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Transposable elements (TEs) are widespread genomic components with substantial roles in genome evolution and sex chromosome differentiation. In this study, we compared the TE composition of three closely related fish with different sex chromosome systems: Megaleporinus elongatus (Z1Z1Z2Z2/Z1W1Z2W2), Megaleporinus macrocephalus (ZZ/ZW) (both with highly differentiated W sex chromosomes), and Leporinus friderici (without heteromorphic sex chromosomes). We created custom TE libraries for each species using clustering methods and manual annotation and prediction, and we predicted TE temporal dynamics through divergence-based analysis. The TE abundance ranged from 16% to 21% in the three mobilomes, with L. friderici having the lowest overall. Despite the recent amplification of TEs in all three species, we observed differing expansion activities, particularly between the two genera. Both Megaleporinus recently experienced high retrotransposon activity, with a reduction in DNA TEs, which could have implications in sex chromosome composition. In contrast, L. friderici showed the opposite pattern. Therefore, despite having similar TE compositions, Megaleporinus and Leporinus exhibit distinct TE histories that likely evolved after their separation, highlighting a rapid TE expansion over short evolutionary periods. [ABSTRACT FROM AUTHOR]

Simple Summary: Long terminal repeat retrotransposons (LTR-RTNs) are vital in genome evolution and diversity. The compact genomes of Tetraodontiformes provide an excellent model for studying LTR-RTN dynamics. An analysis of the genomes of ten tetraodontiform species revealed a total of 819 full-length LTR retrotransposon sequences classified into nine families spanning four distinct superfamilies. Among them, the Gypsy superfamily displayed the highest level of diversity. Takifugu stood out for having the highest abundance of LTR families and sequences. Evidence of recent LTR-RTN activity and multiple invasions was observed in specific tetraodontiform genomes. This investigation provides valuable insights into the evolution of LTR retrotransposons and their impact on the structure and evolution of compact tetraodontiform genomes. This study aimed to investigate the evolutionary profile (including diversity, activity, and abundance) of retrotransposons (RTNs) with long terminal repeats (LTRs) in ten species of Tetraodontiformes. These species, Arothron firmamentum, Lagocephalus sceleratus, Pao palembangensis, Takifugu bimaculatus, Takifugu flavidus, Takifugu ocellatus, Takifugu rubripes, Tetraodon nigroviridis, Mola mola, and Thamnaconus septentrionalis, are known for having the smallest genomes among vertebrates. Data mining revealed a high diversity and wide distribution of LTR retrotransposons (LTR-RTNs) in these compact vertebrate genomes, with varying abundances among species. A total of 819 full-length LTR-RTN sequences were identified across these genomes, categorized into nine families belonging to four different superfamilies: ERV (Orthoretrovirinae and Epsilon retrovirus), Copia, BEL-PAO, and Gypsy (Gmr, Mag, V-clade, CsRN1, and Barthez). The Gypsy superfamily exhibited the highest diversity. LTR family distribution varied among species, with Takifugu bimaculatus, Takifugu flavidus, Takifugu ocellatus, and Takifugu rubripes having the highest richness of LTR families and sequences. Additionally, evidence of recent invasions was observed in specific tetraodontiform genomes, suggesting potential transposition activity. This study provides insights into the evolution of LTR retrotransposons in Tetraodontiformes, enhancing our understanding of their impact on the structure and evolution of host genomes. [ABSTRACT FROM AUTHOR]

Miiuy croaker, Miichthys miiuy is an ecologically important teleost species which is widely distributed in southeast coast of China. In this study, we present a chromosomal-scale genome assembly of the miiuy croaker which is an important Sciaenidae fish and economical species. We adopted Oxford Nanopore and Hi-C sequencing techniques to achieve an assembly with high accuracy and completeness. The investigation of genome characteristic and functional features may provide insights into the study of phylogenetic diversity of miiuy croaker. This study can also be beneficial to improve molecular assisted breeding techniques. Moreover, it can be a great resource to better conduct further study of other sciaenids. [ABSTRACT FROM AUTHOR]

Resolving the genomic basis underlying phenotypic variations is a question of great importance in evolutionary biology. However, understanding how genotypes determine the phenotypes is still challenging. Centuries of artificial selective breeding for beauty and aggression resulted in a plethora of colors, long-fin varieties, and hyper-aggressive behavior in the air-breathing Siamese fighting fish (Betta splendens), supplying an excellent system for studying the genomic basis of phenotypic variations. Combining whole-genome sequencing, quantitative trait loci mapping, genome-wide association studies, and genome editing, we investigated the genomic basis of huge morphological variation in fins and striking differences in coloration in the fighting fish. Results revealed that the double tail, elephant ear, albino, and fin spot mutants each were determined by single major-effect loci. The elephant ear phenotype was likely related to differential expression of a potassium ion channel gene, kcnh8. The albinotic phenotype was likely linked to a cis-regulatory element acting on the mitfa gene and the double-tail mutant was suggested to be caused by a deletion in a zic1 / zic4 coenhancer. Our data highlight that major loci and cis-regulatory elements play important roles in bringing about phenotypic innovations and establish Bettas as new powerful model to study the genomic basis of evolved changes. [ABSTRACT FROM AUTHOR]

Testing among competing demographic models of divergence has become an important component of evolutionary research in model and non-model organisms. However, the effect of unaccounted demographic events on model choice and parameter estimation remains largely unexplored. Using extensive simulations, we demonstrate that under realistic divergence scenarios, failure to account for population size (N e) changes in daughter and ancestral populations leads to strong biases in divergence time estimates as well as model choice. We illustrate these issues reconstructing the recent demographic history of North Sea and Baltic Sea turbots (Scophthalmus maximus) by testing 16 isolation with migration (IM) and 16 secondary contact (SC) scenarios, modeling changes in N e as well as the effects of linked selection and barrier loci. Failure to account for changes in N e resulted in selecting SC models with long periods of strict isolation and divergence times preceding the formation of the Baltic Sea. In contrast, models accounting for N e changes suggest recent (<6 kya) divergence with constant gene flow. We further show how interpreting genomic landscapes of differentiation can help discerning among competing models. For example, in the turbot data, islands of differentiation show signatures of recent selective sweeps, rather than old divergence resisting secondary introgression. The results have broad implications for the study of population divergence by highlighting the potential effects of unmodeled changes in N e on demographic inference. Tested models should aim at representing realistic divergence scenarios for the target taxa, and extreme caution should always be exercised when interpreting results of demographic modeling. [ABSTRACT FROM AUTHOR]

Genomics is increasingly applied in breeding programmes for farmed fish and shellfish species around the world. However, current applications do not include information on genome functional activity, which can enhance opportunities to predict relationships between genotypes and phenotypes and hence increase the accuracy of selection. Here, we review prospects for improving aquaculture breeding practises through the uptake of functional genomics data in light of the EU Horizon 2020 project AQUA-FAANG: ' Advancing European Aquaculture by Genome Functional Annotation'. This consortium targeted the six major farmed fish species in European aquaculture, producing thousands of functional genomic datasets from samples representing embryos to mature adults of both sexes, and following immunological stimulation. This data was used to catalogue functional activity across the genome of each species, revealing transcribed regions, distinct chromatin states and regulatory elements impacting gene expression. These functional annotations were shared as open data through the Ensembl genome browser using the latest reference genomes for each species. AQUA-FAANG data offers novel opportunities to identify and prioritize causative genetic variants responsible for diverse traits including disease resistance, which can be exploited to enhance selective breeding. Such knowledge and associated resources have the potential to improve sustainability and boost production in aquaculture by accelerating genetic gain for health and robustness to infection, whilst reducing the requirement for animal testing. We further outline directions to advance and leverage genome functional annotation beyond the AQUA-FAANG project. Given the diversity of aquaculture sectors and businesses, the incorporation of functional genomic information into breeding decisions will depend on technological readiness level and scale of operation, with cost-benefit analysis necessary to determine the most profitable approach for each species and production system. • The AQUAFAANG project has produced improved and richly functionally annotated genomes for six fish species. • The prospects for utilising functional genomic information in breeding decisions is critically reviewed. • Future research opportunities and the need to determine the cost benefit of different genomic technologies is highlighted. [ABSTRACT FROM AUTHOR]

