Search

The tumor necrosis superfamily (TNFSF) and their receptors (TNFRs) play an essential role in inflammatory responses. In this study, tnfsf14, tnfrsf1a, tnfrsf1b and tnfrsf14 were identified in spotted gar. All the genes have conserved genomic organization and synteny with their respective homologs in zebrafish and humans. The putative TNFSF protein contains a typical TNF homology domain in the extracellular region. All three TNFRSFs possess characteristic cysteine-rich domains. TNFRSF1a has a death domain in the cytosolic region which is absent in the TNFRSF1b and TNFRSF14. Notably, TNFRSF14 lacks a transmembrane domain and is predicted to be secreted. Protein structure modeling revealed that the key residues involved in the interaction between TNFSF14 and TNFRSF14 are well conserved in spotted gar. All four genes were ubiquitously expressed in the spleen, liver, kidney, gills and intestine. Infection with Klebsiella pneumoniae resulted in remarkable downregulation of tnfsf14 and tnfrsf14 in tissues but upregulation of tnfrsf1a and tnfrsf1b. The results indicate that tnfsf14, tnfrsf1a, tnfrsf1b and tnfrsf14 are involved in the immune response to bacterial infection, and expand knowledge on the TNF system in the primitive ray-finned fish. [ABSTRACT FROM AUTHOR]

Spotted gar (Lepisosteus oculatus) is a primitive ray-finned fish which has not undergone the third round whole genome duplication and commonly used as a model to study the evolution of immune genes. In this study, a pathogenic strain of Klebsiella pneumoniae (termed KPY01) was isolated from a diseased spotted gar, based on the Gram-stain and phylogenetic analysis of the 16S rDNA and khe genes. Further, the virulence genes and drug resistance genes were determined and drug sensitivity tests were performed to explore the virulence and drug resistance of the KPY01. Putative biosynthetic gene clusters (BGCs) for the biosynthesis of secondary metabolites were predicted using the anti-SMASH5.0 online genome mining platform. Histopathological analysis revealed that the immune cells were significantly decreased in the white pulp of spleen of fish infected with K. pneumonia and tissue inflammation became apparent. Besides, the expression of cytokines including interleukin (il) -8, il-10 , il-12a , il-18 and interferon γ (ifn-γ) were shown to be modulated in the spleen, gills and kidney. Our work provides useful information for further investigation on the virulence of K. pneumoniae and host immune responses to K. pneumoniae infection in fish. • A Klebsiella pneumoniae strain was isolated from a diseased spotted gar. • Virulence and drug resistance genes were determined. • K. pneumoniae consists of biosynthetic gene clusters for discovery of bioactive natural products. • K. pneumoniae infection leads to upregulation of proinflammatory cytokines in the kidney and spleen of spotted gar. [ABSTRACT FROM AUTHOR]

Background: The cellular and molecular mechanisms initiating vertebrate cranial dermal bone formation is a conundrum in evolutionary and developmental biology. Decades of studies have determined the developmental processes of cranial dermal bones in various vertebrates and identified possible inducers of dermal bone. However, evolutionarily derived characters of current experimental model organisms, such as non‐homologous frontal bones between teleosts and sarcopterygians, hinder investigations of ancestral and conserved mechanisms of vertebrate cranial dermal bone induction. Thus, investigating such mechanisms with animals diverging at evolutionarily informative phylogenetic nodes is imperative. Results: We investigated the cellular foundations of skull frontal bone formation in the spotted gar Lepisosteus oculatus, a basally branching non‐teleost actinopterygian. Whole‐mount bone and cartilage staining and hematoxylin‐eosin section staining revealed that mesenchymal cell condensations in the frontal bone of spotted gar develop in close association with the underlying cartilage. We also identified novel aspects of frontal bone formation: enrichment of F‐actin, cellular membranes, and E‐cadherin in condensing cells, and extension of podia‐like structures from osteoblasts to the frontal bone, which may be responsible for bone mineral transport. Conclusion: This study highlights the process of frontal bone formation with dynamic architectural changes of mesenchymal cells in spotted gar, an emerging non‐teleost fish model system, illuminating supposedly ancestral and likely conserved developmental mechanisms of skull bone formation among vertebrates. Key Findings: The precise developmental staging of the cranial dermal bones in spotted gar was established.Mesenchymal cell condensations for the frontal bone develop in close association with the underlying cartilage.Enrichment of F‐actin, cellular membranes, and E‐cadherin takes place in condensing mesenchymal cells for the frontal bone. [ABSTRACT FROM AUTHOR]

