Gills de novo assembly reveals oxidative stress, unfolded protein, and immune response on red cusk-eel (Genypterus chilensis) under thermal stress

The heat waves on the South Pacific coast could lead to thermal stress in native fish. The red cusk-eel (Genypterus chilensis) is relevant for Chilean artisanal fisheries and aquaculture diversification. This study examined the effect of high-temperature stress in the gills of G. chilensis in control (14 °C) and high-temperature stress (19 °C) conditions. High-temperature stress induces a significant increase in gills cortisol levels. Additionally, oxidative damage was observed in gills (protein carbonylation and lipoperoxidation). RNA-seq data was used to build the first transcriptome assembly of gills in this species (23,656 annotated transcripts). A total of 1138 down-regulated and 1531 up-regulated transcripts were observed in response to high-temperature stress in gills. The enrichment analysis showed immune response and replication enriched processes (on down-regulated transcripts), and processes related to the folding of proteins, endoplasmic reticulum, and transporter activity (on up-regulated transcripts). The present study showed how gills could be affected by high-temperature stress.

Planococcus notacanthi sp. nov., isolated from the skin of a deep-sea snub-nosed spiny eel

A novel bacterial strain, APC 4016T, was previously isolated from the skin of a snub-nosed spiny eel, Notacanthus chemnitzii, from a depth of 1000 m in the northern Atlantic Ocean. Cells were aerobic, cocci, motile, Gram-positive to Gram-variable staining, and gave rise to orange-pigmented colonies. Growth occurred at 4-40 °C (optimum, 25-28 °C), pH 5.5-12 (optimum, pH 7-7.5), and 0-12 % (w/v) NaCl (optimum, 1 %). 16S rRNA gene phylogenetic analysis confirmed that strain APC 4016T belonged to the genus Planococcus and was most closely related to Planococcus okeanokoites IFO 12536T (98.98 % 16S similarity). However, digital DNA-DNA hybridization and average nucleotide identity values between these two strains were low, at 20.1 and 83.8 %, respectively. Major (>10 %) cellular fatty acids of strain APC 4016T were iso-C14 : 0, anteiso-C15 : 0 and C16 : 1-ω-Alc. The predominant respiratory quinones were menaquinones 5, 6, 7 and 8. The major cellular polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine, and three unknown lipids were also present. The draft genome sequence is 3.6 Mb with a G+C content of 45.25 mol%. This strain was previously shown to have antimicrobial activity and to encode bacteriocin and secondary metabolite biosynthetic gene clusters. Based on the phylogenetic analysis and its distinct phenotypic characteristics, strain APC 4016T is deemed to represent a novel species of the genus Planococcus, and for which the name Planococcus notacanthi sp. nov. is proposed. The type strain of this species is APC 4016T (=DSM 115753T=NCIMB 15463T).

A new snake eel species of the genus Ophichthus (Anguilliformes: Ophichthidae) from the southeast coast of India, Bay of Bengal, with the taxonomic account of Ophichthus chilkensis

A new species of the ophichthid eel of the family Ophichthidae is described based on five specimens collected from the Mudasalodai fish landing center, off Cuddalore coast, southeast coast of India, Bay of Bengal. Ophichthus naevius sp. nov. is distinguished from its congeners by having a unique color pattern: dorsal body with numerous dense dark spots or patches, ventral body pale yellowish green, dorsal-fin origin just before pectoral-fin tip, vertebral formula: 12-14/52-53/134-138, and teeth on jaw uniserial and pointed. The study also reports the range extension and molecular evidence of Ophichthus chilkensis from South India. Molecular analyses were performed for both species, and their phylogenetic relationship suggests that the new species exhibits 10.2% genetic divergence with its congener Ophichthus sangjuensis, followed by Ophichthus brevicaudatus (10.4%), and Ophichthus sp. 1 (11.8%) also forms the closest clade in both Bayesian inference and maximum likelihood (ML) tree. Similarly, according to the topology of the ML tree, the species O. chilkensis forms a clade with Ophichthus sp. 5, Ophichthus remiger, Ophichthus frontalis, Ophichthus sp. 6, and Ophichthus rex, suggesting that it would be the genetically closest congener.

Chromosome-level genome assembly and annotation of eel goby (Odontamblyopus rebecca)

The eel gobies fascinate researchers with many important features, including its unique body structure, benthic lifestyle, and degenerated eyes. However, genome assembly and exploration of the unique genomic composition of the eel gobies are still in their infancy. This has severely limited research progress on gobies. In this study, multi-platform sequencing data were generated and used to assemble and annotate the genome of O. rebecca at the chromosome-level. The assembled genome size of O. rebecca is 918.57 Mbp, which is similar to the estimated genome size (903.03 Mbp) using 17-mer. The scaffold N50 is 41.67 Mbp, and 23 chromosomes were assembled using Hi-C technology with a mounting rate of 99.96%. Genome annotation indicates that 53.29% of the genome is repetitive sequences, and 22,999 protein-coding genes are predicted, of which 21,855 have functional annotations. The chromosome-level genome of O. rebecca will not only provide important genomic resources for comparative genomic studies of gobies, but also expand our knowledge of the genetic origin of their unique features fascinating researchers for decades.

Neuropeptide B (NPB) and NPB receptor 2b (NPBWR2b) in the ricefield eel Monopterus albus: expression and potential involvement in the regulation of gonadotropins

The neuropeptide B/W signaling system is composed of neuropeptide B (NPB), neuropeptide W (NPW), and two cognate receptors, NPBWR1 and NPBWR2, which are involved in diverse physiological processes, including the central regulation of neuroendocrine axes in vertebrates. The components of this signaling system are not well conserved during vertebrate evolution, implicating its functional diversity. The present study characterized the ricefield eel neuropeptide B/W system, generated a specific antiserum against the neuropeptide B/W receptor, and examined the potential roles of the system in the regulation of adenohypophysial functions. The ricefield eel genome contains npba, npbb, and npbwr2b but lacks the npw, npbwr1, and npbwr2a genes. The loss of npw and npbwr1 probably occurred at the base of ray-finned fish radiation and that of npbwr2a species specifically in ray-finned fish. Npba and npbb genes are produced through whole-genome duplication (WGD) in ray-finned fish. The ricefield eel npba was expressed in the brain and some peripheral tissues, while npbb was predominantly expressed in the brain. The ricefield eel npbwr2b was also expressed in the brain and in some peripheral tissues, such as the pituitary, gonad, heart, and eye. Immunoreactive Npbwr2b was shown to be localized to Lh and Fsh cells but not to Gh or Prl cells in the pituitary of ricefield eels. Npba upregulated the expression of fshb and cga but not lhb mRNA in pituitary fragments of ricefield eels cultured in vitro. The results of the present study suggest that the NPB system of ricefield eels may be involved in the neuroendocrine regulation of reproduction.