Abstract Background The electric organ of Tetronarce californica (an electric ray formerly known as Torpedo californica) is a classic preparation for biochemical studies of cholinergic neurotransmission. To broaden the usefulness of this preparation, we have performed a transcriptome assembly of the presynaptic component of the electric organ (the electric lobe). We combined our assembled transcriptome with a previous transcriptome of the postsynaptic electric organ, to define a MetaProteome containing pre- and post-synaptic components of the electric organ. Results Sequencing yielded 102 million paired-end 100 bp reads. De novo Trinity assembly was performed at Kmer 25 (default) and Kmers 27, 29, and 31. Trinity, generated around 103,000 transcripts, and 78,000 genes per assembly. Assemblies were evaluated based on the number of bases/transcripts assembled, RSEM-EVAL scores and informational content and completeness. We found that different assemblies scored differently according to the evaluation criteria used, and that while each individual assembly contained unique information, much of the assembly information was shared by all assemblies. To generate the presynaptic transcriptome (electric lobe), while capturing all information, assemblies were first clustered and then combined with postsynaptic transcripts (electric organ) downloaded from NCBI. The completness of the resulting clustered predicted MetaProteome was rigorously evaluated by comparing its information against the predicted proteomes from Homo sapiens, Callorhinchus milli, and the Transporter Classification Database (TCDB). Conclusions In summary, we obtained a MetaProteome containing 92%, 88.5%, and 66% of the expected set of ultra-conserved sequences (i.e., BUSCOs), expected to be found for Eukaryotes, Metazoa, and Vertebrata, respectively. We cross-annotated the conserved set of proteins shared between the T. californica MetaProteome and the proteomes of H. sapiens and C. milli, using the H. sapiens genome as a reference. This information was used to predict the position in human pathways of the conserved members of the T. californica MetaProteome. We found proteins not detected before in T. californica, corresponding to processes involved in synaptic vesicle biology. Finally, we identified 42 transporter proteins in TCDB that were detected by the T. californica MetaProteome (electric fish) and not selected by a control proteome consisting of the combined proteomes of 12 widely diverse non-electric fishes by Reverse-Blast-Hit Blast. Combined, the information provided here is not only a unique tool for the study of cholinergic neurotransmission, but it is also a starting point for understanding the evolution of early vertebrates.

Treated sewage discharge has been reported to affect multiple levels of biological organization in fish and fish community structure. In this study, a split-plot ANOVA design was used to test species diversity of fish assemblages in Taiwan. The samples were collected seasonally, from 2005 to 2016, at three different stations near the ocean outfall pipeline of a sewage treatment plant in northern Taiwan. The significance of differences in abundance, species richness, and phylogenetic diversity of fish assemblages were tested. Using the ANOVA model, the significance of yearly and seasonal differences could be tested simultaneously. The results suggest that yearly and seasonal effects were not significant for any of the three components of diversity tested during the 12-year period. The results also suggest that the distance from the outfall of the ocean pipeline had no significant impact on species diversity. [ABSTRACT FROM AUTHOR]

Crustacean hemocytes, which have usually been classified morphologically based on methods using Giemsa or May-Giemsa stains, have recently been categorized using monoclonal antibodies or marker genes. However, these latter techniques are not yet widely used, and different classification methods are used for hemocytes among laboratories. Therefore, we aimed to develop a molecular classification method that can be widely used by researchers. The method we have developed uses lectins and magnetic-activated cell sorting (MACS) to isolate sub-populations of hemocytes. Two lectins, wheat germ agglutinin (WGA) and tomato lectin (Lycopersicon esculentum lectin; LEL), characteristically bind to hemocytes, which allows them to be classified into three sub-populations. Furthermore, different sub-populations of hemocyte can be isolated by using LEL and MACS. These sub-populations were characterized as non-granular and granular hemocytes, and the accumulation patterns of the gene transcripts were consistent with the results of a functional analysis reported previously. The lectin-based hemocyte isolation method developed in this study has good reproducibility. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Phylogenomics reveals extensive paraphy in Schizothoracinae. • Convergent evolution of morphology prevails in Schizothoracinae. • Similar niches is the underlying mechanism of convergence. • Convergent evolution mislead taxonomy. • An overhaul of taxonomy of the HSG fishes is imperative. Abstract Highly specialized grade (HSG; genera Gymnocypris , Oxygymnocypris , Schizopygopsis , Platypharodon and Chuanchia) of the Schizothoracinae (Cypriniformes: Cyprinidae) are endemic to the Qinghai-Tibet Plateau (QTP). Previously, two distinct ecomorphs were recognized according to trophic traits. One was a limnetic omnivore with normal lower jaw morphology, terminal mouth, and moderate or dense gill rakers, mostly inhabiting in open water of lakes, including Gymnocypris and Oxygymnocypris. Another was a benthic feeder with inferior mouth, sparse gill rakers and sharp horny sheath on the lower jaw for scraping of attached prey off hard substrates, including Schizopygopsis , Platypharodon and Chuanchia. However, traditional taxonomy of HSG based on these trophic traits presented extensive conflicts with the molecular studies in recent years. The possible cause could be convergent evolution in morphology, retention of ancestral polymorphisms or mitochondrial introgression, but these hypotheses could not be assessed due to incomplete taxon sampling and only mitochondrial data employed in previous works. Here, we conducted the most comprehensive molecular analysis on HSG fishes to date, using four mitochondrial loci and 152,464 genome-wide SNPs, and including 21 of 24 putative species and one undescribed Schizopygopsis species. Both SNP and mtDNA trees confirmed extensive paraphyly of genera Gymnocypris and Schizopygopsis , where species often were clustered together by watershed instead of by genus. Basal split into the north clade B and the south clade C (ca. 3.03 Ma) approximately by the Tanggula-Tanitawen Mountains in SLAF tree coincided with a violent uplift of the QTP during the phase A of 'Qingzang movement' (ca. 3.6 Ma). Ancestral state reconstruction of the trophic ecomorph showed that the limnetic omnivore ecomorph had evolved repeatedly in clade B and C. Furthermore, we presented a striking case of convergent evolution between two 'subspecies' Gymnocypris chui chui and G. chui longimandibularis , which had diverged as early as two million years ago (ca. 2.42 Ma). Ecological analyses revealed that similar food utilization, particularly in zooplankton, was the main underlying driving force. This work showed an example of taxonomy with the most extensive errors at the genus/species levels due to convergent evolution and suggested that trophic traits could be misleading in fish taxonomy. Therefore, we propose a major generic revision for HSG species. [ABSTRACT FROM AUTHOR]

The Congolese and Lower Guinean ichthyological provinces are understudied hotspots of the global fish diversity. Here, we barcoded 741 specimens from the Lower and Middle Congo River and from three major drainage basins of the Lower Guinean ichthyological province, Kouilou‐Niari, Nyanga and Ogowe. We identified 194 morphospecies belonging to 82 genera and 25 families. Most morphospecies (92.8%) corresponded to distinct clusters of DNA barcodes. Of the four morphospecies present in both neighbouring ichthyological provinces, only one showed DNA barcode divergence <2.5%. A small fraction of the fishes barcoded here (12.9% of the morphospecies and 16.1% of the barcode clusters representing putative species) were also barcoded in a previous large‐scale DNA analysis of freshwater fishes of the Lower Congo published in 2011 (191 specimens, 102 morphospecies). We compared species assignments before and after taxonomic updates and across studies performed by independent research teams and observed that most cases of inconsistent species assignments were due to unknown diversity (undescribed species and unknown intraspecific variation). Our results report more than 17 putative new species and show that DNA barcode data provide a measure of genetic variability that facilitates the inventory of underexplored ichthyofaunae. However, taxonomic scrutiny, associated with revisions and new species descriptions, is indispensable to delimit species and build a coherent reference library. [ABSTRACT FROM AUTHOR]

The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that antipredator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here, we present a de novo chromosome‐scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single‐molecule real‐time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi‐C‐based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein‐coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes. [ABSTRACT FROM AUTHOR]