The tumor necrosis superfamily (TNFSF) and their receptors (TNFRs) play an essential role in inflammatory responses. In this study, tnfsf14, tnfrsf1a, tnfrsf1b and tnfrsf14 were identified in spotted gar. All the genes have conserved genomic organization and synteny with their respective homologs in zebrafish and humans. The putative TNFSF protein contains a typical TNF homology domain in the extracellular region. All three TNFRSFs possess characteristic cysteine-rich domains. TNFRSF1a has a death domain in the cytosolic region which is absent in the TNFRSF1b and TNFRSF14. Notably, TNFRSF14 lacks a transmembrane domain and is predicted to be secreted. Protein structure modeling revealed that the key residues involved in the interaction between TNFSF14 and TNFRSF14 are well conserved in spotted gar. All four genes were ubiquitously expressed in the spleen, liver, kidney, gills and intestine. Infection with Klebsiella pneumoniae resulted in remarkable downregulation of tnfsf14 and tnfrsf14 in tissues but upregulation of tnfrsf1a and tnfrsf1b. The results indicate that tnfsf14, tnfrsf1a, tnfrsf1b and tnfrsf14 are involved in the immune response to bacterial infection, and expand knowledge on the TNF system in the primitive ray-finned fish.

We developed an ex silico evolutionary‐based systematic synteny approach to define and name the duplicated genes in vertebrates. The first convention for the naming of genes relied on historical precedent, the order in the human genome, and mutant phenotypes in model systems. However, total‐genome duplication that resulted in teleost genomes required the naming of duplicated orthologous genes (ohnologs) in a specific manner. Unfortunately, as we review here, such naming has no defined criteria, and some ohnologs and their orthologs have suffered from incorrect nomenclature, thus creating confusion in comparative genetics and disease modeling. We sought to overcome this barrier by establishing an ex silico evolutionary‐based systematic approach to naming ohnologs in teleosts. We developed software and compared gene synteny in zebrafish using the spotted gar genome as a reference, representing the unduplicated ancestral state. Using new criteria, we identified several hundred potentially misnamed ohnologs and validated the principle manually. Also see the video abstract here: https://youtu.be/UKNLa_TvSgY [ABSTRACT FROM AUTHOR]

Olfactomedin-like (OLFML) proteins are members of the olfactomedin domain–containing secreted glycoprotein (OLF) family. OLFML2A and OLFML2B are representative molecules of these glycoproteins. Olfactomedins are critical for the development and functional organization of the nervous system and retina, which is a highly conserved structure in vertebrates, having almost identical anatomical and physiological characteristics in multiple taxa. Spotted gar, a member of the Lepisosteidae family, is a freshwater fish that inhabits rivers, bayous, swamps, and brackish waters. Recently, the complete genome has been sequenced, providing a unique bridge between fish medical models to human biology, making it an excellent animal model. This study was aimed to understanding the evolution OLFML2A and OLFML2B in the retina of spotted gar through looking for the expression of these genes. Spotted gar retina was analyzed with hematoxylin-eosin staining assays to provide an overall view of the retina structure and an immunofluorescence assay to identify OLFML2A and OLFML2B protein expression. A phylogenetic tree was created using the neighbor-joining method. Forces that direct the evolution of the fish genes were tested. Spotted gar retina, as in other vertebrates, is made of several layers. OLFML2A and OLFML2B proteins were detected in the rod and cone photoreceptor layer (PRL), outer nuclear layer (ONL), and inner nuclear layer (INL). Phylogenetic tree analysis confirms the orthology within the OLFML2A gene. Purifying selection is the evolutionary force that directs the OLFML2A genes. OLFML2A genes have a well-conserved function over time and species. [ABSTRACT FROM AUTHOR]

Background: p63 is an evolutionarily ancient transcription factor essential to vertebrate tooth development. Our recent gene expression screen comparing wild‐type and "toothless" p63−/− mouse embryos implicated in tooth development several new genes that we hypothesized act downstream of p63 in dental epithelium, where p63 is also expressed. Results: Via in situ hybridization and immunohistochemistry, we probed mouse embryos (embryonic days 10.5‐14.5) and spotted gar fish embryos (14 days postfertilization) for these newly linked genes, Cbln1, Cldn23, Fermt1, Krt15, Pltp and Prss8, which were expressed in mouse and gar dental epithelium. Loss of p63 altered expression levels but not domains. Expression was comparable between murine upper and lower tooth organs, implying conserved gene functions in maxillary and mandibular dentitions. Our meta‐analysis of gene expression databases supported that these genes act within a p63‐driven gene regulatory network important to tooth development in mammals and more evolutionary ancient vertebrates (fish, amphibians). Conclusions: Cbln1, Cldn23, Fermt1, Krt15, Pltp, and Prss8 were expressed in mouse and fish dental epithelium at placode, bud, and/or cap stages. We theorize that these genes participate in cell‐cell adhesion, cell polarity, and extracellular matrix signaling to support dental epithelium integrity, folding, and epithelial‐mesenchymal cross talk during tooth development. Key Findings: Our study discovered that Cbln1, Cldn23, Fermt1, Krt15, Pltp and Prss8 are expressed in dental epithelium of upper and lower tooth organs from E10.5 to E14.5 in mouse, and in tooth organ of 14 dpf spotted gar fish.We found that these genes in mouse and gar have homologues in other vertebrate classes, supporting that these genes are important to vertebrate odontogenesis.As such, our work provides new foundational insights into genes underpinning tooth morphogenesis and, potentially, evolution. [ABSTRACT FROM AUTHOR]