FoxH1 Represses the Promoter Activity of cyp19a1a in the Ricefield Eel (Monopterus albus)

Forkhead box H1 (FoxH1) is a sexually dimorphic gene in Oreochromis niloticus, Oplegnathus fasciatus, and Acanthopagrus latus, indicating that it is essential for gonadal development. In the present study, the molecular characteristics and potential function of FoxH1 and the activation of the cyp19a1a promoter in vitro were evaluated in Monopterus albus. The levels of foxh1 in the ovaries were three times higher than those in the testes and were regulated by gonadotropins (Follicle-Stimulating Hormone and Human Chorionic Gonadotropin). FoxH1 colocalized with Cyp19a1a in the oocytes and granulosa cells of middle and late vitellogenic follicles. In addition, three FoxH1 binding sites were identified in the proximal promoter of cyp19a1a, namely, FH1 (-871/-860), FH2 (-535/-524), and FH3 (-218/-207). FoxH1 overexpression significantly attenuated the activity of the cyp19a1a promoter in CHO cells, and FH1/2 mutation increased promoter activity. Taken together, these results suggest that FoxH1 may act as an important regulator in the ovarian development of M. albus by repressing cyp19a1a promoter activity, which provides a foundation for the study of FoxH1 function in bony fish reproductive processes.

Establishment of cell-lines stably expressing recombinant Japanese eel follicle-stimulating hormone and luteinizing hormone using CHO-DG44 cells: fully induced ovarian development at different modes

The gonadotropins (Gth), follicle-stimulating hormone (Fsh) and luteinizing hormone (Lh), play central roles in gametogenesis in vertebrates. However, available information on their differential actions in teleost, especially in vivo, is insufficient. In this study, we established stable CHO-DG44 cell lines expressing long-lasting recombinant Japanese eel Fsh and Lh with extra O-glycosylation sites (Fsh-hCTP and Lh-hCTP), which were produced in abundance. Immature female eels received weekly intraperitoneal injections of Gths. Fsh-hCTP induced the entire ovarian development by 8 weeks from the beginning of injection; thus, the ovaries of most fish were at the migratory nucleus stage while the same stage was observed in eels after 4 weeks in the Lh-hCTP-treated group. In contrast, all pretreated and saline-injected eels were in the pre-vitellogenic stage. Gonadosomatic indices in the Fsh-hCTP-treated group were significantly higher than those in the Lh-hCTP group at the migratory nucleus stage because of the significantly higher frequency of advanced ovarian follicles. Ovarian mRNA levels of genes related to E2 production (cyp11a1, cyp17a1, cyp19a1, hsd3b, fshr, and lhr) were measured using real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR). All genes were induced by both Fsh-hCTP and Lh-hCTP, with a peak at either the mid- or late vitellogenic stages. Transcript abundance of cyp19a1 and fshr in the Lh-hCTP group were significantly higher than those in the Fsh-hCTP group, whereas no difference in the expression of other genes was observed between the groups. Fluctuations in serum levels of sex steroid hormones (estradiol-17β, 11-ketotestosterone, and testosterone) in female eels were comparable in the Fsh-hCTP and Lh-hCTP groups, thus increasing toward the maturational phase. Furthermore, the fecundity of the eels induced to mature by Fsh-hCTP was significantly higher than that induced by Lh-hCTP. These findings indicate that Fsh and Lh can induce ovarian development in distinctively different modes in the Japanese eel.

A chromosome-level reference genome assembly of the Reeve's moray eel (Gymnothorax reevesii)

Due to potentially hostile behaviors and elusive habitats, moray eels (Muraenidae) as one group of apex predators in coral reefs all across the globe have not been well investigated. Here, we constructed a chromosome-level genome assembly for the representative Reeve's moray eel (Gymnothorax reevesii). This haplotype genome assembly is 2.17 Gb in length, and 97.87% of the sequences are anchored into 21 chromosomes. It contains 56.34% repetitive sequences and 23,812 protein-coding genes, of which 96.77% are functionally annotated. This sequenced marine species in Anguilliformes makes a good complement to the genetic resource of eel genomes. It not only provides a genetic resource for in-depth studies of the Reeve's moray eel, but also enables deep-going genomic comparisons among various eels.

Characterization and expression analysis of the interferon regulatory factor (IRF) gene family in zig-zag eel (Mastacembelus armatus) against Aeromonas veronii infection

Interferon regulatory factors (IRFs) play an important role in innate and adaptive immune system. However, in teleosts, the data on IRFs is still scarce. Here, for the first time, we identified 11 members of IRFs from the zig-zag eel Mastacembelus armatus (MarIRF1-10). The deduced protein sequences are highly conserved among different fish species especially in DBD and IAD domain. Phylogenetic analysis indicated that MarIRFs preferentially grouped with fish species in Synbranchiformes or Perciformes. Expression analysis showed that MarIRFs were expressed in all nine tissues including spleen, gill, muscle and intestine. After infected by Aeromonas veronii, expression of MarIRF2, MaIRF4b and MaIRF5 were significantly upregulated in spleen, MarIRF1, MarIRF2 were significantly upregulated in kidney, but in liver, nearly all MarIRFs were downregulated. Taken together, this study first reported molecular characterization and expression patterns of 11 IRFs in the zig-zag eel. All these results will contribute a lot to better understanding the antibacterial mechanism of IRFs in teleosts.

Genome structures resolve the early diversification of teleost fishes

Accurate species phylogenies are a prerequisite for all evolutionary research. Teleosts are the largest and most diversified group of extant vertebrates, but relationships among their three oldest extant lineages remain unresolved. On the basis of seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (arapaima, elephantnose fish) in a monophyletic sister group to all other teleosts, i.e., the Clupeocephala lineage (zebrafish, medaka). This finding resolves more than 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies.

Circular RNA expression profiles and CircSnd1-miR-135b/c-foxl2 axis analysis in gonadal differentiation of protogynous hermaphroditic ricefield eel Monopterus albus

BACKGROUND

The expression and biological functions of circular RNAs (circRNAs) in reproductive organs have been extensively reported. However, it is still unclear whether circRNAs are involved in sex change. To this end, RNA sequencing (RNA-seq) was performed in gonads at 5 sexual stages (ovary, early intersexual stage gonad, middle intersexual stage gonad, late intersexual stage gonad, and testis) of ricefield eel, and the expression profiles and potential functions of circRNAs were studied.

RESULTS

Seven hundred twenty-one circRNAs were identified, and the expression levels of 10 circRNAs were verified by quantitative real-time PCR (qRT-PCR) and found to be in accordance with the RNA-seq data, suggesting that the RNA-seq data were reliable. Then, the sequence length, category, sequence composition and the relationship between the parent genes of the circRNAs were explored. A total of 147 circRNAs were differentially expressed in the sex change process, and GO and KEGG analyses revealed that some differentially expressed (such as novel_circ_0000659, novel_circ_0004005 and novel_circ_0005865) circRNAs were closely involved in sex change. Furthermore, expression pattern analysis demonstrated that both circSnd1 and foxl2 were downregulated in the process of sex change, which was contrary to mal-miR-135b. Finally, dual-luciferase reporter assay and RNA immunoprecipitation showed that circSnd1 and foxl2 can combine with mal-miR-135b and mal-miR-135c. These data revealed that circSnd1 regulates foxl2 expression in the sex change of ricefield eel by acting as a sponge of mal-miR-135b/c.

CONCLUSION

Our results are the first to demonstrate that circRNAs have potential effects on sex change in ricefield eel; and circSnd1 could regulate foxl2 expression in the sex change of ricefield eel by acting as a sponge of mal-miR-135b/c. These data will be useful for enhancing our understanding of sequential hermaphroditism and sex change in ricefield eel or other teleosts.