The goldfish (Carassius auratus) is a domesticated cyprinid teleost closely related to the crucian carp. Goldfish domestication occurred in South China around 1,000 years ago. At least 180 variants and 70 genetically established strains are currently produced. These strains possess diverse phenotypes in body shape, colouration, scales, and fin, eye and hood morphology. These include biologically interesting phenotypes that have not been observed in mutants of zebrafish or medaka. In addition, goldfish strains have been maintained in a non-wild environment for several hundreds of generations, and certain goldfish strains have phenotypes similar to some human diseases. The recent progress in the assembly of the whole-genome sequence of goldfish provides strong tools for a genetic analysis of these phenotypes. The whole-genome duplication (WGD) event occurred in the goldfish genome 8–14 million years ago; this is one of the latest WGD in vertebrates. Goldfish are a useful model for studying genome evolution after the WGD event. This review focuses on the potential for goldfish as a model system in understanding the molecular basis of vertebrate development and evolution and human diseases. [ABSTRACT FROM AUTHOR]

The geographic structure of marine fish populations is an important element used in defining stock units, and genetic data have historically been used for this purpose. Here, genetic data were used to elicit population genomic patterns for Atlantic Croakers Micropogonias undulatus collected at five locations in the Gulf of Mexico (hereafter, "Gulf") and a single location in the southern U.S. Atlantic. Mitochondrial DNA (mtDNA) haplotypes were used as a baseline for historical lineage delineation and in a comparison with a previous Atlantic Croaker study that was centered on the Atlantic coast. A genomic data set consisting of 3,682 single-nucleotide polymorphism (SNP)-containing loci was used to assess contemporary gene flow throughout the sampled area. Both the mtDNA and SNP data sets showed significant between-basin estimates of genetic divergence (Φst = 0.049 and FST = 0.002, respectively), while pairwise FST implied a low magnitude of divergence (FST ≤ 0.002) at all geographic scales. Comparison of patterns obtained from putatively "neutral" versus "outlier" SNP loci suggested contrasting genetic patterns at the extremes of the sampling distribution in the Gulf. Putatively neutral SNPs implied a single stock in the Gulf, whereas a handful of outliers suggested distinct populations in the eastern and western Gulf. The pattern observed at outlier loci could imply either the presence of natural selection impacting a small number of loci or otherwise could be explained as a remnant pattern reflective of historical geographic isolation. In either case, the weak population structure observed at a small number of SNP loci may be indicative of a more significant demographic structure; for this reason, caution is urged when treating Atlantic Croakers as a single stock in the Gulf. [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]

Abstract MicroRNAs (miRNAs) play key roles in the stress response in animals. The rainbow trout is a widely cultivated cold-water fish species that usually encounters heat stress, which affects its growth and may cause diseases. However, there is limited information on the miRNAs involved in heat stress in this species. To identify the heat-responsive miRNAs at the genome level in rainbow trout, we conducted high-throughput sequencing of 6 small RNA libraries from the liver tissues of rainbow trout specimens under control and heat-treated conditions. A total of 363 conserved miRNAs and 638 novel miRNAs were identified, among which 39 (21 conserved and 18 novel) miRNAs were differentially expressed in response to heat stress. Eight important miRNAs were further validated using quantitative real-time PCR. GO enrichment and KEGG pathway analyses of the potential target genes of the DE miRNAs, revealed DNA replication and protein folding and unfolding were affected by heat stress. Several key pathways involved in the heat stress response were characterized, such as protein processing in the endoplasmic reticulum, NOD-like receptor signaling pathway, and progesterone-mediated oocyte maturation. In addition, 20 important functional interaction pairs among the 65 negatively correlated miRNA-mRNA pairs were identified using integrated miRNA-mRNA analysis and miRNA prediction algorithms, which including potential important miRNAs and target genes such as miR-301a, miR-301d, let-7c, novel_1181 and HSP90BA , HSP90BB , HSP40 , PDIA3. This study showed that the identified miRNAs probably play important roles in the heat stress response and lay a foundation for further studies on the thermal adaptation mechanisms in rainbow trout. Highlights • We sequenced 6 miRNA libraries from rainbow trout livers in 18 °C and 24 °C. • A total of 363 conserved miRNAs and 638 novel miRNAs were identified. • 21 conserved and 18 novel miRNAs were differentially expressed. • 20 important miRNA-mRNA interaction pairs were involved in heat stress response. [ABSTRACT FROM AUTHOR]

Background: The cartilaginous fishes diverged from other jawed vertebrates ~ 450 million years ago (mya). Despite this key evolutionary position, the only high-quality cartilaginous fish genome available is for the elephant shark (Callorhinchus milii), a chimaera whose ancestors split from the elasmobranch lineage ~ 420 mya. Initial analysis of this resource led to proposals that key components of the cartilaginous fish adaptive immune system, most notably their array of T cell subsets, was primitive compared to mammals. This proposal is at odds with the robust, antigen-specific antibody responses reported in elasmobranchs following immunization. To explore this discrepancy, we generated a multi-tissue transcriptome for small-spotted catshark (Scyliorhinus canicula), a tractable elasmobranch model for functional studies. We searched this, and other newly available sequence datasets, for CD4+ T cell subset-defining genes, aiming to confirm the presence or absence of each subset in cartilaginous fishes. Results: We generated a new transcriptome based on a normalised, multi-tissue RNA pool, aiming to maximise representation of tissue-specific and lowly expressed genes. We utilized multiple transcriptomic datasets and assembly variants in phylogenetic reconstructions to unambiguously identify several T cell subset-specific molecules in cartilaginous fishes for the first time, including interleukins, interleukin receptors, and key transcription factors. Our results reveal the inability of standard phylogenetic reconstruction approaches to capture the site-specific evolutionary processes of fast-evolving immune genes but show that site-heterogeneous mixture models can adequately do so. Conclusions: Our analyses reveal that cartilaginous fishes are capable of producing a range of CD4+ T cell subsets comparable to that of mammals. Further, that the key molecules required for the differentiation and functioning of these subsets existed in the jawed vertebrate ancestor. Additionally, we highlight the importance of considering phylogenetic diversity and, where possible, utilizing multiple datasets for individual species, to accurately infer gene presence or absence at higher taxonomic levels. [ABSTRACT FROM AUTHOR]

The South African (SAF) yellowfin tuna (Thunnus albacares) fishery represents a potential example of misalignment between management units and biological processes. The SAF fishery spans an operational stock with a boundary at 20°E, either side of which fish are considered part of Atlantic or Indian Ocean regional stocks. However, the actual recruitment of fish from Atlantic and Indian Ocean spawning populations into SAF waters is unknown. To address this knowledge gap, genomic analysis (11 101 SNPs) was performed on samples from Atlantic and Indian Ocean spawning sites, including SAF sites spanning the current stock boundary. Outlier loci conferred high discriminatory power to assignment tests and revealed that all SAF fish were assigned to the Indian Ocean population and that no Atlantic Ocean fish appeared in the SAF samples. Additionally, several Indian Ocean migrants were detected at the Atlantic spawning site demonstrating asymmetric dispersal and the occurrence of a mixed-stock fishery in Atlantic waters. This study highlights both the spatial inaccuracy of current stock designations and a misunderstanding of interactions between the underlying biological units, which must be addressed in light of local and global declines of the species. Specifically, the entire SAF fishery must be managed as part of the Indian Ocean stock. [ABSTRACT FROM AUTHOR]