One of the earliest patterning events in the vertebrate neural plate is the specification of mes/r1, the territory comprising the prospective mesencephalon and the first hindbrain rhombomere. Within mes/r1, an interface of gene expression defines the midbrain–hindbrain boundary (MHB), a lineage restriction that separates the mesencephalon and rhombencephalon. wnt1 is critical to mes/r1 development and functions within the MHB as a component of the MHB gene regulatory network (GRN). Despite its importance to these critical and early steps of vertebrate neurogenesis, little is known about the factors responsible for wnt1 transcriptional regulation. In the zebrafish, wnt1 and its neighboring paralog, wnt10b, are expressed in largely overlapping patterns, suggesting co-regulation. To understand wnt1 and wnt10b transcriptional control, we used a comparative genomics approach to identify relevant enhancers. We show that the wnt1-wnt10b locus contains multiple cis-regulatory elements that likely interact to generate the wnt1 and wnt10b expression patterns. Two of 11 conserved enhancers tested show activity restricted to the midbrain and MHB, an activity that is conserved in the distantly related spotted gar orthologous elements. Three non-conserved elements also play a likely role in wnt1 regulation. The identified enhancers display dynamic modes of chromatin accessibility, suggesting controlled deployment during embryogenesis. Our results suggest that the control of wnt1 and wnt10b expression is under complex regulation involving the interaction of multiple enhancers. [ABSTRACT FROM AUTHOR]

Novel molecular data from both mitochondrial (cytochrome c oxidase subunit 1) and ribosomal regions (18S, ITS1-5.8S, ITS2, and 28S) are provided for Sebekia mississippiensis Overstreet, Self, & Vliet, 1985 , a pentastome infecting the American alligator, Alligator mississippiensis Daudin, 1801, and the spotted gar, Lepisosteus oculatus Winchell, 1864. Adult and nymphal pentastomes are described from the lungs and liver of the type host, A. mississippiensis, collected from Mississippi, while additional nymphs are described from the esophageal lining of L. oculatus specimens collected from Louisiana. This sequencing data will facilitate more accurate identification of various life cycle stages of S. mississippiensis, enabling future work to resolve many ambiguities in the literature regarding this species. Additionally, histopathological data are provided from both the definitive and intermediate hosts. [ABSTRACT FROM AUTHOR]

Background: Many physiological processes are influenced by nicotinic acetylcholine receptors (nAChR), ranging from neuromuscular and parasympathetic signaling to modulation of the reward system and long-term memory. Due to the complexity of the nAChR family and variable evolutionary rates among its members, their evolution in vertebrates has been difficult to resolve. In order to understand how and when the nAChR genes arose, we have used a broad approach of analyses combining sequence-based phylogeny, chromosomal synteny and intron positions. Results: Our analyses suggest that there were ten subunit genes present in the vertebrate predecessor. The two basal vertebrate tetraploidizations (1R and 2R) then expanded this set to 19 genes. Three of these have been lost in mammals, resulting in 16 members today. None of the ten ancestral genes have kept all four copies after 2R. Following 2R, two of the ancestral genes became triplicates, five of them became pairs, and three seem to have remained single genes. One triplet consists of CHRNA7, CHRNA8 and the previously undescribed CHRNA11, of which the two latter have been lost in mammals but are still present in lizards and ray-finned fishes. The other triplet consists of CHRNB2, CHRNB4 and CHRNB5, the latter of which has also been lost in mammals. In ray-finned fish the neuromuscular subunit gene CHRNB1 underwent a local gene duplication generating CHRNB1.2. The third tetraploidization in the predecessor of teleosts (3R) expanded the repertoire to a total of 31 genes, of which 27 remain in zebrafish. These evolutionary relationships are supported by the exon-intron organization of the genes. Conclusion: The tetraploidizations explain all gene duplication events in vertebrates except two. This indicates that the genome doublings have had a substantial impact on the complexity of this gene family leading to a very large number of members that have existed for hundreds of millions of years. [ABSTRACT FROM AUTHOR]

A sensory deficit both at the individual and at the species level can be compensated by increased acuity in other senses. The loss of vision in blind cavefish, Astyanax mexicanus, appears to be partially counterbalanced by enhanced chemosensory perception. Whether such improvement also involves adaptive changes in chemosensory receptor repertoires was unknown. The typical bitter taste receptor repertoire of teleost fish is reported as 3-5 genes, much smaller than that of many terrestrial species. Interestingly, several fish species, for example, mudskipper, have evolved a terrestrial lifestyle, but again it was unknown, whether this change in habitat is reflected in the size of gustatory receptor repertoires. We have searched the genomes of 15 fish species and performed a thorough phylogenetic analysis to delineate their bitter taste receptor repertoires. We report no adaptation for 4 mudskipper species, which exhibit 3–4 bitter taste receptor genes, and thus a typical teleost repertoire, shaped by few gene losses and minor gene duplications from an ancestral repertoire of 4 genes. However, and in sharp contrast to all other teleost fish species analyzed, blind cavefish possess more than 20 intact bitter taste receptors and several pseudogenes, rivaling the complexity of the human bitter taste receptor repertoire. The gene duplications giving rise to the current cavefish bitter taste receptor repertoire appear to have occurred well before the loss of vision, consistent with this increase in repertoire size constituting a preadaptive trait that conceivably could compensate to some extent for the lack of visual cues. [ABSTRACT FROM AUTHOR]

