together, the results show that despite generally conserved migratory patterns, heterochronic alterations in the timing of emigration and pattern of migration of CNC cells accompanies morphological diversity of ray-finned fishes.
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Affiliation(s)
- Jan Stundl
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Vodnany, Czech Republic.
| | - Anna Pospisilova
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Tereza Matějková
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Martin Psenicka
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Vodnany, Czech Republic
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Robert Cerny
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic.
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237
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Aardema ML, Stiassny MLJ, Alter SE. Genomic Analysis of the Only Blind Cichlid Reveals Extensive Inactivation in Eye and Pigment Formation Genes. Genome Biol Evol 2020; 12:1392-1406. [PMID: 32653909 PMCID: PMC7502198 DOI: 10.1093/gbe/evaa144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2020] [Indexed: 12/21/2022] Open
Abstract
Trait loss represents an intriguing evolutionary problem, particularly when it occurs across independent lineages. Fishes in light-poor environments often evolve “troglomorphic” traits, including reduction or loss of both pigment and eyes. Here, we investigate the genomic basis of trait loss in a blind and depigmented African cichlid, Lamprologus lethops, and explore evolutionary forces (selection and drift) that may have contributed to these losses. This species, the only known blind cichlid, is endemic to the lower Congo River. Available evidence suggests that it inhabits deep, low-light habitats. Using genome sequencing, we show that genes related to eye formation and pigmentation, as well as other traits associated with troglomorphism, accumulated inactivating mutations rapidly after speciation. A number of the genes affected in L. lethops are also implicated in troglomorphic phenotypes in Mexican cavefish (Astyanax mexicanus) and other species. Analysis of heterozygosity patterns across the genome indicates that L. lethops underwent a significant population bottleneck roughly 1 Ma, after which effective population sizes remained low. Branch-length tests on a subset of genes with inactivating mutations show little evidence of directional selection; however, low overall heterozygosity may reduce statistical power to detect such signals. Overall, genome-wide patterns suggest that accelerated genetic drift from a severe bottleneck, perhaps aided by directional selection for the loss of physiologically expensive traits, caused inactivating mutations to fix rapidly in this species.
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Affiliation(s)
- Matthew L Aardema
- Department of Biology, Montclair State University.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, New York
| | - S Elizabeth Alter
- Department of Ichthyology, American Museum of Natural History, New York, New York.,The Graduate Center, City University of New York.,Department of Biology, York College/The City University of New York
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238
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Swann JB, Holland SJ, Petersen M, Pietsch TW, Boehm T. The immunogenetics of sexual parasitism. Science 2020; 369:1608-1615. [PMID: 32732279 DOI: 10.1126/science.aaz9445] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 07/17/2020] [Indexed: 01/29/2023]
Abstract
Sexual parasitism has evolved as a distinctive mode of reproduction among deep-sea anglerfishes. The permanent attachment of males to host females observed in these species represents a form of anatomical joining, which is otherwise unknown in nature. Pronounced modifications to immune facilities are associated with this reproductive trait. The genomes of species with temporarily attaching males lack functional aicda genes that underpin affinity maturation of antibodies. Permanent attachment is associated with additional alterations, culminating in the loss of functional rag genes in some species, abolishing somatic diversification of antigen receptor genes, the hallmark of canonical adaptive immunity. In anglerfishes, coevolution of innate and adaptive immunity has been disentangled, implying that an alternative form of immunity supported the emergence of this evolutionarily successful group of vertebrates.
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Affiliation(s)
- Jeremy B Swann
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany.
| | - Stephen J Holland
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Malte Petersen
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Theodore W Pietsch
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98105-5020, USA
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany.