Rag1 and Rag2 Gene Expressions Identify Lymphopoietic Tissues in Larvae of Rice-Field Eel (Monopterus albus)

In immature lymphocytes, recombination activating genes 1 and 2 are necessary for antigen receptor V (D) J recombination, representing immature lymphocyte biomarkers. Herein, we cloned and sequenced rice-field eel rag1 and rag2 genes. Their expressions in the thymus, liver, and kidney were significant from 0 days post hatching (dph) to 45 dph, peaking at 45 dph in these three tissues. In situ hybridization detected high rag1 and rag2 expressions in the liver, kidney, and thymus of rice-field eel from 2 to 45 dph, suggesting that multiple tissues of rice-field eel contain lymphocyte lineage cells and undergo lymphopoiesis. Tissue morphology was used to observe lymphopoiesis development in these three tissues. The thymus primordium began to develop at 2 dph, while the kidney and liver have generated. Our findings verified that the thymus is the primary lymphopoietic tissue and suggested that, in rice-field eel, lymphocyte differentiation also occurs in the liver and kidney.

Complete Depletion of Primordial Germ Cells Results in Masculinization of Monopterus albus, a Protogynous Hermaphroditic Fish

Primordial germ cells (PGCs) play an important role in sexual fate determination and gonadal development in gonochoristic fish, such as zebrafish and medaka. However, little is known about the function of PGCs in hermaphroditic fish. Rice field eel (Monopterus albus), a protogynous hermaphroditic fish, is an economically valuable aquaculture species. We eliminated PGCs in rice field eels during embryogenesis via morpholino-mediated knockdown dead end (dnd). The PGCs-depleted gonads developed into testis-like structures with Sertoli cells and Leydig cells. The gene expression pattern of 15-month-old PGCs-depleted gonads showed that male-biased genes, dmrt1, sox9a, gsdf, and amh, were significantly higher than that of the WT, whereas female-biased genes, foxl2 and cyp19a1a, were significantly decreased. These results indicate that PGCs are essential for ovarian differentiation in rice field eel, and PGCs-depleted gonads develop into sterile males without undergoing the female and intersex stages. Our study is the first to identify the role of PGCs in sex differentiation in rice field eel, a protogynous hermaphrodite teleost. And it is of great significance in rice field eel for discovering the underlying mechanism of sex differentiation and establishing sex control technology.

Expression of transport proteins in the rete mirabile of european silver and yellow eel

BACKGROUND

In physoclist fishes filling of the swimbladder requires acid secretion of gas gland cells to switch on the Root effect and subsequent countercurrent concentration of the initial gas partial pressure increase by back-diffusion of gas molecules in the rete mirabile. It is generally assumed that the rete mirabile functions as a passive exchanger, but a detailed analysis of lactate and water movements in the rete mirabile of the eel revealed that lactate is diffusing back in the rete. In the present study we therefore test the hypothesis that expression of transport proteins in rete capillaries allows for back-diffusion of ions and metabolites, which would support the countercurrent concentrating capacity of the rete mirabile. It is also assumed that in silver eels, the migratory stage of the eel, the expression of transport proteins would be enhanced.

RESULTS

Analysis of the transcriptome and of the proteome of rete mirabile tissue of the European eel revealed the expression of a large number of membrane ion and metabolite transport proteins, including monocarboxylate and glucose transport proteins. In addition, ion channel proteins, Ca2+-ATPase, Na+/K+-ATPase and also F1F0-ATP synthase were detected. In contrast to our expectation in silver eels the expression of these transport proteins was not elevated as compared to yellow eels. A remarkable number of enzymes degrading reactive oxygen species (ROS) was detected in rete capillaries.

CONCLUSIONS

Our results reveal the expression of a large number of transport proteins in rete capillaries, so that the back diffusion of ions and metabolites, in particular lactate, may significantly enhance the countercurrent concentrating ability of the rete. Metabolic pathways allowing for aerobic generation of ATP supporting secondary active transport mechanisms are established. Rete tissue appears to be equipped with a high ROS defense capacity, preventing damage of the tissue due to the high oxygen partial pressures generated in the countercurrent system.

Nr5a homologues in the ricefield eel Monopterus albus: Alternative splicing, tissue-specific expression, and differential roles on the activation of cyp19a1a promoter in vitro

Nr5a (Fushi tarazu factor 1, Ftz-F1) homologues belong to the nuclear receptor superfamily, and are involved in the regulation of reproduction in vertebrates. Four genes encoding Nr5a homologues were present in the genome of ricefield eel, which are designated as nr5a1a, nr5a1b, nr5a2, and nr5a5 in the present study. Alternatively spliced transcripts were identified for nr5a1a and nr5a1b genes. Sequence analysis indicated that nr5a5 is possibly a paralog of nr5a2, and nr5a1b is lost during evolution in some teleosts including tilapia and medaka. Ricefield eel nr5a genes exhibit tissue-specific expression patterns, with nr5a1a and nr5a1b resembling that of the SF-1/Ad4BP (NR5A1) subfamily, and nr5a2 and nr5a5 resembling that of the NR5A2/LRH/FTF subfamily. Transcriptomic analysis revealed parallel expression profiles of nr5a1a, foxl2, and cyp19a1a in ovarian follicles during vitellogenesis, with peak values at the late vitellogenic stage. Real-time PCR indicated that the expression levels of nr5a1a and foxl2 in gonads were decreased significantly during the sexual transition from female to the late intersexual stage. In vitro transient transfection assay showed that Nr5a1a up-regulated ricefield eel cyp19a1a promoter activities synergistically with Foxl2. However, Nr5a1b, Nr5a2, and Nr5a5 could neither activate ricefield eel cyp19a1a promoter alone nor enhance the stimulatory effects of Foxl2 on cyp19a1a promoter activities. Collectively, the above data suggest that Nr5a homologues may have diverse and differential roles in the tissues of ricefield eels. The up-regulation of gonadal nr5a1a and foxl2 during vitellogenesis may be important for the ovarian development whereas their down-regulation during the sexual transition period may be important for the sex change process of ricefield eels, possibly through the regulation of cyp19a1a gene expression.

Molecular characterization, expression, and apoptosis regulation of siva1 in protogynous hermaphrodite fish ricefield eel (Monopterus albus)

Siva1, which induces extensive apoptosis, has been well characterized. To elucidate the molecular function of Siva1 in ricefield eel, molecular characterization and phylogenetic analysis were performed, and the mRNA expression in the ovary at different developmental stages and ovary tissues exposed to H₂O₂ and Z-VAD-FMK in vitro were also evaluated. The results indicated that ricefield eel Siva1 was highly conserved and contains three conserved motifs, despite 83 amino acid differences upstream of the initiation codon. Phylogenetic analysis demonstrated that ricefield eel Siva1 clusters together with the Siva1 protein of the other fish, with high sequence homology with that of Lates calcarifer. Quantitative real-time polymerase chain reaction analysis showed high siva1 expression levels in the ovary and low expression levels in the liver. The higher mRNA levels of siva1 were detected in the IE and IM, and the lower siva1 mRNA levels were found in the OM, IL, and TE during gonadal development. Additionally, siva1 expression levels in the ovarian tissues were significantly increased at 1 h post incubation (hpi) with H₂O₂ and then significantly decreased at 2 hpi; however, siva1 expression was upregulated significantly at 4 and 8 hpi, similar to the patterns observed with caspase3, which was used as a molecular marker of apoptosis. Moreover, the siva1 mRNAs were elevated significantly than that in control groups at 1 hpi, but the expression of siva1 was down-regulated dramatically at 2, 4, and 8 hpi, which were similar with that of caspase3 expression profiles after Z-VAD-FMK incubation. What's more, Pearson's correlation coefficients showed strongly positive relationships between siva1 and caspase3. These findings suggest that Siva1 plays an important apoptosis role in gonadal development of ricefield eel.