Common carp ( Cyprinus carpio, carp) are a widespread and ecologically destructive invasive fish species. Carp management is critical for maintaining healthy aquatic ecosystems, and many control options are available, but most have proven to be ineffective. Carp abundances have increased at The Nature Conservancy's Emiquon Preserve, Illinois, since its restoration in 2007 despite management efforts to suppress this species. We conducted a comparative diet study in Illinois, Tennessee, and Wisconsin to test whether bowfin ( Amia calva), spotted gar ( Lepisosteus oculatus, gar), and largemouth bass ( Micropterus salmoides) commonly preyed upon carp. We focused on bowfin and gar because they are hypoxia-tolerant, similar to carp. We also assessed whether specific fish community characteristics were correlated with carp relative abundances. We found no evidence that bowfin, gar, and bass consumed large numbers of carp. However, carp may be limited in some ecosystems (e.g., Reelfoot Lake, Tennessee) through alternative mechanisms associated with bowfin, gar, bass, and bluegill ( Lepomis macrochirus) included in a diverse native fish community. [ABSTRACT FROM AUTHOR]

Several whole genome duplication (WGD) events followed by rediploidization took place in the evolutionary history of vertebrates. Acipenserids represent a convenient model group for investigation of the consequences of WGD as their representatives underwent additional WGD events in different lineages resulting in ploidy level variation between species, and these processes are still ongoing. Earlier, we obtained a set of sterlet (Acipenser ruthenus) chromosome-specific libraries by microdissection and revealed that they painted two or four pairs of whole sterlet chromosomes, as well as additional chromosomal regions, depending on rediploidization status and chromosomal rearrangements after genome duplication. In this study, we employed next generation sequencing to estimate the content of libraries derived from different paralogous chromosomes of sterlet. For this purpose, we aligned the obtained reads to the spotted gar (Lepisosteus oculatus) reference genome to reveal syntenic regions between these two species having diverged 360 Mya. We also showed that the approach is effective for synteny prediction at various evolutionary distances and allows one to clearly distinguish paralogous chromosomes in polyploid genomes. We postulated that after the acipenserid-specific WGD sterlet karyotype underwent multiple interchromosomal rearrangements, but different chromosomes were involved in this process unequally. [ABSTRACT FROM AUTHOR]

The spotted gar ( Lepisosteus oculatus) shows a disjunct natural distribution, with a core population extending from the central Mississippi River Basin to the U.S. gulf coast and a peripheral population in the southern Great Lakes Basin. Despite significant conservation concerns for this species in the Great Lakes watersheds where it occurs, few genetic examinations and comparisons of these populations have been performed. We investigated inter- and intrapopulational variation in several mitochondrial genetic markers (cytochrome oxidase subunit I, COI; cytochrome oxidase subunit II, COII; and 16S rRNA, 16S) from spotted gars taken from core and peripheral populations. Genetic diversity was highest in the Mississippi River Basin and lowest in the Great Lakes Basin, while the Nueces River Basin (Texas) population showed the greatest level of divergence from other populations. Average genetic distance among core and peripheral populations was over an order of magnitude less than that seen between L. oculatus and its sister species, the Florida gar ( L. platyrhincus), although a significant correlation was found between genetic and geographical distance in L. oculatus. Genetic divergence in spotted gars is likely to be related to a combination of geographic isolation and founder effects associated with recent colonization following glacial retreat. Despite its apparent lack of significant genetic differentiation or haplotype diversity, the Great Lakes population of spotted gars has previously been shown to be a unique component of the species, and additional studies are needed to determine the genetic mechanisms underlying regional adaptations as well as potential morphological differentiation among spotted gar populations. [ABSTRACT FROM AUTHOR]