Abstract The wrasses (Labridae) are one of the most successful and species-rich families of the Perciformes order of teleost fish. Its members display great morphological diversity, and occupy distinct trophic levels in coastal waters and coral reefs. The cleaning behaviour displayed by some wrasses, such as corkwing wrasse (Symphodus melops), is of particular interest for the salmon aquaculture industry to combat and control sea lice infestation as an alternative to chemicals and pharmaceuticals. There are still few genome assemblies available within this fish family for comparative and functional studies, despite the rapid increase in genome resources generated during the past years. Here, we present a highly continuous genome assembly of the corkwing wrasse using PacBio SMRT sequencing (x28.8) followed by error correction with paired-end Illumina data (x132.9). The present genome assembly consists of 5040 contigs (N50 = 461,652 bp) and a total size of 614 Mbp, of which 8.5% of the genome sequence encode known repeated elements. The genome assembly covers 94.21% of highly conserved genes across ray-finned fish species. We find evidence for increased copy numbers specific for corkwing wrasse possibly highlighting diversification and adaptive processes in gene families including N-linked glycosylation (ST8SIA6) and stress response kinases (HIPK1). By comparative analyses, we discover that de novo repeats, often not properly investigated during genome annotation, encode hundreds of immune-related genes. This new genomic resource, together with the ballan wrasse (Labrus bergylta), will allow for in-depth comparative genomics as well as population genetic analyses for the understudied wrasses. Highlights • Sequencing and assembly of the corkwing wrasse genome. • Possible adaptations related to stress response and glycosylation. • Comparative analysis of gene copy numbers in wrasses. • De novo repeats, often discarded, encode hundreds of immune-related genes in wrasses. [ABSTRACT FROM AUTHOR]

Nonsexual complexes which lack typical reproductive isolation and show multiple conspecific and heterospecific mating options among hybrids and parental species are excellent models to study mate choice based on genetics. The allopolyploid fish complex Squalius alburnoides includes multiple fertile male and female genomotypes reproducing among each other and with the sympatric species of the Squalius genus. We used this hybridogenetic complex to study the relationship between mate preference and mates' genetic background, focusing on a population whose mating options include 2 Squalius species. The preference of S. alburnoides hybrid females towards multiple male genomotypes was assessed in affiliation trials, and the levels of admixture between the genomes of the 2 Squalius species were measured using next-generation genotyping. The genome of the most recent Squalius species in the drainage was admixed with variable genetic portions typically allocated to the other species, but not the opposite, suggesting that the newer species in the drainage may be more prone to interspecific crosses. Female mate preferences were related to males' genetic background, but also to the genetic background of the choosy female itself. Overall, females showed higher preference towards males with admixed genomes over pure males, and towards males with a genetic background more similar to their own. This trend favors crosses between the hybrids and the most recent Squalius species in the drainage, promoting the flow of its genome into the hybridogenetic complex. These findings highlight an intricate interplay between mate choice and mates' genomes, which may be directly related to genetic benefits. [ABSTRACT FROM AUTHOR]

Alzheimer’s disease is the most common form of age-related dementia. At least 15 mutations in the human gene PRESENILIN 2 (PSEN2) have been found to cause familial Alzheimer’s disease (fAD). Zebrafish possess an orthologous gene, psen2, and present opportunities for investigation of PRESENILIN function related to Alzheimer’s disease. The most prevalent and best characterized fAD mutation in PSEN2 is N141I. The equivalent codon in zebrafish psen2 is N140. We used genome editing technology in zebrafish to target generation of mutations to the N140 codon. We isolated two mutations: psen2N140fs, (hereafter “N140fs”), causing truncation of the coding sequence, and psen2T141_L142delinsMISLISV, (hereafter “T141_L142delinsMISLISV”), that deletes the two codons immediately downstream of N140 and replaces them with seven codons coding for amino acid residues MISLISV. Thus, like almost every fAD mutation in the PRESENILIN genes, this latter mutation does not truncate the gene’s open reading frame. Both mutations are homozygous viable although N140fs transcripts are subject to nonsense-mediated decay and lack any possibility of coding for an active γ-secretase enzyme. N140fs homozygous larvae initially show grossly normal melanotic skin pigmentation but subsequently lose this as they grow while retaining pigmentation in the retinal pigmented epithelium. T141_L142delinsMISLISV homozygotes retain faint skin melanotic pigmentation as adults, most likely indicating that the protein encoded by this allele retains weak γ-secretase activity. Null mutations in the human PRESENILIN genes do not cause Alzheimer’s disease so these two mutations may be useful for future investigation of the differential effects of null and fAD-like PRESENILIN mutations on brain aging. [ABSTRACT FROM AUTHOR]

The estimation of stock specific exploitation is imperative to fisheries management and the conservation of biodiversity, particularly in instances where fisheries simultaneously exploit mixtures of stocks. Mixed stock harvests are particularly common in species that have extensive marine migrations, such as Atlantic and Pacific salmon. Here we develop a range-wide genetic baseline for Atlantic salmon ( Salmo salar ) from North American and European rivers to allow regional assignment of individuals targeted in international mixed stock fisheries. A combination of published data and additional genotyping was used to assemble a dataset of 96 SNPs for 285 range-wide Atlantic salmon populations for regional assignment. Clustering of baseline samples identified 20 North American and eight European reporting groups with mean individual assignment accuracy of 90% (range 70–100%). This baseline was applied to disentangle the stock composition of individuals in a subset of individuals from the West Greenland Atlantic salmon fishery. Genetic mixture analysis revealed that both European and North American individuals originated from multiple regions, with 92% of European individuals originating from the United Kingdom and Ireland, and North American individuals originating from three regions; Gulf of St. Lawrence (28%), Gaspé Peninsula (23%), and coastal Labrador (21%). The baseline represents a significant resource for the management of Atlantic salmon fisheries and the quantification of salmon migration patterns at sea. [ABSTRACT FROM AUTHOR]

Arctic charr have a circumpolar distribution, persevere under extreme environmental conditions, and reach ages unknown to most other salmonids. The Salvelinus genus is primarily composed of species with genomes that are structured more like the ancestral salmonid genome than most Oncorhynchus and Salmo species of sister genera. It is thought that this aspect of the genome may be important for local adaptation (due to increased recombination) and anadromy (the migration of fish from saltwater to freshwater). In this study, we describe the generation of a new genetic map, the sequencing and assembly of the Arctic charr genome (GenBank accession: GCF_002910315.2) using the newly created genetic map and a previous genetic map, and present several analyses of the Arctic charr genes and genome assembly. The newly generated genetic map consists of 8,574 unique genetic markers and is similar to previous genetic maps with the exception of three major structural differences. The N50, identified BUSCOs, repetitive DNA content, and total size of the Arctic charr assembled genome are all comparable to other assembled salmonid genomes. An analysis to identify orthologous genes revealed that a large number of orthologs could be identified between salmonids and many appear to have highly conserved gene expression profiles between species. Comparing orthologous gene expression profiles may give us a better insight into which genes are more likely to influence species specific phenotypes. [ABSTRACT FROM AUTHOR]

Abstract: The current ease of obtaining thousands of molecular markers challenges the notion that full phylogenetic concordance, as proposed by phylogenetic species concepts, is a requirement for defining species delimitations. Indeed, the presence of genomic islands of divergence, which may be the cause, or in some cases the consequence, of speciation, precludes concordance. Here, we explore this issue using thousands of RAD markers on two sister species of surgeonfishes (Teleostei: Acanthuridae), Zebrasoma flavescens and Z. scopas, and several populations within each species. Species are readily distinguished based on their colors (solid yellow and solid brown, respectively), yet populations and species are neither distinguishable using mitochondrial markers (cytochrome c oxidase 1), nor using 5193 SNPs (pairwise Φst = 0.034). In contrast, when using outlier loci, some of them presumably under selection, species delimitations, and strong population structure follow recognized taxonomic positions (pairwise Φst = 0.326). Species and population delimitation differences based on neutral and selected markers are likely due to local adaptation, thus being consistent with the idea that these genomic islands of divergence arose as a consequence of isolation. These findings, which are not unique, raise the question of a potentially important pathway of divergence based on local adaptation that is only evident when looking at thousands of loci. [ABSTRACT FROM AUTHOR]