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239
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Unravelling the Complex Duplication History of Deuterostome Glycerol Transporters. Cells 2020; 9:cells9071663. [PMID: 32664262 PMCID: PMC7408487 DOI: 10.3390/cells9071663] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 12/12/2022] Open
Abstract
Transmembrane glycerol transport is an ancient biophysical property that evolved in selected subfamilies of water channel (aquaporin) proteins. Here, we conducted broad level genome (>550) and transcriptome (>300) analyses to unravel the duplication history of the glycerol-transporting channels (glps) in Deuterostomia. We found that tandem duplication (TD) was the major mechanism of gene expansion in echinoderms and hemichordates, which, together with whole genome duplications (WGD) in the chordate lineage, continued to shape the genomic repertoires in craniates. Molecular phylogenies indicated that aqp3-like and aqp13-like channels were the probable stem subfamilies in craniates, with WGD generating aqp9 and aqp10 in gnathostomes but aqp7 arising through TD in Osteichthyes. We uncovered separate examples of gene translocations, gene conversion, and concerted evolution in humans, teleosts, and starfishes, with DNA transposons the likely drivers of gene rearrangements in paleotetraploid salmonids. Currently, gene copy numbers and BLAST are poor predictors of orthologous relationships due to asymmetric glp gene evolution in the different lineages. Such asymmetries can impact estimations of divergence times by millions of years. Experimental investigations of the salmonid channels demonstrated that approximately half of the 20 ancestral paralogs are functional, with neofunctionalization occurring at the transcriptional level rather than the protein transport properties. The combined findings resolve the origins and diversification of glps over >800 million years old and thus form the novel basis for proposing a pandeuterostome glp gene nomenclature.
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240
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Machado AM, Muñoz-Merida A, Fonseca E, Veríssimo A, Pinto R, Felício M, da Fonseca RR, Froufe E, Castro LFC. Liver transcriptome resources of four commercially exploited teleost species. Sci Data 2020; 7:214. [PMID: 32636445 PMCID: PMC7340784 DOI: 10.1038/s41597-020-0565-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 06/09/2020] [Indexed: 01/10/2023] Open
Abstract
The generation of omic resources is central to develop adequate management strategies for species with economic value. Here, we provide high-coverage RNA-seq datasets of liver tissue (containing between 80,2 and 88,4 million of paired-end reads) from four wildtype teleost species with high commercial value: Trachurus trachurus (TTR; Atlantic horse mackerel), Scomber scombrus (SSC; Atlantic mackerel), Trisopterus luscus (TLU; pout), and Micromesistius poutassou (MPO; blue whiting). A comprehensive assembly pipeline, using de novo single and multi-kmer assembly approaches, produced 64 single high-quality liver transcriptomes - 16 per species. The final assemblies, with N50 values ranging from 2,543-3,700 bp and BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness values between 81.8-86.5% of the Actinopterygii gene set, were subjected to open reading frame (ORF) prediction and functional annotation. Our study provides the first transcriptomic resources for these species and offers valuable tools to evaluate both neutral and selected genetic variation among populations, and to identify candidate genes for environmental adaptation assisting in the investigation of the effects of global changes in fisheries.
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Affiliation(s)
- André M Machado
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto - University of Porto, Porto, Portugal.
| | - Antonio Muñoz-Merida
- CIBIO-InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Elza Fonseca
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto - University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Porto, Portugal
| | - Ana Veríssimo
- CIBIO-InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Porto, Portugal
| | - Rui Pinto
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto - University of Porto, Porto, Portugal
| | - Mónica Felício
- Portuguese Institute for the Sea and Atmosphere, I.P. (IPMA), Lisbon, Portugal
| | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Elsa Froufe
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto - University of Porto, Porto, Portugal
| | - L Filipe C Castro
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto - University of Porto, Porto, Portugal.
- Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Porto, Portugal.