The study of the nitrergic system, formed by the networks of neurons containing the enzyme nitric oxide synthase (NOS), has been extremely useful in unraveling neuroanatomical features of the organization of the central nervous system of vertebrates. Thus, data are available for representatives of most vertebrate classes and, in particular, several studies have detailed the organization of this system in teleosts. In contrast, no information is available regarding this neurotransmission system in the brains of holosteans, an early diverged and poorly understood group of actinopterygian fishes, currently considered a sister group of teleosts that contains only 8 species. The present study provides the first detailed information on the distribution of nitrergic cell bodies and fibers in 2 holostean species of the genus Lepisosteus, the spotted gar L. oculatus and the Florida gar L. platyrhincus. NOS immunohistochemistry and the NADPH diaphorase (NADPH-d) histochemical reaction were used, and both techniques yielded identical results, with the exception of the primary olfactory and terminal nerve fibers, which only labeled for NADPH-d exclusively in L. oculatus. Double immunohistochemistry was conducted for the simultaneous detection of NOS with tyrosine hydroxylase, choline acetyltransferase, calbindin, calretinin, and serotonin to accurately establish the localization of the nitrergic neurons and fibers in the brain of holosteans, the neuroanatomy of which has been mostly neglected, and to assess possible interactions between these neuroactive substances. Distinct groups of nitrergic cells were located in subpallial areas, the basal hypothalamus, posterior tubercle, optic tectum and mesencephalic tegmentum, reticular formation, solitary tract nucleus, spinal cord, and amacrine cells in the retina. In addition, low numbers of nitrergic cells were observed in the pallium, suprachiasmatic nucleus, prethalamic and thalamic areas, torus lateralis and torus semicircularis, cerebellar and laterodorsal tegmental nuclei, and the ventral octavolateral area. Comparison of these results with those from other classes of vertebrates, and including a segmental analysis to correlate cell populations, reveals that the pattern of the nitrergic system in holosteans is very close to that in ancestral actinopterygian fishes and highlights conserved and derived traits. [ABSTRACT FROM AUTHOR]

Perilipin (PLIN) proteins constitute an ancient family important in lipid droplet (LD) formation and triglyceride metabolism. We identified an additional PLIN clade (plin6) that is unique to teleosts and can be traced to the two whole genome duplications that occurred early in vertebrate evolution. Plin6 is highly expressed in skin xanthophores, which mediate red/yellow pigmentation and trafficking, but not in tissues associated with lipid metabolism. Biochemical and immunochemical analyses demonstrate that zebrafish Plin6 protein targets the surface of pigment-containing carotenoid droplets (CD). Protein kinase A (PKA) activation, which mediates CD dispersion in xanthophores, phosphorylates Plin6 on conserved residues. Knockout of plin6 in zebrafish severely impairs the ability of CD to concentrate carotenoids and prevents tight clustering of CD within carotenoid bodies. Ultrastructural and functional analyses indicate that LD and CD are homologous structures, and that Plin6 was functionalized early in vertebrate evolution for concentrating and trafficking pigment.

Synovial joints are the lubricated connections between the bones of our body that are commonly affected in arthritis. It is assumed that synovial joints first evolved as vertebrates came to land, with ray-finned fishes lacking lubricated joints. Here, we examine the expression and function of a critical lubricating protein of mammalian synovial joints, Prg4/Lubricin, in diverse ray-finned fishes. We find that Prg4 homologs are specifically enriched at the jaw and pectoral fin joints of zebrafish, stickleback, and gar, with genetic deletion of the zebrafish prg4b gene resulting in the same age-related degeneration of joints as seen in lubricin-deficient mice and humans. Our data support lubricated synovial joints evolving much earlier than currently accepted, at least in the common ancestor of all bony vertebrates. Establishment of the first arthritis model in the highly regenerative zebrafish will offer unique opportunities to understand the aetiology and possible treatment of synovial joint disease.

Genome duplication, thought to have happened twice early in vertebrate evolution and a third time in teleost fishes, gives rise to gene paralogs that can evolve subfunctions or neofunctions via sequence and regulatory changes. To explore the evolution and functions of corticotropin-releasing hormone (CRH), we searched sequenced teleost genomes for CRH paralogs. Our phylogenetic and synteny analyses indicate that two CRH genes, crha and crhb, evolved via duplication of crh1 early in the teleost lineage. We examined the expression of crha and crhb in two teleost species from different orders: an African cichlid, Burton’s mouthbrooder, (Astatotilapia burtoni; Order Perciformes) and zebrafish (Danio rerio; Order Cypriniformes). Furthermore, we compared expression of the teleost crha and crhb genes with the crh1 gene of an outgroup to the teleost clade: the spotted gar (Lepisosteus oculatus). In situ hybridization for crha and crhb mRNA in brains and eyes revealed distinct expression patterns for crha in different teleost species. In the cichlid, crha mRNA was found in the retina but not in the brain. In zebrafish, however, crha mRNA was not found in the retina, but was detected in the brain, restricted to the ventral hypothalamus. Spotted gar crh1 was found in the retina as well as the brain, suggesting that the ancestor of teleost fishes likely had a crh1 gene expressed in both retina and brain. Thus, genome duplication may have freed crha from constraints, allowing it to evolve distinct sequences, expression patterns, and likely unique functions in different lineages.