Toll-like receptors (TLRs) play an essential role in the immune response. Here two Toll-like receptors from golden pompano ( Trachinotus ovatus ), ToTLR1 and ToTLR2, were characterized, the full-length cDNAs were 3126 bp and 7430 bp, and the deduced proteins consisted of 801 and 825 amino acids, respectively. ToTLR1 and ToTLR2 both contained the typical TLR domain architecture including signal peptide, leucine rich repeat (LRR), C-terminal LRR domain at the extracellular region and Toll/interleukin (IL)-1 receptor (TIR) domain in the cytoplasmic region. ToTLR1 only had one intron and two exons, but ToTLR2 consisted of twelve introns and thirteen exons. The promoters of ToTLR1 and ToTLR2 contained several putative transcription factor binding sites. Phylogenetic analysis showed that ToTLR1 and ToTLR2 were clustered into the clade of TLR1 and TLR2, respectively. Tissues distribution analysis indicated that both genes were ubiquitously expressed in all examined tissues, with higher expression levels observed in blood, head-kidney and spleen. After injection with poly inosinic:cytidylic [poly(I:C)], flagellin and lipopolysaccharides (LPS), ToTLR1 and ToTLR2 mRNAs were significantly up-regulated in the immune related tissues, indicating the possible the role of ToTLR1 and ToTLR2 in defense against pathogenic microbes. Further research should be carried out to identify ligands of fish TLR1 and TLR2 in order to understand the function of these receptors. [ABSTRACT FROM AUTHOR]

Examination of the genetic basis of the timing of the return migration of Atlantic salmon (Salmo salar) to fresh water from the sea, a trait of economic and conservation interest, was carried out using a genome-wide association study. We examined genotype data of 52 731 single nucleotide polymorphic (SNP) markers from 73 early and 49 late running two-sea-winter salmon from five rivers in eastern Scotland. A single region of the Atlantic salmon chromosome Ssa09 was identified, containing nine SNP markers significantly associated with run timing, a region previously linked to variation in sea age at maturity. Validation of the markers in a group of 233 one- and two-sea-winter fish, including adults from a novel river, again showed significant associations between the trait and the Ssa09 region, explaining ∼24% of the trait variance. The SNP loci identified provide the ability to examine trait variation in populations of Atlantic salmon and so help facilitate conservation management of the differing run timing phenotypes. [ABSTRACT FROM AUTHOR]

Summary: Minisatellites, a class of variable number tandem repeats (VNTRs), are abundant throughout the control region in animal mitochondrial DNA (mtDNA) but rare in other regions of animal mtDNA. Here, we reported a novel minisatellite in fish mitochondrial genomes. We first determined the complete mitochondrial genomes of two schizothoracine fishes (Herzensteinia microcephalus and Schizopygopsis pylzovi) and found a type of minisatellites in a novel region between the tRNA‐Thr and tRNA‐Pro genes in their mtDNA. To explore the origin and evolution of the minisatellites in different schizothoracine and closely related fishes, we analyzed the available 80 fish mitogenomes which represent five closely related tribes of cyprinine fishes. The results from the phylogenetic analyses show that the schizothoracine fishes sensu stricto is not a monophyletic group and is divided into two clades (Schizothoracini and Schizopygopsini); and the minisatellite is only present in Schizopygopsini distributed in the region between the two tRNA genes (tRNA‐Thr and tRNA‐Pro) of the mtDNA. This is the first record of a minisatellite in a non‐control region of fish mitogenome. [ABSTRACT FROM AUTHOR]

Abstract: Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next‐generation sequencing, in conjunction with novel bioinformatic tools, allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here, we scanned the published Atlantic salmon genome to identify 706 microsatellite loci, from which we developed a final panel of 101 microsatellites distributed across the genome (average 3.4 loci per chromosome). Using samples from 35 Atlantic salmon populations (n = 1,485 individuals) from coastal Labrador, Canada, a region characterized by low levels of differentiation in this species, this panel identified 844 alleles (average of 8.4 alleles per locus). Simulation‐based evaluations of assignment and mixture identification accuracy revealed unprecedented resolution, clearly identifying 26 rivers or groups of rivers spanning 500 km of coastline. This baseline was used to examine the stock composition of 696 individuals harvested in the Labrador Atlantic salmon fishery and revealed that coastal fisheries largely targeted regional groups (<300 km). This work suggests that the development and application of large sequenced microsatellite panels presents great potential for stock resolution in Atlantic salmon and more broadly in other exploited anadromous and marine species. [ABSTRACT FROM AUTHOR]

We sequenced the complete mitochondrial genomes of three pairs of congeneric peripheral fishes distributed on either side of the Isthmus of Panama in order to test their status as geminate species pairs. Our phylogenetic analysis did not support a sister relationship between Gobiomorus dormitor and G. maculatus and therefore they cannot be considered geminates. The average genetic distance of protein-coding genes between Sicydium altum and S. salvini was more than two times larger than between Atlantic and Pacific Awaous banana, suggesting different timings for their divergence across the Isthmus of Panama. [ABSTRACT FROM AUTHOR]

Background: Salinity is an important abiotic stress that influences the physiological and metabolic activity, reproduction, growth and development of marine fish. It has been suggested that half-smooth tongue sole (Cynoglossus semilaevis), a euryhaline fish species, uses a large amount of energy to maintain osmotic pressure balance when exposed to fluctuations in salinity. To delineate the molecular response of C. semilaevis to different levels of salinity, we performed RNA-seq analysis of the liver to identify the genes and molecular and biological processes involved in responding to salinity changes. Results: The present study yielded 330.4 million clean reads, of which 83.9% were successfully mapped to the reference genome of C. semilaevis. One hundred twenty-eight differentially expressed genes (DEGs), including 43 up-regulated genes and 85 down-regulated genes, were identified. These DEGs were highly represented in metabolic pathways, steroid biosynthesis, terpenoid backbone biosynthesis, butanoate metabolism, glycerolipid metabolism and the 2-oxocarboxylic acid metabolism pathway. In addition, genes involved in metabolism, osmoregulation and ion transport, signal transduction, immune response and stress response, and cytoskeleton remodeling were affected during acclimation to low salinity. Genes acat2, fdps, hmgcr, hmgcs1, mvk, pmvk, ebp, lss, dhcr7, and dhcr24 were up-regulated and abat, ddc, acy1 were down-regulated in metabolic pathways. Genes aqp10 and slc6a6 were down-regulated in osmoregulation and ion transport. Genes abat, fdps, hmgcs1, mvk, pmvk and dhcr7 were first reported to be associated with salinity adaptation in teleosts. Conclusions: Our results revealed that metabolic pathways, especially lipid metabolism were important for salinity adaptation. The candidate genes identified from this study provide a basis for further studies to investigate the molecular mechanism of salinity adaptation and transcriptional plasticity in marine fish. [ABSTRACT FROM AUTHOR]

A single Atoh1 basic-helix-loop-helix transcription factor specifies multiple neuron types in the mammalian cerebellum and anterior hindbrain. The zebrafish genome encodes three paralagous atoh1 genes whose functions in cerebellum and anterior hindbrain development we explore here. With use of a transgenic reporter, we report that zebrafish atoh1c- expressing cells are organized in two distinct domains that are separated both by space and developmental time. An early isthmic expression domain gives rise to an extracerebellar population in rhombomere 1 and an upper rhombic lip domain gives rise to granule cell progenitors that migrate to populate all four granule cell territories of the fish cerebellum. Using genetic mutants we find that of the three zebrafish atoh1 paralogs, atoh1c and atoh1a are required for the full complement of granule neurons. Surprisingly, the two genes are expressed in non-overlapping granule cell progenitor populations, indicating that fish use duplicate atoh1 genes to generate granule cell diversity that is not detected in mammals. Finally, live imaging of granule cell migration in wildtype and atoh1c mutant embryos reveals that while atoh1c is not required for granule cell specification per se, it is required for granule cells to delaminate and migrate away from the rhombic lip. [ABSTRACT FROM AUTHOR]

Channel catfish (Ictalurus punctatus) is a highly adaptive species and has been used as a research model for comparative immunology, physiology, and toxicology among ectothermic vertebrates. It is also economically important for aquaculture. As such, its reference genome was generated and annotated with protein coding genes. However, the repetitive elements in the catfish genome are less well understood. In this study, over 417.8 Megabase (MB) of repetitive elements were identified and characterized in the channel catfish genome. Among them, the DNA/TcMar-Tc1 transposons are the most abundant type, making up ~20% of the total repetitive elements, followed by the microsatellites (14%). The prevalence of repetitive elements, especially the mobile elements, may have provided a driving force for the evolution of the catfish genome. A number of catfish-specific repetitive elements were identified including the previously reported Xba elements whose divergence rate was relatively low, slower than that in untranslated regions of genes but faster than the protein coding sequences, suggesting its evolutionary restrictions. [ABSTRACT FROM AUTHOR]