New records of two deep-sea eels collected from the Western Pacific Ocean based on COI and 16S rRNA genes

BACKGROUND

Two deep-sea eels collected from the Western Pacific Ocean are described in this study. Based on their morphological characteristics, the two deep-sea eel specimens were assumed to belong to the cusk-eel family Ophidiidae and the cutthroat eel family Synaphobranchidae.

METHODS AND RESULTS

To accurately identify the species of the deep-sea eel specimens, we sequenced the mitochondrial genes (cytochrome c oxidase subunit I [COI] and 16S ribosomal RNA [16S rRNA]). Through molecular phylogenetic analysis based on mtDNA COI and 16S rRNA gene sequences, these species clustered with the genera Bassozetus and Synaphobranchus, suggesting that the deep-sea eel specimens collected are two species from the genera Bassozetus and Synaphobranchus in the Western Pacific Ocean, respectively.

CONCLUSIONS

This is the first study to report new records of the genera Bassozetus and Synaphobranchus from the Western Pacific Ocean based on COI and 16S rRNA genes.

A new species of the genus Cirrhimuraena (Anguilliformes: Ophichthidae) from the Bay of Bengal, India

A new species of the genus Cirrhimuraena (Anguilliformes: Ophichthidae), Cirrhimuraena indica sp. nov., is described based on eight specimens collected from the Paradip (Odisha) and Petuaghat harbours (West Bengal) along the Bay of Bengal. The species is distinct in having the upper jaw fringed with 16-17 cirri before posterior nostril and 4-5 in between the anterior and posterior nostrils on the side; dorsal fin originates above the level of gill opening, predorsal length is 9.3-10.9 in total length; the head is relatively large, the length is 9.3-9.8 in total length; no infraorbital pores are observed between the nostrils; teeth are numerous, small, conical and in bands on each jaw; pores are present before the gill opening 10-11 and before anus 47-48; pectoral-fin length is 2.4-2.8 in head length; predorsal vertebrae are 8-10, pre-anal vertebrae 43-47 and total vertebrae 164-169. In the maximum likelihood tree analysis for COI gene, the new species belongs to the same clade as the other congener of Cirrhimuraena chinensis and is separated from the species morphologically and genetically.

Anguillid herpesvirus 1 (AngHV) ORF95 encodes a late, structural envelope protein

Anguillid herpesvirus 1 (AngHV) is one of the vital pathogenic agents found in the wild and cultured eel populations, which has brought significant losses to eel culture industry in China. In this study, AngHV ORF95 was characterized. Bioinformatics analysis showed that ORF95 putatively encodes a structural protein that is homologous to hemagglutinin-esterase (HE) protein of infectious salmon anemia virus (ISAV). Temporal transcription and expression analysis indicated that ORF95 is a viral late gene. Subcellular localization analysis revealed that ORF95 was predominantly localized in the cytoplasm. Further, western blot analysis indicated that ORF95 is a structural protein of virion envelope. These results provide a novel basis to make further efforts to clarify the function of ORF95 in the process of AngHV infection and the possibility to use ORF95 as antigen to develop AngHV subunit vaccine.

Two forms of G protein-coupled estrogen receptor 1 in the ricefield eel: Expression and functional characterization in relation to ovarian follicle development

G protein-coupled estrogen receptor 1 (Gper1) mediates many rapid, non-genomic estrogenic effects in vertebrates, and plays an important reproductive role in the maintenance of oocyte meiotic arrest in teleost fishes. In the present study, two genes for Gper1, namely gper1a and gper1b, were identified in the genome of a teleost fish, the ricefield eel (Monopterus albus) through Blast and syntenic analysis. Although genes neighboring gper1b are of high synteny, ricefield eel Gper1b shares very low (around 15) percent identities with Gper1 homologues of other vertebrates. In transiently transfected HEK293T cells, both ricefield eel Gper1a and Gper1b responded to estradiol (E₂) and estradiol-BSA (E₂-BSA) challenges by activating pCRE but not pSRE luciferase reporters, which were abolished by G-15 and NF-449. The production of cAMP was also increased in HEK293T cells transfected with Gper1a or Gper1b expression construct after E₂-BSA challenge, which was also abolished by G-15. Surprisingly, both Gper1a and Gper1b showed ligand-independent effects on pCRE luciferase reporters at higher transfected doses (10 ng). RT-PCR analysis showed that the transcript of gper1a is broadly expressed in tissues of both female and male fish while the expression of gper1b in tissues demonstrates obvious sexual dimorphism, with transcripts detected in all tissues examined in female whereas they were barely detectable in some peripheral tissues of male including the testis. In the ovary, the expression of both gper1a and gper1b was detected in the oocyte but not the follicular layer, with the mRNA levels increased during vitellogenesis, peaked at the late vitellogenic stage, and decreased precipitously at the full-grown and germinal vesicle breakdown (GVBD) stages. Moreover, E₂ and E₂-BSA induced cAMP production in the in vitro incubated follicles at mid-vitellogenic stage but not the GVBD stage, and the induction could be completely abolished by G-15, a Gper1 inhibitor. Taken together, these results suggest that both Gper1a and Gper1b may play important roles in the development and maturation of ovarian follicles in ricefield eels, possibly through inhibition of oocyte meiotic resumption.

Molecular cloning and functional characterization of growth hormone-releasing hormone in Mastacembelus armatus

Growth hormone-releasing hormone (GHRH) is a neuropeptide that controls growth hormone (GH) synthesis and release. In this study, the full-length cDNA of Mastacembelus armatus ghrh was obtained by rapid amplification of cDNA ends method. Sequence analysis showed that the cloned sequence is 1090 bp in length, containing an open reading frame (ORF) of 429 bp that encodes a precursor protein of 142 amino acids. Sequence alignment revealed that the 27-amino acid mature peptide of Ghrh in M. armatus is conserved. Real-time PCR showed that ghrh is highly expressed in the brain, with very low or no expression in other tissues. During embryonic and larval development, ghrh expression was low in embryos but increased gradually in the stages of larval development. The biological function of Ghrh peptide was further investigated in vivo. Ghrh injection could significantly upregulate the mRNA expression of growth hormone (gh) and insulin-like growth factor-1/2 (igf-1/2) in M. armatus. Our data indicate that Ghrh is able to activate the GH-IGFs axis in M. armatus.

