Seeing the rainbow: mechanisms underlying spectral sensitivity in teleost fishes.
Ontology highlight
ABSTRACT:
SUBMITTER: Carleton KL
PROVIDER: S-EPMC7188444 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Fish viviparity project, draft genome assemblies
| PRJNA1066408 | ENA
Project description:Rhodopsin mediates an essential step in image capture and is tightly associated with visual adaptations of aquatic organisms, especially species that live in dim light environments (e.g., the deep sea). The rh1 gene encoding rhodopsin was formerly considered a single-copy gene in genomes of vertebrates, but increasing exceptional cases have been found in teleost fish species. The main objective of this study was to determine to what extent the visual adaptation of teleosts might have been shaped by the duplication and loss of rh1 genes. For that purpose, homologous rh1/rh1-like sequences in genomes of ray-finned fishes from a wide taxonomic range were explored using a PCR-based method, data mining of public genetic/genomic databases, and subsequent phylogenomic analyses of the retrieved sequences. We show that a second copy of the fish-specific intron-less rh1 is present in the genomes of most anguillids (Elopomorpha), Hiodon alosoides (Osteoglossomorpha), and several clupeocephalan lineages. The phylogenetic analysis and comparisons of alternative scenarios for putative events of gene duplication and loss suggested that fish rh1 was likely duplicated twice during the early evolutionary history of teleosts, with one event coinciding with the hypothesized fish-specific genome duplication and the other in the common ancestor of the Clupeocephala. After these gene duplication events, duplicated genes were maintained in several teleost lineages, whereas some were secondarily lost in specific lineages. Alternative evolutionary schemes of rh1 and comparison with previous studies of gene evolution are also reviewed.
| S-EPMC6218077 | biostudies-literature
Project description:Recent advances in carbohydrate chemistry, chemical biology, and mass spectrometric techniques have opened the door to rapid progress in uncovering the function and diversity of glycan structures associated with human health and disease. These strategies can be equally well applied to advance non-human health care research. To date, the glycomes of only a handful of non-human, non-domesticated vertebrates have been analyzed in depth due to the logistic complications associated with obtaining or handling wild-caught or farm-raised specimens. In contrast, the last 2 decades have seen advances in proteomics, glycoproteomics, and glycomics that have significantly advanced efforts to identify human serum/plasma biomarkers for various diseases. In this study, we investigated N-glycan structural diversity in serum harvested from five cultured fish species. This biofluid is a useful starting point for glycomic analysis because it is rich in glycoproteins, can be acquired in a sustainable fashion, and its contents reflect dynamic physiologic changes in the organism. Sera acquired from two chondrostrean fish species, the Atlantic sturgeon and shortnose sturgeon, and three teleost fish species, the Atlantic salmon, Arctic char, and channel catfish, were delipidated by organic extraction and the resulting protein-rich preparations sequentially treated with trypsin and PNGaseF to generate released N-glycans for structural analysis. Released N-glycans were analyzed as their native or permethylated forms by nanospray ionization mass spectrometry in negative or positive mode. While the basic biosynthetic pathway that initiates the production of glycoprotein glycan core structures is well-conserved across the teleost fish species examined in this study, species-specific structural differences were detected across the five organisms in terms of their monosaccharide composition, sialylation pattern, fucosylation, and degree of O-acetylation. Our methods and results provide new contributions to a growing library of datasets describing fish N-glycomes that can eventually establish species-normative baselines for assessing N-glycosylation dynamics associated with pathogen invasion, environmental stress, and fish immunologic responses.
| S-EPMC8631502 | biostudies-literature
Project description:Myoglobin (Mb) is the classic vertebrate oxygen-binding protein present in aerobic striated muscles. It functions principally in oxygen delivery and provides muscle with its characteristic red colour. Members of the Antarctic icefish family (Channichthyidae) are widely thought to be extraordinary for lacking cardiac Mb expression, a fact that has been attributed to their low metabolic rate and unusual evolutionary history. Here, we report that cardiac Mb deficit, associated with pale heart colour, has evolved repeatedly during teleost evolution. This trait affects both gill- and air-breathing species from temperate to tropical habitats across a full range of salinities. Cardiac Mb deficit results from total pseudogenization in three-spined stickleback and is associated with a massive reduction in mRNA level in two species that evidently retain functional Mb. The results suggest that near or complete absence of Mb-assisted oxygen delivery to heart muscle is a common facet of teleost biodiversity, even affecting lineages with notable oxygen demands. We suggest that Mb deficit may affect how different teleost species deal with increased tissue oxygen demands arising under climate change.