Shrimp hemocyte iridescent virus (SHIV) is a recently reported shrimp virus, which threats the cultured white-leg shrimp Litopenaeus vannamei and can cause huge economic loss in shrimp farming industry in China. A quantitative real time polymerase chain reactio (qPCR) assay was developed using a TaqMan probe to detect and quantify SHIV. A pair of qPCR primers, which amplify a 188 bp DNA fragment, and a TaqMan probe were selected from ATPase gene (ORF114R) of the SHIV genome. The primers and TaqMan probe used in this assay were shown to be specific for SHIV and did not react with White spot syndrome virus (WSSV), Infectious hypodermal and hematopoietic necrosis virus (IHHNV), Hepatopancreatic parvovirus (HPV), Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease (VP AHPND ), and Enterocytozoon hepatopenaei (EHP), or healthy shrimp DNA. The detection limit of the qPCR method was as low as 4 copies per reaction. The diagnostic sensitivity and the diagnostic specificity of the qPCR compared with nested PCR were 95.3% and 99.2%, respectively. The resulting standard curves showed high correlation coefficient values (R 2  = 0.998) in the range of 4 × 10 9 to 4 × 10 0 DNA copies/reaction. Test of farm samples showed that SHIV was detected in L. vannamei , Fenneropenaeus chinensis and Macrobrachium rosenbergii contained SHIV ranged from 1.21E+02 to 7.95E+07 copies (μg DNA) −1 . Quantitative detection of different tissues in artificial infected shrimp showed that haemolymph contained the highest SHIV load and muscle contained lowest SHIV load. [ABSTRACT FROM AUTHOR]

Background: Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod (Gadus morhua) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss of the major histocompatibility complex (MHC) II genes 100 million years ago. An improved version of the Atlantic cod genome assembly shows an extreme density of tandem repeats compared to other vertebrate genome assemblies. Highly contiguous assemblies are therefore needed to further investigate the unusual immune system of the Gadiformes, and whether the high density of tandem repeats found in Atlantic cod is a shared trait in this group. Results: Here, we have sequenced and assembled the genome of haddock (Melanogrammus aeglefinus) – a relative of Atlantic cod – using a combination of PacBio and Illumina reads. Comparative analyses reveal that the haddock genome contains an even higher density of tandem repeats outside and within protein coding sequences than Atlantic cod. Further, both species show an elevated number of tandem repeats in genes mainly involved in signal transduction compared to other teleosts. A characterization of the immune gene repertoire demonstrates a substantial expansion of MCHI in Atlantic cod compared to haddock. In contrast, the Toll-like receptors show a similar pattern of gene losses and expansions. For the NOD-like receptors (NLRs), another gene family associated with the innate immune system, we find a large expansion common to all teleosts, with possible lineage-specific expansions in zebrafish, stickleback and the codfishes. Conclusions: The generation of a highly contiguous genome assembly of haddock revealed that the high density of short tandem repeats as well as expanded immune gene families is not unique to Atlantic cod – but possibly a feature common to all, or most, codfishes. A shared expansion of NLR genes in teleosts suggests that the NLRs have a more substantial role in the innate immunity of teleosts than other vertebrates. Moreover, we find that high copy number genes combined with variable genome assembly qualities may impede complete characterization of these genes, i.e. the number of NLRs in different teleost species might be underestimates. [ABSTRACT FROM AUTHOR]

Massive parallel sequencing allows scientists to gather DNA sequences composed of millions of base pairs that can be combined into large datasets and analyzed to infer organismal relationships at a genome-wide scale in non-model organisms. Although the use of these large datasets is becoming more widespread, little to no work has been done in estimating phylogenetic relationships using UCEs in deep-sea fishes. Among deep-sea animals, the 257 species of lanternfishes (Myctophiformes) are among the most important open-ocean lineages, representing half of all mesopelagic vertebrate biomass. With this relative abundance, they are key members of the midwater food web where they feed on smaller invertebrates and fishes in addition to being a primary prey item for other open-ocean animals. Understanding the evolution and relationships of midwater organisms generally, and this dominant group of fishes in particular, is necessary for understanding and preserving the underexplored deep-sea ecosystem. Despite substantial congruence in the evolutionary relationships among deep-sea lanternfishes at higher classification levels in previous studies, the relationships among tribes, genera, and species within Myctophidae often conflict across phylogenetic studies or lack resolution and support. Herein we provide the first genome-scale phylogenetic analysis of lanternfishes, and we integrate these data from across the nuclear genome with additional protein-coding gene sequences and morphological data to further test evolutionary relationships among lanternfishes. Our phylogenetic hypotheses of relationships among lanternfishes are entirely congruent across a diversity of analyses that vary in methods, taxonomic sampling, and data analyzed. Within the Myctophiformes, the Neoscopelidae is inferred to be monophyletic and sister to a monophyletic Myctophidae. The current classification of lanternfishes is incongruent with our phylogenetic tree, so we recommend revisions that retain much of the traditional tribal structure and recognize five subfamilies instead of the traditional two subfamilies. The revised monophyletic taxonomy of myctophids includes the elevation of three former lampanyctine tribes to subfamilies. A restricted Lampanyctinae was recovered sister to Notolychninae. These two clades together were recovered as the sister group to the Gymnoscopelinae. Combined, these three subfamilies were recovered as the sister group to a clade composed of a monophyletic Diaphinae sister to the traditional Myctophinae. Our results corroborate recent multilocus molecular studies that infer a polyphyletic Myctophum in Myctophinae, and a para- or polyphyletic Lampanyctus and Nannobrachium within Lampanyctinae . We resurrect Dasyscopelus and Ctenoscopelus for the independent clades traditionally classified as species of Myctophum , and we place Nannobrachium into the synonymy of Lampanyctus. [ABSTRACT FROM AUTHOR]

Background: As one of the most popular and valuable commercial marine fishes in China and East Asian countries, the Chinese black porgy (Acanthopagrus schlegelii), also known as the blackhead seabream, has some attractive characteristics such as fast growth rate, good meat quality, resistance to diseases, and excellent adaptability to various environments. Furthermore, the black porgy is a good model for investigating sex changes in fish due to its protandrous hermaphroditism. Here, we obtained a high-quality genome assembly of this interesting teleost species and performed a genomic survey on potential genes associated with the sex-change phenomenon. Findings: We generated 175.4 gigabases (Gb) of clean sequence reads using a whole-genome shotgun sequencing strategy. The final genome assembly is approximately 688.1 megabases (Mb), accounting for 93% of the estimated genome size (739.6 Mb). The achieved scaffold N50 is 7.6 Mb, reaching a relatively high level among sequenced fish species. We identified 19 465 protein-coding genes, which had an average transcript length of 17.3 kb. By performing a comparative genomic analysis, we found 3 types of genes potentially associated with sex change, which are useful for studying the genetic basis of the protandrous hermaphroditism. Conclusions: We provide a draft genome assembly of the Chinese black porgy and discuss the potential genetic mechanisms of sex change. These data are also an important resource for studying the biology and for facilitating breeding of this economically important fish. [ABSTRACT FROM AUTHOR]

The Erythrinidae family (Teleostei: Characiformes) is a small Neotropical fish group with a wide distribution throughout South America, where Hoplias malabaricus corresponds to the most widespread and cytogenetically studied taxon. This species possesses significant genetic variation, as well as huge karyotype diversity among populations, as reflected by its seven major karyotype forms (i.e., karyomorphs A-G) identified up to now. Although morphological differences in their bodies are not outstanding, H. malabaricus karyomorphs are easily identified by differences in 2n, morphology and size of chromosomes, as well as by distinct evolutionary steps of sex chromosomes development. Here, we performed comparative genomic hybridization (CGH) to analyse both the intra- and inter-genomic status in terms of repetitive DNA divergence among all but one (E) H. malabaricus karyomorphs. Our results indicated that they have close relationships, but with evolutionary divergences among their genomes, yielding a range of non-overlapping karyomorph-specific signals. Besides, male-specific regions were uncovered on the sex chromosomes, confirming their differential evolutionary trajectories. In conclusion, the hypothesis that H. malabaricus karyomorphs are result of speciation events was strengthened. [ABSTRACT FROM AUTHOR]