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241
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Genomes of major fishes in world fisheries and aquaculture: Status, application and perspective. AQUACULTURE AND FISHERIES 2020. [DOI: 10.1016/j.aaf.2020.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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242
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Dalziel AC, Tirbhowan S, Drapeau HF, Power C, Jonah LS, Gbotsyo YA, Dion‐Côté A. Using asexual vertebrates to study genome evolution and animal physiology: Banded ( Fundulus diaphanus) x Common Killifish ( F. heteroclitus) hybrid lineages as a model system. Evol Appl 2020; 13:1214-1239. [PMID: 32684956 PMCID: PMC7359844 DOI: 10.1111/eva.12975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/27/2022] Open
Abstract
Wild, asexual, vertebrate hybrids have many characteristics that make them good model systems for studying how genomes evolve and epigenetic modifications influence animal physiology. In particular, the formation of asexual hybrid lineages is a form of reproductive incompatibility, but we know little about the genetic and genomic mechanisms by which this mode of reproductive isolation proceeds in animals. Asexual lineages also provide researchers with the ability to produce genetically identical individuals, enabling the study of autonomous epigenetic modifications without the confounds of genetic variation. Here, we briefly review the cellular and molecular mechanisms leading to asexual reproduction in vertebrates and the known genetic and epigenetic consequences of the loss of sex. We then specifically discuss what is known about asexual lineages of Fundulus diaphanus x F. heteroclitus to highlight gaps in our knowledge of the biology of these clones. Our preliminary studies of F. diaphanus and F. heteroclitus karyotypes from Porter's Lake (Nova Scotia, Canada) agree with data from other populations, suggesting a conserved interspecific chromosomal arrangement. In addition, genetic analyses suggest that: (a) the same major clonal lineage (Clone A) of F. diaphanus x F. heteroclitus has remained dominant over the past decade, (b) some minor clones have also persisted, (c) new clones may have recently formed, and iv) wild clones still mainly descend from F. diaphanus ♀ x F. heteroclitus ♂ crosses (96% in 2017-2018). These data suggest that clone formation may be a relatively rare, but continuous process, and there are persistent environmental or genetic factors causing a bias in cross direction. We end by describing our current research on the genomic causes and consequences of a transition to asexuality and the potential physiological consequences of epigenetic variation.
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Affiliation(s)
| | - Svetlana Tirbhowan
- Department of BiologySaint Mary's UniversityHalifaxNSCanada
- Département de biologieUniversité de MonctonMonctonNBCanada
| | | | - Claude Power
- Département de biologieUniversité de MonctonMonctonNBCanada
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243
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Nishiya K, Sawada M, Dijkstra JM, Miyamae J, Okano M, Katakura F, Moritomo T. A fish cytokine related to human IL-3, IL-5, and GM-CSF, induces development of eosinophil/basophil/mast-cell type (EBM) granulocytes. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 108:103671. [PMID: 32147469 DOI: 10.1016/j.dci.2020.103671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/04/2020] [Accepted: 03/04/2020] [Indexed: 06/10/2023]
Abstract
Interleukin-3 (IL-3), IL-5, and granulocyte-macrophage colony-stimulating factor (GM-CSF) are related cytokines that signal through receptors possessing the β common (βc) chain. As a family, these cytokines combine rather non-specific hematopoietic growth factor properties with a special importance for eosinophils, basophils, and mast cells. In fish the cytokines of this family are called IL-5fam, and the present study, using carp, constitutes their first functional analysis. Carp il-5fam expression was enhanced by stimulation with phytohemagglutinin and killed bacteria. Reminiscent of mammalian IL-3/IL-5/GM-CSF family members, recombinant carp IL-5fam (rcIL-5fam) induced activation of transcription factor STAT5 and efficiently promoted proliferation and colony-formation of eosinophil/basophil/mast-cell type (EBM) granulocytes. Upon addition of recombinant carp βc the growth effect of rcIL-5fam was reduced, suggesting βc participation in the signaling route. In summary, despite differences in individual cytokines and cell populations, fish and mammalian IL-3/IL-5/GM-CSF family members share growth factor functions for non-neutrophil granulocytes.