| S-EPMC4090546 | biostudies-literature
Project description:Many studies have shown that 5-HTTLPR genotype interacts with exposure to stress in conferring risk for psychopathology. However, the specific neural mechanisms through which this gene-by-environment interaction confers risk remain largely unknown, and no study to date has directly examined the modulatory effects of 5-HTTLPR on corticolimbic circuit responses during exposure to acute stress.An acute laboratory stressor was administered to 51 healthy women during blood-oxygen-level-dependent functional magnetic resonance imaging. In this task, participants were threatened with electric shocks of uncertain intensity, which were unpredictably delivered to the wrist after a long anticipatory cue period of unpredictable duration.Relative to women carrying the L allele, those with the SS genotype showed enhanced activation during threat anticipation in a network of regions, including the amygdala, hippocampus, anterior insula, thalamus, pulvinar, caudate, precuneus, anterior cingulate cortex, and medial prefrontal cortex. Individuals with the SS genotype also displayed enhanced positive coupling between medial prefrontal cortex activation and anxiety experience, whereas enhanced negative coupling between insula activation and perceived success at regulating anxiety was observed in individuals carrying the L allele.These findings suggest that during stress exposure, neural systems that enhance fear and arousal, modulate attention toward threat, and perseverate on emotional salience of the threat may be engaged preferentially in individuals with the SS genotype. This may be one mechanism underlying the risk for psychopathology conferred by the S allele upon exposure to life stressors.
| S-EPMC3761065 | biostudies-literature
Project description:The opercle is a prominent craniofacial bone supporting the gill cover in all bony fish and has been the subject of morphological, developmental, and genetic investigation. We surveyed the shapes of this bone among 110 families spanning the teleost tree and examined its pattern of occupancy in a principal component-based morphospace. Contrasting with expectations from the literature that suggest the local morphospace would be only sparsely occupied, we find primarily dense, broad filling of the morphological landscape, indicating rich diversity. Phylomorphospace plots suggest that dynamic evolution underlies the observed spatial patterning. Evolutionary transits through the morphospaces are sometimes long, and occur in a variety of directions. The trajectories seem to represent both evolutionary divergences and convergences, the latter supported by convevol analysis. We suggest that that this pattern of occupancy reflects the various adaptations of different groups of fishes, seemingly paralleling their diverse marine and freshwater ecologies and life histories. Opercle shape evolution within the acanthomorphs, spiny ray-finned fishes, appears to have been especially dynamic.
| S-EPMC5744915 | biostudies-literature
Project description:BackgroundGene and genome duplication play important roles in the evolution of gene function. Compared to individual duplicated genes, gene clusters attract particular attention considering their frequent associations with innovation and adaptation. Here, we report for the first time the expansion of the apolipoprotein D (ApoD) ligand-transporter genes in a cluster manner specific to teleost fishes.ResultsBased on comparative genomic and transcriptomic analyses, protein 3D structure comparison, positive selection detection and breakpoints detection, the single ApoD gene in the ancestor expanded into two clusters following a dynamic evolutionary pattern in teleost fishes. Orthologous genes show conserved expression patterns, whereas lineage-specific duplicated genes show tissue-specific expression patterns and even evolve new gene expression profiles. Positive selection occurred in branches before and after gene duplication, especially for lineage-specific duplicated genes. Cluster analyses based on protein 3D structure comparisons, especially comparisons of the four loops at the opening side, show gene duplication-segregating patterns. Duplicated ApoD genes are predicted to be associated with forkhead transcription factors and MAPK genes. ApoD clusters are located next to the breakpoints of genome rearrangements.ConclusionsHere, we report the expansion of ApoD genes specific to teleost fishes in a cluster manner for the first time. Neofunctionalization and subfunctionalization were observed at both the protein and expression levels after duplication. Evidence from different aspects-i.e., abnormal expression-induced disease in humans, fish-specific expansion, predicted associations with forkhead transcription factors and MAPK genes, specific expression patterns in tissues related to sexual selection and adaptation, duplicated genes under positive selection and their location next to the breakpoints of genome rearrangements-suggests the potentially advantageous roles of ApoD genes in teleost fishes. The cluster expansion of ApoD genes specific to teleost fishes provides thus an ideal evo-devo model for studying gene duplication, cluster maintenance and new gene function emergence.