Accumulating evidence suggests that peroxiredoxins (Prxs) eliminate excessive cellular H 2 O 2 and are important factors in redox signaling pathways. In this study, we cloned the full-length cDNAs and genomic sequences of Prx3 and Prx4 from common carp. The common carp Prx3 and Prx4 open reading frames were 753 base pairs (bp) and 783 bp in length, respectively, and contained seven exons and six introns. Multiple sequence alignment and phylogenetic analyses revealed that the common carp Prx1–4 proteins share high identities and similar characteristics with other known animal Prxs. Prx3 and Prx4 mRNA were constitutively expressed in all tissues, and the highest Prx3 and Prx4 transcript abundances occurred in head kidney. Although the highest Prx4 protein and mRNA expression were also observed in head kidney, many differences were detected between Prx4 mRNA and protein expression levels in other tissues. Prx3 expression increased significantly in the head kidney 12 h after an Aeromonas hydrophila challenge. The A. hydrophila challenge upregulated Prx3 mRNA expression in liver and spleen, increased Prx4 mRNA expression levels in liver and spleen excluding at 36 h in spleen, but decreased Prx4 mRNA expression level in the head kidney. The mature Prx4 peptide was recombinantly expressed and purified using Dextrin Beads 6FF and it exhibited thioredoxin (Trx)-dependent peroxidase activity. These data suggest that Prx3 and Prx4 are constitutive and inducible proteins that might play important roles in innate immune function. The Trx-dependent peroxidase activity analysis of recombinant Prx4 further verified the important role of Prxs in the redox system of fish. [ABSTRACT FROM AUTHOR]

Abstract: Butterflyfish are among the most iconic of the coral reef fishes and represent a model system to study general questions of biogeography, evolution and population genetics. We assembled and annotated the genome sequence of the blacktail butterflyfish (Chaetodon austriacus), an Arabian region endemic species that is reliant on coral reefs for food and shelter. Using available bony fish (superclass Osteichthyes) genomes as a reference, a total of 28 926 high‐quality protein‐coding genes were predicted from 13 967 assembled scaffolds. The quality and completeness of the draft genome of C. austriacus suggest that it has the potential to serve as a resource for studies on the co‐evolution of reef fish adaptations to the unique Red Sea environment, as well as a comparison of gene sequences between closely related congeneric species of butterflyfish distributed more broadly across the tropical Indo‐Pacific. [ABSTRACT FROM AUTHOR]

In the last 15 years, considerable attempts have been undertaken to develop the obligately parthenogenetic marbled crayfish Procambarus virginalis as a new model in biology. Its main advantage is the production of large numbers of offspring that are genetically identical to the mother, making this crustacean particularly suitable for research in epigenetics. Now, a draft genome, transcriptome and genome-wide methylome are available opening new windows for research. In this article, I summarize the biological advantages and genomic and epigenetic features of marbled crayfish and, based on first promising data, discuss what this new model could contribute to answering of ''big'' biological questions. Genome mining is expected to reveal new insights into the genetic specificities of decapod crustaceans, the genetic basis of arthropod reproduction, moulting and immunity, and more general topics such as the genetic underpinning of adaptation to fresh water, omnivory, biomineralization, sexual system change, behavioural variation, clonal genome evolution, and resistance to cancer. Epigenetic investigations with the marbled crayfish can help clarifying the role of epigenetic mechanisms in gene regulation, tissue specification, adult stem cell regulation, cell ageing, organ regeneration and disease susceptibility. Marbled crayfish is further suitable to elucidate the relationship between genetic and epigenetic variation, the transgenerational inheritance of epigenetic signatures and the contribution of epigenetic phenotype variation to the establishment of social hierarchies, environmental adaptation and speciation. These issues can be tackled by experiments with highly standardized laboratory lineages, comparison of differently adapted wild populations and the generation of genetically and epigenetically edited strains. [ABSTRACT FROM AUTHOR]

The gonadosomatic index (GSI) is an economically important trait in the large yellow croaker ( Larimichthys crocea ), a mariculture fish species with high commercial value in Southeast China. However, progress in the genetic research on this species is relatively lacking. To identify the relevant genes and chromosome regions associated with the GSI, we performed a genome-wide association study (GWAS) on a population of 500 individuals (237 males and 263 females), using single marker analysis and Bayesian methods. The genotyping-by-sequencing method was used to construct the libraries, and 29,748 SNPs were subsequently found in the genome of Larimichthys crocea . A total of six different SNPs, located on LG3, LG6, LG8, and LG16, were determined to be significantly associated with the GSI. Among them, only two SNPs were found by both GWAS methods. By integrating the results of two GWAS methods with the biological functions of the genes, six candidate genes (viz., FZD3 , DDX4 , EDC3 , CITED3 , SOX9-b, and LOC106602108 ) were revealed to be associated with the GSI in the large yellow croaker. These functional genes are involved in gonadal development or gonadogenesis, providing the basis for further study on genetic mechanisms and marker-assisted selection in this fish species. In this study, we found that the combination of single marker analysis and Bayesian methods could identify more SNP loci associated with the phenotypes. Thus, we suggest performing these two methods simultaneously in GWAS. [ABSTRACT FROM AUTHOR]

To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species. Localization of repeats on chromosomes of hundreds of fish species and populations originating from diversified environments have revealed the biological importance of this genomic fraction. Ribosomal genes (rDNA) belong to the most informative repeats and in fish, they are subject to a more relaxed regulation than in higher vertebrates. This can result in formation of a literal 'rDNAome' consisting of more than 20,000 copies with their high proportion employed in extra-coding functions. Because rDNA has high rates of transcription and recombination, it contributes to genome diversification and can form reproductive barrier. Our overall knowledge of fish cytogenomics grows rapidly by a continuously increasing number of fish genomes sequenced and by use of novel sequencing methods improving genome assembly. The recently revealed exceptional compositional heterogeneity in an ancient fish lineage (gars) sheds new light on the compositional genome evolution in vertebrates generally. We highlight the power of synergy of cytogenetics and genomics in fish cytogenomics, its potential to understand the complexity of genome evolution in vertebrates, which is also linked to clinical applications and the chromosomal backgrounds of speciation. We also summarize the current knowledge on fish cytogenomics and outline its main future avenues. [ABSTRACT FROM AUTHOR]

A study with DNA microarrays was performed to investigate the effects of two diarrhetic and one azaspiracid shellfish poison, okadaic acid (OA), dinophysistoxin-1 (DTX-1) and azaspiracid-1 (AZA-1) respectively, on the whole-genome mRNA expression of undifferentiated intestinal Caco-2 cells. Previously, the most responding genes were used to develop a dedicated array tube test to screen shellfish samples on the presence of these toxins. In the present study the whole genome mRNA expression was analyzed in order to reveal modes of action and obtain hints on potential biomarkers suitable to be used in alternative bioassays. Effects on key genes in the most affected pathways and processes were confirmed by qPCR. OA and DTX-1 induced almost identical effects on mRNA expression, which strongly indicates that OA and DTX-1induce similar toxic effects. Biological interpretation of the microarray data indicates that both compounds induce hypoxia related pathways/processes, the unfolded protein response (UPR) and endoplasmic reticulum (ER) stress. The gene expression profile of AZA-1 is different and shows increased mRNA expression of genes involved in cholesterol synthesis and glycolysis, suggesting a different mode of action for this toxin. Future studies should reveal whether identified pathways provide suitable biomarkers for rapid detection of DSPs in shellfish. [ABSTRACT FROM AUTHOR]

