Largest Group Of Vertebrates Research Articles

Climate change can impair bacterial pathogen defences in sablefish via hypoxia-mediated effects on adaptive immunity

Low-oxygen levels (hypoxia) in aquatic habitats are becoming more common because of global warming and eutrophication. However, the effects on the health/disease status of fishes, the world's largest group of vertebrates, are unclear. Therefore, we assessed how long-term hypoxia affected the immune function of sablefish, an ecologically and economically important North Pacific species, including the response to a formalin-killed Aeromonas salmonicida bacterin. Sablefish were held at normoxia or hypoxia (100% or 40% air saturated seawater, respectively) for 6–16 weeks, while we measured a diverse array of immunological traits. Given that the sablefish is a non-model organism, this involved the development of a species-specific methodological toolbox comprised of qPCR primers for 16 key immune genes, assays for blood antibacterial defences, the assessment of blood immunoglobulin (IgM) levels with ELISA, and flow cytometry and confocal microscopy techniques. We show that innate immune parameters were typically elevated in response to the bacterial antigens, but were not substantially affected by hypoxia. In contrast, hypoxia completely prevented the ∼1.5-fold increase in blood IgM level that was observed under normoxic conditions following bacterin exposure, implying a serious impairment of adaptive immunity. Since the sablefish is naturally hypoxia tolerant, our results demonstrate that climate change-related deoxygenation may be a serious threat to the immune competency of fishes.

Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon (Salmo salar).

Chitin is one of the most abundant polysaccharides in nature, forming important structures in insects, crustaceans, and fungal cell walls. Vertebrates on the other hand are generally considered "nonchitinous" organisms, despite having highly conserved chitin metabolism-associated genes. Recent work has revealed that the largest group of vertebrates, the teleosts, have the potential to both synthesize and degrade endogenous chitin. Yet, little is known about the genes and proteins responsible for these dynamic processes. Here, we used comparative genomics, transcriptomics, and chromatin accessibility data to characterize the repertoire, evolution, and regulation of genes involved in chitin metabolism in teleosts, with a particular focus on Atlantic salmon. Reconstruction of gene family phylogenies provides evidence for an expansion of teleost and salmonid chitinase and chitin synthase genes after multiple whole-genome duplications. Analyses of multi-tissue gene expression data demonstrated a strong bias of gastrointestinal tract expression for chitin metabolism genes, but with different spatial and temporal tissue specificities. Finally, we integrated transcriptomes from a developmental time series of the gastrointestinal tract with chromatin accessibility data to identify putative transcription factors responsible for regulating chitin metabolism gene expression (CDX1 and CDX2) as well as tissue-specific divergence in the regulation of gene duplicates (FOXJ2). The findings presented here support the hypothesis that chitin metabolism genes in teleosts play a role in developing and maintaining a chitin-based barrier in the teleost gut and provide a basis for further investigations into the molecular basis of this barrier.

Neural activation patterns associated with mouthbrooding, maternal care, infanticide and fry release in an African cichlid fish.

Parental care has evolved several times and is present across taxa. Parental care behaviors, such as food provisioning and protection, are critical for offspring success. However, infanticide can co-exist with parental care in the same species. The mechanisms underlying the switch from care to consumption and from offspring dependence to independence are relatively unknown, especially in fishes, the oldest and largest group of vertebrates. Mouthbrooding, an extreme example of parental care present in dozens of genera of fishes, provides an excellent opportunity to investigate the brain regions important for parental care. The maternal mouthbrooding African cichlid fish Astatotilapia burtoni broods developing young inside the mouth for approximately 14 days, then provides post-release maternal care by protecting fry inside the mouth when threatened. Following the post-release maternal care phase, females can exhibit infanticide and consume their own offspring. We used immunohistochemistry for the neural activation marker pS6 to identify differences in neural activation among mouthbrooding, maternal-care-providing and infanticide-exhibiting females, and between pre- and post-release fry. We identified five brain regions (Dc-5, ATn, nPPa, Vd-c and Dl-g) that are differentially activated among mouthbrooding, maternal care and infanticide females as well as six regions (Dm, Vv, Vd, Vs-m, TPp, PGZ and INL of retina) differentially activated between pre- and post-release fry. This study identifies both shared and distinct circuitry that may support transitions between parental care states and from care to infanticide, as well as regions in developed fry that support the transition from pre- to post-release.