Chromosome Mapping of 5S Ribosomal Genes in Indo-Pacific and Atlantic Muraenidae: Comparative Analysis by Dual Colour Fluorescence In Situ Hybridisation

The Muraenidae is one of the largest and most complex anguilliform families. Despite their abundance and important ecological roles, morays are little studied, especially cytogenetically, and both their phylogenetic relationships and the taxonomy of their genera are controversial. With the aim of extending the karyology of this fish group, the chromosomal mapping of the 5S ribosomal gene family was performed on seven species belonging to the genera Muraena and Gymnothorax from both the Atlantic and Pacific oceans. Fluorescence in situ hybridisation (FISH) experiments were realized using species-specific 5S rDNA probes; in addition, two-colour FISH was performed to investigate the possible association with the 45S ribosomal gene family. Multiple 5S rDNA clusters, located either in species-specific or in possibly homoeologous chromosomes, were found. Either a syntenic or different chromosomal location of the two ribosomal genes was detected. Our results revealed variability in the number and location of 5S rDNA clusters and confirmed a substantial conservation of the number and location of the 45S rDNA.

A review of the genus Strophidon (Anguilliformes: Muraenidae), with description of a new species

Strophidon McClelland is a muraenid genus with characteristic appearance of a very elongated body, a large mouth cleft and anteriorly placed eyes. The nomenclature and taxonomic history of species within Strophidon are contentious and its members are easily misidentified. In the present study, species of the genus Strophidon are revised based on morphological and molecular data, and five species are considered valid, including S. dawydoffi Prokofiev, S. dorsalis (Seale), S. sathete (Hamilton), S. ui Tanaka and a new species, S. tetraporus. Strophidon tetraporus sp. nov. is described based on 15 specimens from Indonesia, the Philippines, Taiwan and Vietnam with the unique characteristic of the constant presence of the fourth infraorbital pore among species of Strophidon. The intraspecific variation of vertebral formula within S. dorsalis is discussed based on molecular data. Muraena macrurus Bleeker and Thyrsoidea longissima Kaup are synonyms of S. sathete that can be distinguished from the most similar congener S. ui by a longer tail, smaller eyes and more inner maxillary and inner dentary teeth. A key to identify species of Strophidon is provided. The distribution and maximum size of each species are also re-evaluated.

Transcriptome analysis of blood for the discovery of sex-related genes in ricefield eel Monopterus albus

The blood acts as a transfer channel for a variety of factors in the whole body. The ricefield eel (Monopterus albus) is a protogynous hermaphrodite vertebrate. Until now, no research has reported an analysis of the blood transcriptome during the process of sexual development in the ricefield eel. In this study, the transcriptome sequencing of blood samples from male and female ricefield eels was completed with a total of 34.70 Gb clean data. The clean data of each sample all reached 5.23 GB, and the percent of the Q30 basic group was 88.62% and above. A total of 106,369 unigenes were obtained after assembly, including 13,296 unigenes with a length of more than 1 kb. Further functional annotation analysis showed that there are 28,522 unigenes that can be annotated. The annotations of genes with differential expression revealed that there were 563 genes with significant differential expression in the blood of male and female ricefield eels, including 91 upregulated genes and 472 downregulated genes. Among which, 14 genes may be closely related to sex differentiation, the qPCR was used to confirmed the expression pattern of those genes and result shown that 11 genes were downregulated and 3 genes were upregulated, consistent with the results of our RNA-Seq analysis. This blood transcript dataset will open future research avenues on ricefield eel sex development and differentiation.

Expression and regulation of Smad2 by gonadotropins in the protogynous hermaphroditic ricefield eel (Monopterus albus)

Smad2, a receptor-activated Smad, plays a critical role in regulating gametogenesis. In this study, a smad2 homologue was identified and sequenced from ricefield eel ovary cDNA, and its mRNA and protein expression levels were analysed during oocyte development. The cDNA sequence of ricefield eel smad2 consisted of 1863 bp encoding a 467-amino acid protein that had high sequence homology with Smad proteins in other teleosts, especially in Poeciliopsis prolifica. The results of real-time quantitative PCR (RT-qPCR) analysis revealed that smad2 is expressed in the ovary during gonad development, increased continuously until the early vitellogenic stage in the ovaries, and then decreased with ovary maturation. Smad2 protein immunoreactivity was localized in the cytoplasm of follicular cells, oogonia, and primary growth stage oocytes. In vitro experiments revealed that follicle-stimulating hormone (FSH) and human chorionic gonadotropin (hCG) promoted smad2 expression in ovary tissue in a time- and dose-dependent manner, respectively. In summary, Smad2 plays a potentially vital role in ricefield eel ovary development.

Identification and Evaluation of Long Noncoding RNAs in Response to Handling Stress in Red Cusk-Eel (Genypterus chilensis) via RNA-seq

The red cusk-eel (Genypterus chilensis) is a native species with strong potential to support Chilean aquaculture diversification. Under commercial conditions, fish are exposed to several stressors. To date, little is known about the mechanism involved in the stress response of red cusk-eel, and there is no information related to the regulation mediated by long noncoding RNAs (lncRNAs). The objective of this work was to identify for the first time the lncRNAs in the transcriptome of G. chilensis and to evaluate the differential expression levels of lncRNAs in the liver, head kidney, and skeletal muscle in response to handling stress. We used previously published transcriptome data to identify the lncRNAs by applying a series of filters based on annotation information in several databases to discard coding sequences. We identified a total of 14,614 putative lncRNAs in the transcriptome of red cusk-eel, providing a useful lncRNA reference resource to be used in future studies. We evaluated their differential expression in response to handling stress in the liver, head kidney, and skeletal muscle, identifying 112, 323, and 108 differentially expressed lncRNAs, respectively. The results suggest that handling stress in red cusk-eel generate an altered metabolic status in liver, altered immune response in head kidney, and skeletal muscle atrophy through an important coding and noncoding gene network. This is the first study that identifies lncRNAs in Genypterus genus and that evaluates the relation between handling stress and lncRNAs in teleost fish, thereby providing valuable information regarding noncoding responses to stress in Genypterus species.

Molecular diet analysis of Anguilliformes leptocephalus larvae collected in the western North Pacific

Natural diets of leptocephalus larvae have been enigmatic. In this study, we collected DNA samples from the gut contents and body surface of leptocephali belonging to the five Anguilliform families (Anguillidae, Chlopsidae, Congridae, Muraenidae, and Serrivomeridae) from the northwest Pacific and performed next-generation 18S rDNA sequencing. Wide variety of eukaryotes was detected in both samples, from which eight eukaryotic groups (jellyfish, conoid parasite, tunicate, copepod, krill, segmented worm, fungi, and dinoflagellate) were selected on the basis of abundance. All groups except conoid parasites were common in both the samples. Cnidarian 18S rDNA reads were the most abundant in both the samples; however, the number of samples having cnidarian reads and the read counts were significantly higher in the body surface scraping samples than in the gut content samples, regardless of careful rinsing of the body surface. These results indicate that the cnidarian DNAs are most likely found because of cross contamination from the body surface and/or environment. 18S rDNA read counts of copepod and tunicate in the gut contents were greater than or comparable with those in the body surface scraping samples, which may correspond to the previous observations of fecal pellets and larvacean houses in the leptocephali gut. Thus, the present study supports previous implications that leptocephali utilize detritus materials, so called marine snow.