The genus Gymnotus (Gymnotiformes) contains over 40 species of freshwater electric fishes exhibiting a wide distribution throughout Central and South America, and being particularly prevalent in the Amazon basin. Cytogenetics has been an important tool in the cytotaxonomy and elucidation of evolutionary processes in this genus, including the unraveling the variety of diploid chromosome number (2n = from 34 to 54), the high karyotype diversity among species with a shared diploid number, different sex chromosome systems, and variation in the distribution of several Repetitive DNAs and colocation and association between those sequences. Recently whole chromosome painting (WCP) has been used for tracking the chromosomal evolution of the genus, showing highly reorganized karyotypes and the conserved synteny of the NOR bearing par within the clade G. carapo. In this study, painting probes derived from the chromosomes of G. carapo (GCA, 2n = 42, 30 m/sm + 12 st/a) were hybridized to the mitotic metaphases of G. arapaima (GAR, 2n = 44, 24 m/sm + 20 st/a). Our results uncovered chromosomal rearrangements and a high number of repetitive DNA regions. From the 12 chromosome pairs of G. carapo that can be individually differentiated (GCA1-3, 6, 7, 9, 14, 16, and 18-21), six pairs (GCA 1, 9, 14, 18, 20, 21) show conserved homology with GAR, five pairs (GCA 1, 9, 14, 20, 21) are also shared with cryptic species G. carapo 2n = 40 (34 m/sm + 6 st/a) and only the NOR bearing pair (GCA 20) is shared with G. capanema (GCP 2n = 34, 20 m/sm + 14 st/a). The remaining chromosomes are reorganized in the karyotype of GAR. Despite the close phylogenetic relationships of these species, our chromosome painting studies demonstrate an extensive reorganization of their karyotypes. [ABSTRACT FROM AUTHOR]

Background: The assembly and annotation of a genome is a valuable resource for a species, with applications ranging from conservation genomics to gene discovery. Genomic resource development is especially important for species in culture, such as the California Yellowtail (Seriola dorsalis), the likely candidate for the establishment of commercial offshore aquaculture production in southern California. Genomic resource development for this species will improve the understanding of sex and other phenotypic traits, and allow for rapid increases in genetic improvement for and economic gain in culture production. Results: We describe the assembly and annotation of the S. dorsalis genome, and present resequencing data from 45 male and 45 female wild-caught S. dorsalis used to identify a sex-determining region and marker in this species. The genome assembly captured approximately 93% of the total 685 MB genome with an average coverage depth of 180×. Using the assembled genome, resequencing data from the 90 fish were aligned to place boundaries on the sex-determining region. Sex-specific markers were developed based on a female-specific, 61 nucleotide deletion identified in that region. We hypothesize that Estradiol 17-beta-dehydrogenase is the putative sex-determining gene and propose a plausible genetic mechanism for ZW sex determination in S. dorsalis involving a female-specific deletion of a transcription factor binding motif that may be targeted by Sox3. Conclusions: Understanding the mechanism of sex determination and development of assays to determine sex is critical both for management of wild fisheries and for development of efficient and sustainable aquaculture practices. In addition, this genome assembly for S. dorsalis will be a substantial resource for a variety of future research applications. [ABSTRACT FROM AUTHOR]

Transposable elements (TEs) are important for host gene regulation and genome evolution. Consensus sequences of TEs can assist investigators in accelerating studies on TE origins, amplification, functions and evolution, as well as comparative analyses and prediction of TEs in different species. In evolution, physiology, ecology and heredity research, fish are important models. However, to date, no comprehensive resource for TE consensus sequences exists for fish. Here, we collected genome-wide data and developed a novel database, FishTEDB, including 27 bony fishes, 1 cartilaginous fish, 1 lamprey and 1 lancelet. De novo, structure-based and homology-based approaches were combined to detect TEs. The database is open-source and user-friendly, and users can browse, search and download all data. FishTEDB also provides GetORF, BLAST and HMMER tools to analyze sequences. Database URL : http://www.fishtedb.org/ [ABSTRACT FROM AUTHOR]

The phenotypic, geographic, and species diversity of cichlid fishes have made them a group of great interest for studying evolutionary processes. Here we present a targeted-exon next-generation sequencing approach for investigating the evolutionary relationships of cichlid fishes (Cichlidae), with focus on the Neotropical subfamily Cichlinae using a set of 923 primarily single-copy exons designed through mining of the Nile tilapia ( Oreochromis niloticus ) genome. Sequence capture and assembly were robust, leading to a complete dataset of 415 exons for 139 species (147 terminals) that consisted of 128 Neotropical species, six African taxa, and five Indo-Malagasy cichlids. Gene and species trees were calculated using alternative partitioning schemes and reconstruction methods. In general, all methods yielded similar topologies to previously hypothesized relationships within the Cichlinae and clarified several relationships that were previously poorly supported or in conflict. Additional work will be needed to fully resolve all aspects of Cichlinae phylogeny. Overall, this approach yielded a well-resolved phylogeny of Neotropical cichlids that will be of utility for future assessments of the evolutionary and ecological processes within this diverse group of fishes. Furthermore, the general methodology employed here of exon targeting and capture should be applicable to any group of organisms with the availability of a reference genome. [ABSTRACT FROM AUTHOR]

Efforts to taxonomically delineate species are often confounded with conflicting information and subjective interpretation. Advances in genomic methods have resulted in a new approach to taxonomic identification that stands to greatly reduce much of this conflict. This approach is ideal for species complexes, where divergence times are recent (evolutionarily) and lineages less well defined. The California Roach/Hitch fish species complex is an excellent example, experiencing a convoluted geologic history, diverse habitats, conflicting species designations and potential admixture between species. Here we use this fish complex to illustrate how genomics can be used to better clarify and assign taxonomic categories. We performed restriction-site associated DNA (RAD) sequencing on 255 Roach and Hitch samples collected throughout California to discover and genotype thousands of single nucleotide polymorphism (SNPs). Data were then used in hierarchical principal component, admixture, and FST analyses to provide results that consistently resolved a number of ambiguities and provided novel insights across a range of taxonomic levels. At the highest level, our results show that the CA Roach/Hitch complex should be considered five species split into two genera (4 + 1) as opposed to two species from distinct genera (1 +1). Subsequent levels revealed multiple subspecies and distinct population segments within identified species. At the lowest level, our results indicate Roach from a large coastal river are not native but instead introduced from a nearby river. Overall, this study provides a clear demonstration of the power of genomic methods for informing taxonomy and serves as a model for future studies wishing to decipher difficult species questions. By allowing for systematic identification across multiple scales, taxonomic structure can then be tied to historical and contemporary ecological, geographic or anthropogenic factors. [ABSTRACT FROM AUTHOR]

The Largemouth BassMicropterus salmoidesincludes two recognized subspecies, the Northern Largemouth Bass (NLMB;M. salmoides salmoides) and the Florida Largemouth Bass (FLMB;M. salmoides floridanus), which can hybridize to produce introgressed Largemouth Bass (ILMB; NLMB × FLMB). Largemouth Bass were introduced into Puerto Rico by using source populations from unknown origins (1915), a natural intergrade zone (1946 and 1947; ILMB), and peninsular Florida (1957; FLMB). All subsequent supplemental stocking efforts used broodstock collected from reservoirs in Puerto Rico with an effort to preferentially propagate non-introgressed FLMB. Here, we document contemporary FLMB-specific alleles and genotypes, changes in allele frequencies over the last decade, and differences in size structure between genotypes of the FLMB and its hybrids (ILMB) in Puerto Rico. Among 12 island reservoirs, FLMB alleles were prevalent at rates similar to estimates from a decade earlier, and the proportion of FLMB alleles (0.77–0.85) was less than that of the hatchery broodstock. No NLMB genotypes were resolved, and the proportion of FLMB genotypes ranged from 0.03 to 0.64. Length frequency distributions differed between the FLMB and ILMB types (KolmogorovD-statistic = 0.172,P= 0.026), with FLMB observed more frequently in larger size-classes. Given their greater sizes and potentially greater longevity, we suggest that FLMB should be used exclusively for future stocking efforts in Puerto Rico. Received January 25, 2017; accepted July 3, 2017 Published online October 11, 2017 [ABSTRACT FROM PUBLISHER]