Genome-wide survey reveals the phylogenomic relationships of Chirolophisjaponicus Herzenstein, 1890 (Stichaeidae, Perciformes).

Fish are the largest vertebrate group, consisting of more than 30 000 species with important ecological and economical value, while less than 3% of fish genomes have been published. Herein, a fish, Chirolophisjaponicus, was sequenced using the next-generation sequencing. Approximately 595.7 megabase pair of the C.japonicus genome was assembled (49 901 contigs with 42.61% GC contents), leading to a prediction of 46 729 protein-coding gene models. A total of 554 136 simple sequence repeats was identified in the whole genome of C.japonicus, and dinucleotide microsatellite motifs were the most abundant, accounting for 59.49%. Phylogenomic analysis of 16 genomes based on the 694 single-copy genes suggests that C.japonicus is closely related with Anarrhichthysocellatus, Cebidichthysviolaceus, and Pholisgunnellus. The results provide more thorough genetic information of C.japonicus and a theoretical basis and reference for further genome-wide analysis.

Initial data release and announcement of the 10,000 Fish Genomes Project (Fish10K).

BackgroundWith more than 30,000 species, fish—including bony, jawless, and cartilaginous fish—are the largest vertebrate group, and include some of the earliest vertebrates. Despite their critical roles in many ecosystems and human society, fish genomics lags behind work on birds and mammals. This severely limits our understanding of evolution and hinders progress on the conservation and sustainable utilization of fish.ResultsHere, we announce the Fish10K project, a portion of the Earth BioGenome Project aiming to sequence 10,000 representative fish genomes in a systematic fashion within 10 years, and we officially welcome collaborators to join this effort. As a step towards this goal, we herein describe a feasible workflow for the procurement and storage of biospecimens, as well as sequencing and assembly strategies.ConclusionsTo illustrate, we present the genomes of 10 fish species from a cohort of 93 species chosen for technology development.

The Mechanosensory Lateral Line System Mediates Activation of Socially-Relevant Brain Regions during Territorial Interactions.

Animals use multiple senses during social interactions and must integrate this information in the brain to make context-dependent behavioral decisions. For fishes, the largest group of vertebrates, the mechanosensory lateral line system provides crucial hydrodynamic information for survival behaviors, but little is known about its function in social communication. Our previous work using the African cichlid fish, Astatotilapia burtoni, provided the first empirical evidence that fish use their lateral line system to detect water movements from conspecifics for mutual assessment and behavioral choices. It is unknown, however, where this socially-relevant mechanosensory information is processed in the brain to elicit adaptive behavioral responses. To examine for the first time in any fish species which brain regions receive contextual mechanosensory information, we quantified expression of the immediate early gene cfos as a proxy for neural activation in sensory and socially-relevant brain nuclei from lateral line-intact and -ablated fish following territorial interactions. Our in situ hybridization results indicate that in addition to known lateral line processing regions, socially-relevant mechanosensory information is processed in the ATn (ventromedial hypothalamus homolog), Dl (putative hippocampus homolog), and Vs (putative medial extended amygdala homolog). In addition, we identified a functional network within the conserved social decision-making network (SDMN) whose co-activity corresponds with mutual assessment and behavioral choice. Lateral line-intact and –ablated fight winners had different patterns of co-activity of these function networks and group identity could be determined solely by activation patterns, indicating the importance of mechanoreception to co-activity of the SDMN. These data show for the first time that the mechanosensory lateral line system provides relevant information to conserved decision-making centers of the brain during territorial interactions to mediate crucial behavioral choices such as whether or not to engage in a territorial fight. To our knowledge, this is also the first evidence of a subpallial nucleus receiving mechanosensory input, providing important information for elucidating homologies of decision-making circuits across vertebrates. These novel results highlight the importance of considering multimodal sensory input in mediating context-appropriate behaviors that will provide broad insights on the evolution of decision-making networks across all taxa.