Resolving deep-sea pelagic saccopharyngiform eel mysteries: Identification of Neocyema and Monognathidae leptocephali and establishment of a new fish family "Neocyematidae" based on larvae, adults and mitogenomic gene orders

Deep-sea midwater "saccopharyngiform" eels of the families Cyematidae, Monognathidae, Eurypharyngidae and Saccopharyngidae (order Anguilliformes) are extraordinary fishes having major skeletal reductions and modifications compared to the general anguilliform body structure. Little is known about most aspects of the systematics, phylogeny, and ecology of these families, and few of the approximately 30 species described from adult specimens have been matched with their leptotocephalus larvae. Based on mitogenomic sequence data from rare new specimens, we show that the long-speculated-about larval form referred to as "Leptocephalus holti", which was thought to possibly be the larva of the rare orange-colored eels of Neocyema (5 known specimens; speculated to belong to the Cyematidae) are actually the larvae of the one-jaw eels of the family Monognathidae. One of the 5 types of L. holti larvae that were collected in the Pacific is genetically matched with Monognathus jesperseni, but multiple species exist based on larval sequence data and the morphology of adult specimens. A rare leptocephalus from the Sargasso Sea, with unique morphological characteristics including many small orange spots on the gut, was found to be the larva of Neocyema, which is presently only known from the Atlantic Ocean. We demonstrate that Neocyema constitutes a separate family being most closely related to Eurypharyngidae and Saccopharyngidae based on mitogenomic DNA sequences and unique mitochondrial gene orders.

Identification of genetic linkage group 1-linked sequences in Japanese eel (Anguilla japonica) by single chromosome sorting and sequencing

Japanese eel (Anguilla japonica) constitutes one of the most important food fish in Japan; accordingly, genome sequencing and linkage mapping have been conducted for the purpose of artificial cultivation. In the next stage, integration of genomic sequences within linkage groups (LG) is required to construct higher-resolution genetic markers for quantitative trait loci mapping and selective breeding of beneficial traits in farming. In order to identify LG1-linked scaffolds from the draft genome assembly (323,776 scaffolds) reported previously, we attempted to isolate chromosomes corresponding to LG1 by flow sorting and subsequent analyses. Initially, single chromosomes were randomly collected by chromosome sorting and subjected to whole-genome amplification (WGA). A total of 60 WGA samples were screened by PCR with primers for a known LG1-linked scaffold, and five positive WGA samples were sequenced by next-generation sequencing (NGS). Following reference mapping analysis of the NGS reads, four of the five WGA samples were found to be enriched by LG1-linked sequences. These samples were cytogenetically assigned to chromosome 5 by fluorescence in situ hybridization. Using blastn searches with 82,081 contigs constructed from the NGS reads of the four WGA samples as queries, 2323 scaffolds were identified as putative LG1-linked scaffolds from the draft genome assembly. The total length of the putative LG1-linked scaffolds was 99.0 Mb, comparable to the estimated DNA amounts of chromosome 5 (91.1 Mb). These results suggest that the methodology developed herein is applicable to isolate specific chromosome DNAs and integrate unanchored scaffold sequences onto a particular LG and chromosome even in teleost fishes, in which isolation of specific chromosomes by flow sorting is generally difficult owing to similar morphologies, sizes, and GC-contents among chromosomes in the genome. The putative LG1-linked scaffolds of Japanese eel contain a total of 6833 short tandem repeats which will be available for higher-resolution linkage mapping.

Expression of aryl hydrocarbon receptor-regulated genes and superoxide dismutase in the Antarctic eelpout Pachycara brachycephalum exposed to benzo[a]pyrene

The aryl hydrocarbon receptor (AhR) pathway mediates many, if not all, responses of fish to dioxin-like compounds. The Southern Ocean is progressively exposed to increasing concentrations of anthropogenic pollutants. Antarctic fish are known to accumulate those pollutants, yet nothing is known about their capability to induce chemical biotransformation via the AhR pathway. The objective of the present study was to investigate whether Antarctic eelpout, Pachycara brachycephalum, respond to anthropogenic pollutants by activation of the AhR and its target gene cytochrome P4501A (CYP1A), and of superoxide dismutase (SOD), which served as a representative for oxidative stress. We exposed P. brachycephalum to 10 and 100 mg benzo[a]pyrene (BaP)/kg body weight for 10 d and measured the expression of AhR, CYP1A, and SOD in liver tissue via quantitative polymerase chain reaction. We identified two distinct AhR isoforms in the liver of P. brachycephalum. Antarctic eelpout responded to both BaP exposures by an up-regulation of AhR and SOD, and by a particularly strong induction of CYP1A expression, which remained high until day 10 of the exposure time. Our data suggest that P. brachycephalum possesses the potential to up-regulate xenobiotic biotransformation pathways, at least at the gene expression level. The time course of the AhR and CYP1A response points to an efficient but slow xenobiotics metabolism. Moreover, BaP exposure could include adverse effects such as oxidative stress. Environ Toxicol Chem 2018;37:1487-1495. © 2018 SETAC.

Characterization, expression, and evolutionary analysis of new TLR3 and TLR5M genes cloned from the spiny eel Mastacembelus armatus

Toll-like receptors (TLRs) play an important role in innate and adaptive immunity. Here, we identify two new TLRs from the spiny eel Mastacembelus armatus (TLR3 and membrane TLR5M). Both MaTLR3 and MaTLR5M were expressed in all tested tissues; expression was highest in liver and spleen, respectively. After infection with Vibrio parahaemolyticus, expression of both TLRs fluctuated and differed significantly from controls at several time points. The predicted three-dimensional model of the MaTLR3 and MaTLR5M proteins indicates that most sites under positive selection were located in the extracellular domains of TLRs. Evolutionary analysis detected positively selected sites in the ancestral lineages of vertebrates, amphibians and reptiles. Multiple ML methods recovered 10 positively selected sites in teleost TLR3 and 24 in TLR5M, and most sites were located in leucine-rich repeat domain, possibly related to an "arms-race" co-evolution with pathogens.

Rapid de novo assembly of the European eel genome from nanopore sequencing reads

We have sequenced the genome of the endangered European eel using the MinION by Oxford Nanopore, and assembled these data using a novel algorithm specifically designed for large eukaryotic genomes. For this 860 Mbp genome, the entire computational process takes two days on a single CPU. The resulting genome assembly significantly improves on a previous draft based on short reads only, both in terms of contiguity (N50 1.2 Mbp) and structural quality. This combination of affordable nanopore sequencing and light weight assembly promises to make high-quality genomic resources accessible for many non-model plants and animals.