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Affiliation(s)
- Kohei Nishiya
- Laboratory of Comparative Immunology, Department of Veterinary Medicine, Nihon University, Kameino 1866, Fujisawa, Kanagawa, 252-0880, Japan
| | - Mai Sawada
- Laboratory of Comparative Immunology, Department of Veterinary Medicine, Nihon University, Kameino 1866, Fujisawa, Kanagawa, 252-0880, Japan
| | - Johannes M Dijkstra
- Institute for Comprehensive Medical Science, Fujita Health University, Dengakugakubo 1-98, Toyoake, Aichi, 470-1192, Japan
| | - Jiro Miyamae
- Faculty of Veterinary Medicine, Okayama University of Science, Ikoino-oka 1-3, Imabari, Ehime, 794-8555, Japan
| | - Masaharu Okano
- Laboratory of Comparative Immunology, Department of Veterinary Medicine, Nihon University, Kameino 1866, Fujisawa, Kanagawa, 252-0880, Japan
| | - Fumihiko Katakura
- Laboratory of Comparative Immunology, Department of Veterinary Medicine, Nihon University, Kameino 1866, Fujisawa, Kanagawa, 252-0880, Japan.
| | - Tadaaki Moritomo
- Laboratory of Comparative Immunology, Department of Veterinary Medicine, Nihon University, Kameino 1866, Fujisawa, Kanagawa, 252-0880, Japan
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244
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Li Y, Liu Y, Yang H, Zhang T, Naruse K, Tu Q. Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis. Genome Res 2020; 30:924-937. [PMID: 32591361 PMCID: PMC7370878 DOI: 10.1101/gr.258871.119] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 06/17/2020] [Indexed: 12/13/2022]
Abstract
Medaka (Oryzias latipes) has become an important vertebrate model widely used in genetics, developmental biology, environmental sciences, and many other fields. A high-quality genome sequence and a variety of genetic tools are available for this model organism. However, existing genome annotation is still rudimentary, as it was mainly based on computational prediction and short-read RNA-seq data. Here we report a dynamic transcriptome landscape of medaka embryogenesis profiled by long-read RNA-seq, short-read RNA-seq, and ATAC-seq. By integrating these data sets, we constructed a much-improved gene model set including about 17,000 novel isoforms and identified 1600 transcription factors, 1100 long noncoding RNAs, and 150,000 potential cis-regulatory elements as well. Time-series data sets provided another dimension of information. With the expression dynamics of genes and accessibility dynamics of cis-regulatory elements, we investigated isoform switching, as well as regulatory logic between accessible elements and genes, during embryogenesis. We built a user-friendly medaka omics data portal to present these data sets. This resource provides the first comprehensive omics data sets of medaka embryogenesis. Ultimately, we term these three assays as the minimum ENCODE toolbox and propose the use of it as the initial and essential profiling genomic assays for model organisms that have limited data available. This work will be of great value for the research community using medaka as the model organism and many others as well.
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Affiliation(s)
- Yingshu Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongjie Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hang Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kiyoshi Naruse
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki 444-8585, Aichi, Japan
| | - Qiang Tu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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245
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Escobar-Camacho D, Carleton KL, Narain DW, Pierotti MER. Visual pigment evolution in Characiformes: The dynamic interplay of teleost whole-genome duplication, surviving opsins and spectral tuning. Mol Ecol 2020; 29:2234-2253. [PMID: 32421918 DOI: 10.1111/mec.15474] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 01/06/2023]
Abstract
Vision represents an excellent model for studying adaptation, given the genotype-to-phenotype map that has been characterized in a number of taxa. Fish possess a diverse range of visual sensitivities and adaptations to underwater light, making them an excellent group to study visual system evolution. In particular, some speciose but understudied lineages can provide a unique opportunity to better understand aspects of visual system evolution such as opsin gene duplication and neofunctionalization. In this study, we showcase the visual system evolution of neotropical Characiformes and the spectral tuning mechanisms they exhibit to modulate their visual sensitivities. Such mechanisms include gene duplications and losses, gene conversion, opsin amino acid sequence and expression variation, and A1 /A2 -chromophore shifts. The Characiforms we studied utilize three cone opsin classes (SWS2, RH2, LWS) and a rod opsin (RH1). However, the characiform's entire opsin gene repertoire is a product of dynamic evolution by opsin gene loss (SWS1, RH2) and duplication (LWS, RH1). The LWS- and RH1-duplicates originated from a teleost specific whole-genome duplication as well as characiform-specific duplication events. Both LWS-opsins exhibit gene conversion and, through substitutions in key tuning sites, one of the LWS-paralogues has acquired spectral sensitivity to green light. These sequence changes suggest reversion and parallel evolution of key tuning sites. Furthermore, characiforms' colour vision is based on the expression of both LWS-paralogues and SWS2. Finally, we found interspecific and intraspecific variation in A1 /A2 -chromophores proportions, correlating with the light environment. These multiple mechanisms may be a result of the diverse visual environments where Characiformes have evolved.