Nutrient Sensing in Atlantic Salmon ‐ Exploring the Sensory Systems for Amino Acids in the Gastrointestinal Tract

Over the last years there has been an improved understanding of the underlying mechanisms involved in nutrient sensing, and how the gastrointestinal tract (GIT) conveys information on ingested food to the brain and other organs. In mammals, several receptors from the G protein‐coupled receptors (GPCRs) superfamily have been identified as nutrient sensors that respond to organic nutrients or their breakdown products, i.e. fatty acids, sugars, amino acids (AAs) and proteolytic products. The AAs and peptides sensory mechanisms in the GIT are involved in modulating pancreatic exocrine and endocrine secretions as well as protein digestion in order to optimize nutrient utilization and control feed intake. While it is well acknowledged that the nutrient sensing system is a key player in the control of these functions in mammals, almost no information exist in teleosts, the largest vertebrate group with more than 25000 species. In Atlantic salmon (Salmo salar), a key commercial species in global aquaculture, it is of high interest to understand how specific AA enhance feed intake, growth and fish quality. In addition, Atlantic salmon has undergone an additional and relatively recent whole‐genome duplication event, the salmonid‐specific 4th WGD. Atlantic salmon therefore represent an excellent model system to study the role of gene duplication and adaptation.Key mammalian GPCRs involved in AA and peptide sensing in GIT belong to GPCR family C and A, respectively. The lysophosphatidic acid receptor 5 (LPAR5) belongs to family A and is responsive to peptides. The family C consists of members such as the metabotropic glutamate receptors (mGluRs), calcium‐sensing receptor (CasR), GPCR family C subtype 6A (GPRC6A) and taste receptors (T1Rs). Whereas the mGluRs are monogamous for L‐Glu, the CasR, GPR6A and T1Rs are promiscuous by nature and respond to, e.g., subsets of L‐α‐AAs and divalent cations. Such promiscuity for nutrients by the receptors in relevant tissues allows for a specific nutrient‐sensing capacity of emerging physiological significance.Our study is based on the hypothesis that the nutrient sensing system is conserved throughout vertebrate phylogeny. Based on this hypothesis, we have analyzed the presence of these receptors in the salmon genome. Homologues of vertebrate LPA5R gene were identified in silico and validated by cDNA cloning and sequencing. The salmon LPAR5 shared more than 50% AA sequence similarity with other vertebrate homologues. Members of GPCR family C were also identified in the salmon genome: five T1R1 transcripts, two T1R3, six GPR6A, thirteen mGluR1, seven mGluR4 and three CaSR transcripts. We have now started to validate the different transcript sequences by RT‐PCR amplification and cloning. Sequence comparative analysis indicates that 7 transmembrane domains and sequence motifs of the predicted salmon GPCRs family C are generally maintained across vertebrates. The remarkable conservation of primary sequences within vertebrates supports our hypothesis. This information is fundamental for further comparative studies and to study receptors pharmacology and biological responses in salmon.Support or Funding InformationSupported by RFFVEST (project no. 247978) and University of Bergen

Unique Features of Fish Immune Repertoires: Particularities of Adaptive Immunity Within the Largest Group of Vertebrates.

Fishes (i.e., teleost fishes) are the largest group of vertebrates. Although their immune system is based on the fundamental receptors, pathways, and cell types found in all groups of vertebrates, fishes show a diversity of particular features that challenge some classical concepts of immunology. In this chapter, we discuss the particularities of fish immune repertoires from a comparative perspective. We examine how allelic exclusion can be achieved when multiple Ig loci are present, how isotypic diversity and functional specificity impact clonal complexity, how loss of the MHC class II molecules affects the cooperation between T and B cells, and how deep sequencing technologies bring new insights about somatic hypermutation in the absence of germinal centers. The unique coexistence of two distinct B-cell lineages respectively specialized in systemic and mucosal responses is also discussed. Finally, we try to show that the diverse adaptations of immune repertoires in teleosts can help in understanding how somatic adaptive mechanisms of immunity evolved in parallel in different lineages across vertebrates.