Ammonia stress under high environmental ammonia induces Hsp70 and Hsp90 in the mud eel, Monopterus cuchia

The obligatory air-breathing mud eel (Monopterus cuchia) is frequently being challenged with high environmental ammonia (HEA) exposure in its natural habitats. The present study investigated the possible induction of heat shock protein 70 and 90 (hsp70, hsc70, hsp90α and hsp90β) genes and more expression of Hsp70 and Hsp90 proteins under ammonia stress in different tissues of the mud eel after exposure to HEA (50 mM NH₄Cl) for 14 days. HEA resulted in significant accumulation of toxic ammonia in different body tissues and plasma, which was accompanied with the stimulation of oxidative stress in the mud eel as evidenced by more accumulation of malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) during exposure to HEA. Further, hyper-ammonia stress led to significant increase in the levels of mRNA transcripts for inducible hsp70 and hsp90α genes and also their translated proteins in different tissues probably as a consequence of induction of hsp70 and hsp90α genes in the mud eel. However, hyper-ammonia stress was neither associated with any significant alterations in the levels of mRNA transcripts for constitutive hsc70 and hsp90β genes nor their translated proteins in any of the tissues studied. More abundance of Hsp70 and Hsp90α proteins might be one of the strategies adopted by the mud eel to defend itself from the ammonia-induced cellular damages under ammonia stress. Further, this is the first report of ammonia-induced induction of hsp70 and hsp90α genes under hyper-ammonia stress in any freshwater air-breathing teleost.

Scp3 expression in relation to the ovarian differentiation in the protogynous hermaphroditic ricefield eel Monopterus albus

Synaptonemal complex protein 3 (Scp3), which is encoded by scp3, is a meiotic marker commonly used to trace the timing of gonadal differentiation in vertebrates. In the present study, the ricefield eel scp3 cDNA was cloned, and a fragment encoding amino acids 49 to 244 was overexpressed. The recombinant Scp3 polypeptide was purified and used to generate a rabbit anti-Scp3 polyclonal antiserum. In adult ricefield eels, scp3 mRNA was predominantly detected in the gonads and faintly detected in discrete brain areas. In the gonads, Scp3 immunoreactivities were shown to be localized to the germ cells, including meiotic primary growth oocytes, spermatocytes, and pre-meiotic spermatogonia. During early ovarian differentiation, immunoreactive Scp3 was not detected in the gonads of ricefield eels at 6 days post-hatching (dph) but was found to be abundantly localized in the cytoplasm of some oogonia at 7 dph, coinciding with the appearance of the ovarian cavity and ovarian differentiation. At 14 dph, strong Scp3 immunostaining was detected on one side of the nucleus with a distinct polarity in some germ cells, presumably at the leptotene stage. Consistent with these results, the expression of scp3 mRNA was faintly detected in the gonads of ricefield eels at 6 dph, increased at 8 dph, and then remained relatively high thereafter. Taken together, these results suggest that the appearance of immunoreactive Scp3 in oogonia could be a marker for early ovarian differentiation in ricefield eels. The translocation of the Scp3 protein from the cytoplasm to the nucleus in the oogonium of ricefield eels appears to be a controlled process that warrants further study.

Morphology and Species Composition of Southern Adriatic Sea Leptocephali Evaluated Using DNA Barcoding

Leptocephali are the characteristic larvae of the superorder Elopomorpha that are difficult to identify at the species level. In this study, we used DNA barcoding (i.e. short genetic sequences of DNA used as unique species tags) coupled with classical taxonomic methods to identify leptocephali in the southern Adriatic Sea. This information will provide an assessment of the biodiversity of the eel larvae in this region. A total of 2,785 leptocephali were collected, and using external morphology were assigned to seven morphotypes: Ariosoma balearicum, Conger conger, Gnathophis mystax, Facciolella sp., Nettastoma melanurum, Dalophis imberbis and Chlopsis bicolor. Collectively, these seven morphotypes are considered to be a good proxy for the Anguilliformes community (the main order of the Elopomorpha) in the southern Adriatic Sea (to date, seven families and sixteen species have been recorded in this region). Interestingly, the higher number of G. mystax larvae collected suggests an increased abundance of this genus. To validate the morphological identifications, we sequenced 61 leptocephali (at a 655 bp fragment from the cytochrome oxidase subunit 1 mitochondrial region) and developed barcode vouchers for the seven morphotypes. Using genetic information from reference databases, we validated three of these morphotypes. Where reference sequences were unavailable, we generated barcodes for both adult and juvenile forms to provide additional genetic information. Using this integrated approach allowed us to characterize a new species of Facciolella in the Adriatic Sea for the first time. Moreover, we also revealed a lack of differentiation, at the species level, between G. mistax and G. bathytopos, a western Atlantic Ocean species. Our morphological and barcode data have been published in the Barcoding of the Adriatic Leptocephali database. This work represents the first contribution to a wider project that aims to create a barcode database to support the assessment of leptocephali diversity in the Mediterranean Sea.

A giant anguilliform leptocephalus Thalassenchelys foliaceus Castle & Raju is a junior synonym of Congriscus maldivensis (Norman 1939)

A single specimen of giant leptocephalus Thalassenchelys foliaceus Castle & Raju 1975 was caught in subtropical waters of the western North Pacific Ocean. Mitochondrial coI gene sequence divergence between T. foliaceus and Congriscus maldivensis (Norman 1939) was 0·64 ± 0·27% (mean ± s.e.), and the myomere and vertebral counts of these species were similar, indicating T. foliaceus is a junior synonym of C. maldivensis.

Molecular phylogenetics reveals convergent evolution in lower Congo River spiny eels

BACKGROUND

The lower Congo River (LCR) is a region of exceptional species diversity and endemism in the Congo basin, including numerous species of spiny eels (genus Mastacembelus). Four of these exhibit distinctive phenotypes characterized by greatly reduced optic globes deeply embedded into the head (cryptophthalmia) and reduced (or absent) melanin pigmentation, among other characteristics. A strikingly similar cryptophthalmic phenotype is also found in members of a number of unrelated fish families, strongly suggesting the possibility of convergent evolution. However, little is known about the evolutionary processes that shaped diversification in LCR Mastacembelus, their biogeographic origins, or when colonization of the LCR occurred.

METHODS

We sequenced mitochondrial and nuclear genes from Mastacembelus species collected in the lower Congo River, and compared them with other African species and Asian representatives as outgroups. We analyzed the sequence data using Maximum Likelihood and Bayesian phylogenetic inference.

RESULTS

Bayesian and Maximum Likelihood phylogenetic analyses, and Bayesian coalescent methods for species tree reconstruction, reveal that endemic LCR spiny eels derive from two independent origins, clearly demonstrating convergent evolution of the cryptophthalmic phenotype. Mastacembelus crassus, M. aviceps, and M. simbi form a clade, allied to species found in southern, eastern and central Africa. Unexpectedly, M. brichardi and brachyrhinus fall within a clade otherwise endemic to Lake Tanganikya (LT) ca. 1500 km east of the LCR. Divergence dating suggests the ages of these two clades of LCR endemics differ markedly. The age of the crassus group is estimated at ~4 Myr while colonization of the LCR by the brichardi-brachyrhinus progenitor was considerably more recent, dated at ~0.5 Myr.

CONCLUSIONS

The phylogenetic framework of spiny eels presented here, the first to include LCR species, demonstrates that cryptophthalmia and associated traits evolved at least twice in Mastacembelus: once in M. brichardi and at least once in the M. crassus clade. Timing of diversification is broadly consistent with the onset of modern high-energy flow conditions in the LCR and with previous studies of endemic cichlids. The close genetic relationship between M. brichardi and M. brachyrhinus is particularly notable given the extreme difference in phenotype between these species, and additional work is needed to better understand the evolutionary history of diversification in this clade. The findings presented here demonstrate strong, multi-trait convergence in LCR spiny eels, suggesting that extreme selective pressures have shaped numerous phenotypic attributes of the endemic species of this region.