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Affiliation(s)
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Devika W Narain
- Environmental Sciences, Anton de Kom University of Suriname, Paramaribo, Suriname
| | - Michele E R Pierotti
- Naos Marine Laboratories, Smithsonian Tropical Research Institute, Panama, Republic of Panama
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246
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Thieme P, Moritz T. The osteology of the golden grey mullet Liza aurata (Teleostei: Mugiliformes: Mugilidae) including interactive three-dimensional reconstructions. JOURNAL OF FISH BIOLOGY 2020; 96:1320-1340. [PMID: 32112399 DOI: 10.1111/jfb.14281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/03/2020] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Grey mullets are remarkably characterized by their overall uniform external morphology. Identifying species as well as positioning the Mugiliformes in a phylogenetic context is rather difficult. Most recently they were placed in the newly erected Ovalentaria, but more detailed relationships to potential sister taxa were not resolved. Studying the internal morphology, especially the osteology, might provide new insights into the evolution of the Mugiliformes as well as help clarify their phylogenetic position within the Ovalentaria. A detailed osteology of the golden grey mullet Liza aurata is presented. The use of cleared and stained specimens allowed for a complete examination of bony and cartilaginous structures, and a 3D reconstruction from a μCT data set provided additional information on the positional relationships of the bones. Following this, the data obtained were compared with different mugilid species, particularly with the flathead grey mullet Mugil cephalus. Several differences between these species could be identified, such as the position of the basisphenoid, the shape of the hyomandibular and the composition of the branchial arches. These characters might help in understanding the evolutionary changes happening within the mugiliforms and will provide the basis to study this taxon in detail, finally allowing the reconstruction of the body plan of grey mullets.
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Affiliation(s)
- Philipp Thieme
- Department of Science, Deutsches Meeresmuseum, Stralsund, Germany
- Institute for Zoology and Evolutionary Research, Friedrich-Schiller-University Jena, Jena, Germany
| | - Timo Moritz
- Department of Science, Deutsches Meeresmuseum, Stralsund, Germany
- Institute for Zoology and Evolutionary Research, Friedrich-Schiller-University Jena, Jena, Germany
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247
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Bradshaw WJ, Valenzano DR. Extreme genomic volatility characterizes the evolution of the immunoglobulin heavy chain locus in cyprinodontiform fishes. Proc Biol Sci 2020; 287:20200489. [PMID: 32396805 PMCID: PMC7287348 DOI: 10.1098/rspb.2020.0489] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/14/2020] [Indexed: 12/30/2022] Open
Abstract
The evolution of the adaptive immune system has provided vertebrates with a uniquely sophisticated immune toolkit, enabling them to mount precise immune responses against a staggeringly diverse range of antigens. Like other vertebrates, teleost fishes possess a complex and functional adaptive immune system; however, our knowledge of the complex antigen-receptor genes underlying its functionality has been restricted to a small number of experimental and agricultural species, preventing systematic investigation into how these crucial gene loci evolve. Here, we analyse the genomic structure of the immunoglobulin heavy chain (IGH) gene loci in the cyprinodontiforms, a diverse and important group of teleosts present in many different habitats across the world. We reconstruct the complete IGH loci of the turquoise killifish (Nothobranchius furzeri) and the southern platyfish (Xiphophorus maculatus) and analyse their in vivo gene expression, revealing the presence of species-specific splice isoforms of transmembrane IGHM. We further characterize the IGH constant regions of 10 additional cyprinodontiform species, including guppy, Amazon molly, mummichog and mangrove killifish. Phylogenetic analysis of these constant regions suggests multiple independent rounds of duplication and deletion of the teleost-specific antibody class IGHZ in the cyprinodontiform lineage, demonstrating the extreme volatility of IGH evolution. Focusing on the cyprinodontiforms as a model taxon for comparative evolutionary immunology, this work provides novel genomic resources for studying adaptive immunity and sheds light on the evolutionary history of the adaptive immune system.