Fugu Genome Analysis Provides Evidence for a Whole-Genome Duplication Early During the Evolution of Ray-Finned Fishes

With about 24,000 extant species, teleosts are the largest group of vertebrates. They constitute more than 99% of the ray-finned fishes (Actinopterygii) that diverged from the lobe-finned fish lineage (Sarcopterygii) about 450 MYA. Although the role of genome duplication in the evolution of vertebrates is now established, its role in structuring the teleost genomes has been controversial. At least two hypotheses have been proposed: a whole-genome duplication in an ancient ray-finned fish and independent gene duplications in different lineages. These hypotheses are, however, based on small data sets and lack adequate statistical and phylogenetic support. In this study, we have made a systematic comparison of the draft genome sequences of Fugu and humans to identify paralogous chromosomal regions ("paralogons") in the Fugu that arose in the ray-finned fish lineage ("fish-specific"). We identified duplicate genes in the Fugu by phylogenetic analyses of the Fugu, human, and invertebrate sequences. Our analyses provide evidence for 425 fish-specific duplicate genes in the Fugu and show that at least 6.6% of the genome is represented by fish-specific paralogons. We estimated the ages of Fugu duplicate genes and paralogons using the molecular clock. Remarkably, the ages of duplicate genes and paralogons are clustered, with a peak around 350 MYA. These data strongly suggest a whole-genome duplication event early during the evolution of ray-finned fishes, probably before the origin of teleosts.

Translational machinery of channel catfish: I. A transcriptomic approach to the analysis of 32 40S ribosomal protein genes and their expression

Ribosomal protein (RP) genes have become widely used as markers for phylogenetic studies and comparative genomics. However, they have not been available for evolutionary studies in fish although teleosts are the largest group of vertebrates with more than 23,000 species. Using a transcriptomic approach, we have cloned and sequenced 32 40S RP complementary DNAs (cDNAs) from channel catfish (Ictaluruspunctatus), making them one of the most complete sets of 40S RP gene sequences from a single organism. Most 40S RPs in channel catfish are highly similar to their orthologues in mammalian species, but S19, S21, and S25 are highly divergent. Only one type of cDNA was found for all RP genes except S26 and S27, for which two cDNAs were found in channel catfish. Alternatively spliced transcripts for the S3 and alternatively polyadenylated transcripts for S19 and S21 were found. The 32 40S RP genes are generally highly expressed and together they account for 5.33–11.42% of expression depending on the tissues. Expression levels of the RP genes were highly variable both within a single tissue among different RP genes and among tissues with regard to a single RP gene. Taken together, these data strongly suggest post-transcriptional regulation of RP gene expression, particularly in consideration of the stoichiometry of their representation in ribosomes.

Transformation of fish cells and embryos.

AbstractFish are the largest group of vertebrates. They have diverse features to adapt to a wide variety of environments, which make them excellent models for studies in various areas, including molecular and cellular biology (1,2). Small freshwater species, such as medaka (Oryzias latipes) and zebrafish (Brachydanio rerio) are being studied in a growing number of laboratories because of their advantages as experimental animals (2,3). The procedures for the preparation and maintenance of fish cell cultures do not differ from those of higher vertebrates. In general, fish cells grow in the same medium as mammalian cells and can be preserved by standard methods for freezing. A specific feature of fish cells is that they generally proliferate over a wide range of temperatures, and the optimal growth temperature reflects the environment that each species inhabits (4,5). In addition, fish cells are thought to be naturally immortal. Even cells derived from nonneoplastic tissues can grow continuously (6–8).KeywordsLong Terminal RepeatTransformation EfficiencyFish CellTransgenic FishHerpes Simplex Virus Thymidine KinaseThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.