Macroderoides luki n. sp. (Trematoda: Macroderoididae) is described from the intestine of spotted gar ( Lepisosteus oculatus) collected from multiple locales on the Trinity River in eastern Texas, U.S.A. Members of the new species are most similar to Macroderoides trilobatus in that they possess an ovary composed of 3 lobes rather than an undivided ovary as in the other 6 species in North America. In the new species, the distance between the cirrus sac and ovary is far greater, the eggs are almost twice the size, and the body is longer than in M. trilobatus. This is the eighth species of Macroderoides named in North America and the largest specimens known from this group. [ABSTRACT FROM AUTHOR]

Background: In the duplication-degeneration-complementation (DDC) model, a duplicated gene has three possible fates: it may lose functionality through the accumulation of mutations (nonfunctionalization), acquire a new function (neofunctionalization), or each duplicate gene may retain a subset of functions of the ancestral gene (subfunctionalization). The role that promoter evolution plays in retention of duplicated genes in eukaryotic genomes is not well understood. Fatty acid-binding proteins (Fabp) belong to a multigene family that are highly conserved in sequence and function, but differ in their gene regulation, suggesting selective pressure is exerted via regulatory elements in the promoter. Results: In this study, we describe the PPAR regulation of zebrafish fabp1 a, fabp1 b.1, and fabp1 b.2 promoters and compare them to the PPAR regulation of the spotted gar fabp1 promoter, representative of the ancestral fabp1 gene. Evolution of the fabp1 promoter was inferred by sequence analysis, and differential PPAR-agonist activation of fabp1 promoter activity in zebrafish liver and intestine explant cells, and in HEK293A cells transiently transfected with wild-type and mutated fabp 1promoter-reporter gene constructs. The promoter activity of spotted gar fabp1, representative of the ancestral fabp1, was induced by both PPARa- and PPARy-specific agonists, but displayed a biphasic response to PPARa activation. Zebrafish fabp1a was PPARa-selective, fabp1b.1 was PPARy-selective, and fabp1 b.2 was not regulated by PPAR. Conclusions: The zebrafish fabp1 promoters underwent two successive rounds of subfunctionalization with respect to PPAR regulation leading to retention of three zebrafish fabp1 genes with stimuli-specific regulation. Using a pharmacological approach, we demonstrated here the divergent regulation of the zebrafish fabp1a, fabp1b.1, and fabp1 b.2 with regard to subfunctionalization of PPAR regulation following two rounds of gene duplication. [ABSTRACT FROM AUTHOR]

The neuropeptide QRFP, also called 26RFa, and its G protein-coupled receptor GPR103 have been identified in all vertebrates investigated. In mammals, this peptide-receptor pair has been found to have several effects including stimulation of appetite. Recently, we reported that a QRFP peptide is present in amphioxus, Branchiostoma floridae, and we also identified a QRFP receptor (QRFPR) that mediates a functional response to sub-nanomolar concentrations of the amphioxus peptide as well as short and long human QRFP (Xu et al., submitted). Because the ancestral vertebrate underwent two tetraploidizations, it might be expected that duplicates of the QRFP gene and its receptor gene may exist. Indeed, we report here the identification of multiple vertebrate QRFPR genes. Three QRFPR genes are present in the coelacanth Latimeria chalumnae, representing an early diverging sarcopterygian lineage. Three QRFP receptor genes are present in the basal actinopterygian fish, the spotted gar. Phylogenetic and chromosomal analyses show that only two of these receptor genes are orthologous between the two species, thus demonstrating a total of four distinct vertebrate genes. Three of the QRFPR genes resulted from the early vertebrate tetraploidizations and were copied along with syntenic neuropeptide Y receptor genes. The fourth QRFPR gene may be an even older and distinct lineage. Because mammals and birds have only a single QRFP receptor gene, this means that three genes have been lost in these lineages, and at least one of these was lost independently in mammals and birds because it is still present in a turtle. In conclusion, these results show that the QRFP system gained considerable complexity in the early stages of vertebrate evolution and still does so in some lineages, and that it has been secondarily reduced in mammals.

Functionally indispensable genes are likely to be retained and otherwise to be lost during evolution. This evolutionary fate of a gene can also be affected by factors independent of gene dispensability, including the mutability of genomic positions, but such features have not been examined well. To uncover the genomic features associated with gene loss, we investigated the characteristics of genomic regions where genes have been independently lost in multiple lineages. With a comprehensive scan of gene phylogenies of vertebrates with a careful inspection of evolutionary gene losses, we identified 813 human genes whose orthologs were lost in multiple mammalian lineages: designated 'elusive genes.' These elusive genes were located in genomic regions with rapid nucleotide substitution, high GC content, and high gene density. A comparison of the orthologous regions of such elusive genes across vertebrates revealed that these features had been established before the radiation of the extant vertebrates approximately 500 million years ago. The association of human elusive genes with transcriptomic and epigenomic characteristics illuminated that the genomic regions containing such genes were subject to repressive transcriptional regulation. Thus, the heterogeneous genomic features driving gene fates toward loss have been in place and may sometimes have relaxed the functional indispensability of such genes. This study sheds light on the complex interplay between gene function and local genomic properties in shaping gene evolution that has persisted since the vertebrate ancestor., Competing Interests: YH No competing interests declared, SK Reviewing editor, eLife, (© 2023, Hara and Kuraku.)