| S-EPMC6325677 | biostudies-literature
Project description:Plastic additives that maintain integrity have been extensively studied for potential toxicity to fish; however, chemicals that protect polymers from (artificial) UV degradation are less studied. Benzotriazole UV stabilizers (BUVSs) are the most widely used UV stabilizers in plastics and are often used in sunscreens, cosmetics, paint, and food packaging. BUVSs can negatively affect aquatic wildlife when released into the environment via plastic degradation. In this review, we summarize the distribution of BUVSs globally and discuss neurotoxicological endpoints measured in fish to understand how these plastic additives can affect the neurological health of teleost fishes. BUVSs have been detected in aquatic environments at concentrations ranging from 0.05 up to 99,200 ng/L. Studies show that BUVSs affect behavioral responses and acetylcholinesterase activity, indicators of neurotoxicity. Our computational analysis using transcriptome data suggests certain pathways associated with neurodegeneration are responsive to exposure to BUVSs, like "Complement Activation in Alzheimer's Disease". Based on our review, we identify some research needs for future investigations: (1) molecular studies in the central nervous system to define precise mechanisms of neurotoxicity; (2) a wider range of tests for assessing aberrant behaviors given that BUVSs can affect the activity of larval zebrafish; and (3) histopathology of the nervous system to accompany biochemical analyses. These data are expected to enhance understanding of the neurotoxicity potential of benzotriazoles and other plastic additives.
| S-EPMC10891865 | biostudies-literature
Project description:BackgroundWith more than 36,000 valid fish species, teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. NLRC3 subfamily genes, which are specific to fishes, play vital roles in the immune system of teleosts. The evolution of teleosts has been impacted by several whole-genome duplication (WGD) events, which might be a key reason for the expansions of the NLRC3 subfamily, but detailed knowledge of NLRC3 subfamily evolution in the family Sebastidae is still limited.ResultsPhylogenetic inference of NLRC3 subfamily protein sequences were conducted to evaluate the orthology of NLRC3 subfamily genes in black rockfish (Sebastes schlegilii), 13 other fish species from the families Sebastidae, Serranidae, Gasterosteidae and Cyclopteridae, and three species of high vertebrates (bird, reptile and amphibian). WGD analyses were used to estimate expansions and contractions of the NLRC3 subfamily, and patterns of expression of NLRC3 subfamily genes in black rockfish following bacterial infections were used to investigate the functional roles of these genes in the traditional and mucosal immune system of the Sebastidae. Different patterns of gene expansions and contractions were observed in 17 fish and other species examined, and one and two whole-genome duplication events were observed in two members of family Sebastidae (black rockfish and honeycomb rockfish, Sebastes umbrosus), respectively. Subsequently, 179 copy numbers of NLRC3 genes were found in black rockfish and 166 in honeycomb rockfish. Phylogenetic analyses corroborated the conservation and evolution of NLRC3 orthologues between Sebastidae and other fish species. Finally, differential expression analyses provided evidence of the immune roles of NLRC3 genes in black rockfish during bacterial infections and gene ontology analysis also indicated other functional roles.ConclusionsWe hypothesize that NLRC3 genes have evolved a variety of different functions, in addition to their role in the immune response, as a result of whole genome duplication events during teleost diversification. Importantly, this study had underscored the importance of sampling across taxonomic groups, to better understand the evolutionary patterns of the innate immunity system on which complex immunological novelties arose. Moreover, the results in this study could extend current knowledge of the plasticity of the immune system.
| S-EPMC10648357 | biostudies-literature
Project description:The Mediterranean Sea is a highly diverse, highly studied, and highly impacted biogeographic region, yet no phylogenetic reconstruction of fish diversity in this area has been published to date. Here, we infer the timing and geographic origins of Mediterranean teleost species diversity using nucleotide sequences collected from GenBank. We assembled a DNA supermatrix composed of four mitochondrial genes (12S ribosomal DNA, 16S ribosomal DNA, cytochrome c oxidase subunit I and cytochrome b) and two nuclear genes (rhodopsin and recombination activating gene I), including 62% of Mediterranean teleost species plus 9 outgroups. Maximum likelihood and Bayesian phylogenetic and dating analyses were calibrated using 20 fossil constraints. An additional 124 species were grafted onto the chronogram according to their taxonomic affinity, checking for the effects of taxonomic coverage in subsequent diversification analyses. We then interpreted the time-line of teleost diversification in light of Mediterranean historical biogeography, distinguishing non-endemic natives, endemics and exotic species. Results show that the major Mediterranean orders are of Cretaceous origin, specifically ~100-80 Mya, and most Perciformes families originated 80-50 Mya. Two important clade origin events were detected. The first at 100-80 Mya, affected native and exotic species, and reflects a global diversification period at a time when the Mediterranean Sea did not yet exist. The second occurred during the last 50 Mya, and is noticeable among endemic and native species, but not among exotic species. This period corresponds to isolation of the Mediterranean from Indo-Pacific waters before the Messinian salinity crisis. The Mediterranean fish fauna illustrates well the assembly of regional faunas through origination and immigration, where dispersal and isolation have shaped the emergence of a biodiversity hotspot.
| S-EPMC3348158 | biostudies-literature