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Affiliation(s)
- William J. Bradshaw
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 296, 50937 Cologne, Germany
- CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50937 Cologne, Germany
| | - Dario Riccardo Valenzano
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 296, 50937 Cologne, Germany
- CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50937 Cologne, Germany
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248
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Sun S, Wang Y, Zeng W, Du X, Li L, Hong X, Huang X, Zhang H, Zhang M, Fan G, Liu X, Liu S. The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenetic position of Lobotiformes and biological conservation. Sci Rep 2020; 10:8164. [PMID: 32424221 PMCID: PMC7235238 DOI: 10.1038/s41598-020-64398-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/06/2020] [Indexed: 11/08/2022] Open
Abstract
Mekong tiger perch (Datnioides undecimradiatus) is an ornamental and vulnerable freshwater fish native to the Mekong basin in Indochina, belonging to the order Lobotiformes. Here, we generated 121X stLFR co-barcode clean reads and 18X Oxford Nanopore MinION reads and obtained a 595 Mb Mekong tiger perch genome, which is the first whole genome sequence in the order Lobotiformes. Based on this genome, the phylogenetic tree analysis suggested that Lobotiformes is more closely related to Sciaenidae than to Tetraodontiformes, resolving a long-time dispute. We depicted the genes involved in pigment development in Mekong tiger perch and results confirmed that the four rate-limiting genes of pigment synthesis had been retained after fish-specific genome duplication. We also estimated the demographic history of Mekong tiger perch, which showed that the effective population size suffered a continuous reduction possibly related to the contraction of immune-related genes. Our study provided a reference genome resource for the Lobotiformes, as well as insights into the phylogenetic position of Lobotiformes and biological conservation.
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Affiliation(s)
- Shuai Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yue Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Wenhong Zeng
- Jiangxi University of Traditional Chinese Medicin, Nanchang, 330004, China
| | - Xiao Du
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Lei Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xiaoning Hong
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 236009, China
| | - Xiaoyun Huang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Mengqi Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
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Lin CJ, Maugars G, Lafont AG, Jeng SR, Wu GC, Dufour S, Chang CF. Basal teleosts provide new insights into the evolutionary history of teleost-duplicated aromatase. Gen Comp Endocrinol 2020; 291:113395. [PMID: 31981691 DOI: 10.1016/j.ygcen.2020.113395] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 01/04/2020] [Accepted: 01/20/2020] [Indexed: 11/25/2022]
Abstract
Duplicated cyp19a1 genes (cyp19a1a encoding aromatase a and cyp19a1b encoding aromatase b) have been identified in an increasing number of teleost species. Cyp19a1a is mainly expressed in the gonads, while cyp19a1b is mainly expressed in the brain, specifically in radial glial cells, as largely investigated by Kah and collaborators. The third round of whole-genome duplication that specifically occurred in the teleost lineage (TWGD or 3R) is likely at the origin of the duplicated cyp19a1 paralogs. In contrast to the situation in other teleosts, our previous studies identified a single cyp19a1 in eels (Anguilla), which are representative species of a basal group of teleosts, Elopomorpha. In the present study, using genome data mining and phylogenetic and synteny analyses, we confirmed that the whole aromatase genomic region was duplicated in eels, with most aromatase-neighboring genes being conserved in duplicate in eels, as in other teleosts. These findings suggest that specific gene loss of one of the 3R-duplicated cyp19a1 paralogs occurred in Elopomorpha after TWGD. Similarly, a single cyp19a1 gene was found in the arowana, which is a representative species of another basal group of teleosts, Osteoglossomorpha. In eels, the single cyp19a1 is expressed in both the brain and the gonads, as observed for the single CYP19A1 gene present in other vertebrates. The results of phylogenetic, synteny, closest neighboring gene, and promoter structure analyses showed that the single cyp19a1 of the basal teleosts shared conserved properties with both teleost cyp19a1a and cyp19a1b paralogs, which did not allow us to conclude which of the 3R-duplicated paralogs (cyp19a1a or cyp19a1b) was lost in Elopomorpha. Elopomorpha and Osteoglossomorpha cyp19a1 genes exhibited preserved ancestral functions, including expression in both the gonad and brain. We propose that the subfunctionalization of the 3R-duplicated cyp19a1 paralogs expressed specifically in the gonad or brain occurred in Clupeocephala, after the split of Clupeocephala from Elopomorpha and Osteoglossomorpha, which represented a driving force for the conservation of both 3R-duplicated paralogs in all extant Clupeocephala. In contrast, the functional redundancy of the undifferentiated 3R-duplicated cyp19a1 paralogs in elopomorphs and osteoglossomorphs would have favored the loss of one 3R paralog in basal teleosts.