Genome duplication, thought to have happened twice early in vertebrate evolution and a third time in teleost fishes, gives rise to gene paralogs that can evolve subfunctions or neofunctions via sequence and regulatory changes. To explore the evolution and functions of corticotropin-releasing hormone (CRH), we searched sequenced teleost genomes for CRH paralogs. Our phylogenetic and synteny analyses indicate that two CRH genes, crha and crhb, evolved via duplication of crh1 early in the teleost lineage. We examined the expression of crha and crhb in two teleost species from different orders: an African cichlid, Burton's mouthbrooder, (Astatotilapia burtoni; Order Perciformes) and zebrafish (Danio rerio; Order Cypriniformes). Furthermore, we compared expression of the teleost crha and crhb genes with the crh1 gene of an outgroup to the teleost clade: the spotted gar (Lepisosteus oculatus). In situ hybridization for crha and crhb mRNA in brains and eyes revealed distinct expression patterns for crha in different teleost species. In the cichlid, crha mRNA was found in the retina but not in the brain. In zebrafish, however, crha mRNA was not found in the retina, but was detected in the brain, restricted to the ventral hypothalamus. Spotted gar crh1 was found in the retina as well as the brain, suggesting that the ancestor of teleost fishes likely had a crh1 gene expressed in both retina and brain. Thus, genome duplication may have freed crha from constraints, allowing it to evolve distinct sequences, expression patterns, and likely unique functions in different lineages. [ABSTRACT FROM AUTHOR]

Understanding the spatial context of genetic variation for species at risk is important for effective management and long-term survival of the species. We use multilocus microsatellite data to investigate the population genetic structure of the spotted gar ( Lepisosteus oculatus) across its northern range edge in Canada. We then compare these northern individuals with samples taken from the southern core of the species range. For the northern samples, significant genetic differentiation among groups of individuals forming two major genetically distinct populations, and as many as 7-9 smaller subpopulations, was recovered using hierarchical Bayesian assignment methods and non-equilibrial discriminant function analyses. Spatial genetic variation is present, particularly at higher hierarchical groupings; however, some population admixture at sites is evident and is indicative of dispersal and gene flow among some locations or shared ancestry. Gene flow estimates among populations and subpopulations is very low, ranging from essentially complete isolation to as high as 5 %-suggesting that mechanisms in addition to geographic isolation are operating to create genetic structure. In Lake Erie, the physical isolation of Point Pelee appears to confer distinct genetic differentiation for those populations and provide a source of genetic variation for Lake Erie proper when breaches to the barrier beach occur. Results indicate that the northern edge populations are distinct from southern populations and should be conserved to maintain the overall genetic diversity of this species. Additionally, the asymmetrical genetic connectivity among the Point Pelee and Rondeau Bay sites highlights the sensitivity of Point Pelee to environmental perturbation and habitat degradation. [ABSTRACT FROM AUTHOR]

The neuropeptide QRFP, also called 26RFa, and its G protein-coupled receptor GPR103 have been identified in all vertebrates investigated. In mammals, this peptide-receptor pair has been found to have several effects including stimulation of appetite. Recently, we reported that a QRFP peptide is present in amphioxus, Branchiostoma floridae, and we also identified a QRFP receptor (QRFPR) that mediates a functional response to sub-nanomolar concentrations of the amphioxus peptide as well as short and long human QRFP (Xu et al., submitted). Because the ancestral vertebrate underwent two tetraploidizations, it might be expected that duplicates of the QRFP gene and its receptor gene may exist. Indeed, we report here the identification of multiple vertebrate QRFPR genes. Three QRFPR genes are present in the coelacanth Latimeria chalumnae, representing an early diverging sarcopterygian lineage. Three QRFPR genes are present in the basal actinopterygian fish, the spotted gar. Phylogenetic and chromosomal analyses show that only two of these receptor genes are orthologous between the two species, thus demonstrating a total of four distinct vertebrate genes. Three of the QRFPR genes resulted from the early vertebrate tetraploidizations and were copied along with syntenic neuropeptide Y receptor genes. The fourth QRFPR gene may be an even older and distinct lineage. Because mammals and birds have only a single QRFPR gene, this means that three genes have been lost in these lineages, and at least one of these was lost independently in mammals and birds because it is still present in a turtle. In conclusion, these results show that the QRFP system gained considerable complexity in the early stages of vertebrate evolution and still maintains much of this in some lineages, and that it has been secondarily reduced in mammals. [ABSTRACT FROM AUTHOR]

Background Functionality of the tetrameric hemoglobin molecule seems to be determined by a few amino acids located in key positions. Oxygen binding encompasses structural changes at the interfaces between the α1β2 and α2β1 dimers, but also subunit interactions are important for the oxygen binding affinity and stability. The latter packing contacts include the conserved Arg B12 interacting with Phe GH5, which is replaced by Leu and Tyr in the αA and αD chains, respectively, of birds and reptiles. Results Searching all known hemoglobins from a variety of gnathostome species (jawed vertebrates) revealed the almost invariant Arg B12 coded by the AGG triplet positioned at an exon-intron boundary. Rare substitutions of Arg B12 in the gnathostome β globins were found in pig, tree shrew and scaled reptiles. Phe GH5 is also highly conserved in the β globins, except for the Leu replacement in the β1 globin of five marine gadoid species, gilthead seabream and the Comoran coelacanth, while Cys and Ile were found in burbot and yellow croaker, respectively. Atlantic cod β1 globin showed a Leu/Met polymorphism at position GH5 dominated by the Met variant in northwest-Atlantic populations that was rarely found in northeast-Atlantic cod. Site-specific analyses identified six consensus codons under positive selection, including 122β(GH5), indicating that the amino acid changes identified at this position may offer an adaptive advantage. In fact, computational mutation analysis showed that the replacement of Phe GH5 with Leu or Cys decreased the number of van der Waals contacts essentially in the deoxy form that probably causes a slight increase in the oxygen binding affinity. Conclusions The almost invariant Arg B12 and the AGG codon seem to be important for the packing contacts and pre-mRNA processing, respectively, but the rare mutations identified might be beneficial. The Leu122β1(GH5)Met and Met55β1(D6)Val polymorphisms in Atlantic cod hemoglobin modify the intradimer contacts B12-GH5 and H2-D6, while amino acid replacements at these positions in avian hemoglobin seem to be evolutionary adaptive in air-breathing vertebrates. The results support the theory that adaptive changes in hemoglobin functions are caused by a few substitutions at key positions. [ABSTRACT FROM AUTHOR]

During the past decade, the kisspeptin system has been identified in various vertebrates, leading to the discovery of multiple genes encoding both peptides (Kiss) and receptors (Kissr). The investigation of recently published genomes from species of phylogenetic interest, such as a chondrichthyan, the elephant shark, an early sarcopterygian, the coelacanth, a non-teleost actinopterygian, the spotted gar, and an early teleost, the European eel, allowed us to get new insights into the molecular diversity and evolution of both Kiss and Kissr families. We identified four Kissr in the spotted gar and coelacanth genomes, providing the first evidence of four Kissr genes in vertebrates. We also found three Kiss in the coelacanth and elephant shark genomes revealing two new species, in addition to Xenopus, presenting three Kiss genes. Considering the increasing diversity of kisspeptin system, phylogenetic, and synteny analyses enabled us to clarify both Kiss and Kissr classifications. We also could trace back the evolution of both gene families from the early steps of vertebrate history. Four Kissr and four Kiss paralogs may have arisen via the two whole genome duplication rounds (1R and 2R) in early vertebrates. This would have been followed by multiple independent Kiss and Kissr gene losses in the sarcopterygian and actinopterygian lineages. In particular, no impact of the teleost-specific 3R could be recorded on the numbers of teleost Kissr or Kiss paralogs. The origin of their diversity via 1R and 2R, as well as the subsequent occurrence of multiple gene losses, represent common features of the evolutionary histories of Kiss and Kissr families in vertebrates. In contrast, comparisons also revealed un-matching numbers of Kiss and Kissr genes in some species, as well as a large variability of Kiss/Kissr couples according to species. These discrepancies support independent features of the Kiss and Kissr evolutionary histories across vertebrate radiation. [ABSTRACT FROM AUTHOR]

Spotted Gar ( Lepisosteus oculatus), a species listed as Threatened under the Canadian Species at Risk Act (SARA) was collected during May and June, 2007 from several sites in Rondeau Bay, a shallow coastal wetland of Lake Erie. The first pectoral fin ray was removed from 78 individuals to age the fish and to determine individual growth characteristics. To assess the validity of using pectoral rays to age Spotted Gar, we compared techniques (otoliths, branchiostegal rays and pectoral rays) for ten individuals captured in southwestern Michigan. Agreement between readers and amongst the three structures was high; thus aging of Spotted Gar using sectioned pectoral rays is an effective method. Rondeau Bay specimens varied in age from 3 to 10 years and from 515 to 761 mm total length. Regression analysis of length vs. age data was calculated to be $$ {\hbox{y}} = {19}.{\hbox{217x}} + {491}.{19}\left( {{{\hbox{R}}^{{2}}} = 0.{22}} \right) $$. The low R value is attributed to having males and females, which differ in growth rates, combined. Growth rates of Rondeau Bay specimens were compared to a Louisiana population using ANCOVA. No significant difference was found in the rate of growth between these populations; however, condition was low as compared to a standard weight equation. This may lead to lower fecundity, contributing to the species' rarity in Canada. [ABSTRACT FROM AUTHOR]