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Affiliation(s)
- Chien-Ju Lin
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan; Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Gersende Maugars
- Laboratory Biology of Aquatic Organisms and Ecosystems (BOREA), Muséum National d'Histoire Naturelle, CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Université des Antilles, 75231 Paris Cedex 05, France
| | - Anne-Gaëlle Lafont
- Laboratory Biology of Aquatic Organisms and Ecosystems (BOREA), Muséum National d'Histoire Naturelle, CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Université des Antilles, 75231 Paris Cedex 05, France
| | - Shan-Ru Jeng
- Department of Aquaculture, National Kaohsiung University of Science and Technology, Kaohsiung 811, Taiwan
| | - Guan-Chung Wu
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan; Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Sylvie Dufour
- Laboratory Biology of Aquatic Organisms and Ecosystems (BOREA), Muséum National d'Histoire Naturelle, CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Université des Antilles, 75231 Paris Cedex 05, France.
| | - Ching-Fong Chang
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan; Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan.
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Balla KM, Rice MC, Gagnon JA, Elde NC. Linking Virus Discovery to Immune Responses Visualized during Zebrafish Infections. Curr Biol 2020; 30:2092-2103.e5. [PMID: 32413307 DOI: 10.1016/j.cub.2020.04.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/28/2020] [Accepted: 04/14/2020] [Indexed: 12/12/2022]
Abstract
The discovery of new viruses currently outpaces our capacity for experimental examination of infection biology. To better couple virus discovery with immunology, we genetically modified zebrafish to visually report on virus infections. After generating a strain that expresses green fluorescent protein (GFP) under an interferon-stimulated gene promoter, we repeatedly observed transgenic larvae spontaneously expressing GFP days after hatching. RNA sequencing comparisons of co-housed GFP-positive and GFP-negative zebrafish revealed a naturally occurring picornavirus that induced a canonical interferon-mediated response and hundreds of antiviral defense genes not observed following immunostimulatory treatments or experimental infections with other viruses. Among the many genes induced by picornavirus infection was a large set encoding guanosine triphosphatase (GTPase) of immunity-associated proteins (GIMAPs). The GIMAP gene family is massively expanded in fish genomes and may also play a crucial role in antiviral responses in mammals, including humans. We subsequently detected zebrafish picornavirus in publicly available sequencing data from seemingly asymptomatic zebrafish in many research institutes and found that it altered gene expression in a previous study of zebrafish development. Experiments revealed a horizontal mode of virus transmission, highlighting a system for studying the spread of picornavirus infections within and between individuals. Our study describes a naturally occurring picornavirus that elicits strong antiviral responses in zebrafish and provides new strategies for simultaneously discovering viruses and their impact on vertebrate hosts.
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Affiliation(s)
- Keir M Balla
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Marlen C Rice
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - James A Gagnon
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Nels C Elde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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