Comparative cytogenetics of six Indo-Pacific moray eels (Anguilliformes: Muraenidae) by chromosomal banding and fluorescence in situ hybridization

A comparative cytogenetic analysis, using both conventional staining techniques and fluorescence in situ hybridization, of six Indo-Pacific moray eels from three different genera (Gymnothorax fimbriatus, Gymnothorax flavimarginatus, Gymnothorax javanicus, Gymnothorax undulatus, Echidna nebulosa and Gymnomuraena zebra), was carried out to investigate the chromosomal differentiation in the family Muraenidae. Four species displayed a diploid chromosome number 2n = 42, which is common among the Muraenidae. Two other species, G. javanicus and G. flavimarginatus, were characterized by different chromosome numbers (2n = 40 and 2n = 36). For most species, a large amount of constitutive heterochromatin was detected in the chromosomes, with species-specific C-banding patterns that enabled pairing of the homologous chromosomes. In all species, the major ribosomal genes were localized in the guanine-cytosine-rich region of one chromosome pair, but in different chromosomal locations. The (TTAGGG)n telomeric sequences were mapped onto chromosomal ends in all muraenid species studied. The comparison of the results derived from this study with those available in the literature confirms a substantial conservation of the diploid chromosome number in the Muraenidae and supports the hypothesis that rearrangements have occurred that have diversified their karyotypes. Furthermore, the finding of two species with different diploid chromosome numbers suggests that additional chromosomal rearrangements, such as Robertsonian fusions, have occurred in the karyotype evolution of the Muraenidae.

An Enriched European Eel Transcriptome Sheds Light upon Host-Pathogen Interactions with Vibrio vulnificus

Infectious diseases are one of the principal bottlenecks for the European eel recovery. The aim of this study was to develop a new molecular tool to be used in host-pathogen interaction experiments in the eel. To this end, we first stimulated adult eels with different pathogen-associated molecular patterns (PAMPs), extracted RNA from the immune-related tissues and sequenced the transcriptome. We obtained more than 2x10⁶ reads that were assembled and annotated into 45,067 new descriptions with a notable representation of novel transcripts related with pathogen recognition, signal transduction and the immune response. Then, we designed a DNA-microarray that was used to analyze the early immune response against Vibrio vulnificus, a septicemic pathogen that uses the gills as the portal of entry into the blood, as well as the role of the main toxin of this species (RtxA1₃) on this early interaction. The gill transcriptomic profiles obtained after bath infecting eels with the wild type strain or with a mutant deficient in rtxA1₃ were analyzed and compared. Results demonstrate that eels react rapidly and locally against the pathogen and that this immune-response is rtxA1₃-dependent as transcripts related with cell destruction were highly up-regulated only in the gills from eels infected with the wild-type strain. Furthermore, significant differences in the immune response against the wild type and the mutant strain also suggest that host survival after V. vulnificus infection could depend on an efficient local phagocytic activity. Finally, we also found evidence of the presence of an interbranchial lymphoid tissue in European eel gills although further experiments will be necessary to identify such tissue.

Transcriptome profile analysis reveals specific signatures of pollutants in Atlantic eels

Identifying specific effects of contaminants in a multi-stress field context remain a challenge in ecotoxicology. In this context, "omics" technologies, by allowing the simultaneous measurement of numerous biological endpoints, could help unravel the in situ toxicity of contaminants. In this study, wild Atlantic eels were sampled in 8 sites presenting a broad contamination gradient in France and Canada. The global hepatic transcriptome of animals was determined by RNA-Seq. In parallel, the contamination level of fish to 8 metals and 25 organic pollutants was determined. Factor analysis for multiple testing was used to identify genes that are most likely to be related to a single factor. Among the variables analyzed, arsenic (As), cadmium (Cd), lindane (γ-HCH) and the hepato-somatic index (HSI) were found to be the main factors affecting eel's transcriptome. Genes associated with As exposure were involved in the mechanisms that have been described during As vasculotoxicity in mammals. Genes correlated with Cd were involved in cell cycle and energy metabolism. For γ-HCH, genes were involved in lipolysis and cell growth. Genes associated with HSI were involved in protein, lipid and iron metabolisms. Our study proposes specific gene signatures of pollutants and their impacts in fish exposed to multi-stress conditions.

Aromatase (Cyp19a1b) in the pituitary is dynamically involved in the upregulation of lhb but not fshb in the vitellogenic female ricefield eel Monopterus albus

Aromatase, encoded by Cyp19a1, is expressed in the pituitary of vertebrates; however, its physiological relevance remains poorly defined. In teleosts, the duplicated cyp19a1b is preferentially expressed in the pituitary where LH and FSH are synthesized in distinct gonadotropes. Our present study demonstrated that Cyp19a1b is colocalized with Lhb, but not Fshb, during vitellogenesis in female ricefield eels. The immunoreactive levels of Cyp19a1b and Lhb, as well as their colocalization frequency, increased during vitellogenesis toward maturation. The expression of lhb but not fshb in the pituitary fragments of female ricefield eels was induced by both estradiol (E2) and testosterone (T). In agreement, the promoter of lhb but not fshb was activated by both E2 and T. T is more potent than E2 in inducing lhb expression, whereas E2 is much more effective in activating the lhb promoter. T-induced lhb expression in the pituitary fragments was abolished by the estrogen receptor (Esr) antagonist fulvestrant and suppressed by the aromatase inhibitor letrozole, suggesting that the effect of T on lhb expression at the pituitary is largely mediated by E2. Furthermore, Lhb was shown to colocalize with Esr1 but not Esr2a. Taken together, results of the present study suggest that Cyp19a1b in LH cells may greatly upregulate lhb expression during vitellogenesis, possibly via E2 and Esr1 in an intracrine manner. The absence of Cyp19a1b in FSH cells and the insensitivity of fshb to sex steroids may contribute to the differential expression of lhb and fshb in ricefield eels and possibly other vertebrates as well.

Phylogeography of the Chinese beard eel, Cirrhimuraena chinensis Kaup, inferred from mitochondrial DNA: a range expansion after the last glacial maximum

The Chinese beard eel (Cirrhimuraena chinensis Kaup) is an intertidal fish and a model organism for the study of impacts caused by topological fluctuations during the Pleistocene and current intricate hydrological conditions on fauna living in the coastal areas of China. In this study, we examined the phylogeographical pattern, population genetic profile and demographical history of C. chinensis using mitochondrial DNA (cytochrome b (cyt b) and control region (CR)) from 266 individuals sampled in seven localities across the coastal area of southeastern China. The combined data indicated high levels of haplotype diversity and low levels of nucleotide diversity. Analyses of molecular variance (AMOVA) and F_ST statistics suggested the absence of a significant population structure across the Chinese coast. Neutrality tests, mismatch distributions and Bayesian skyline plots uniformly indicated a recent population expansion. The phylogeographic structure of C. chinensis may be attributed to past population expansion and long-distance pelagic larval dispersal facilitated by present-day ocean currents.

Characterization of thyroid hormone receptors during early development of the Japanese eel (Anguilla japonica)

We studied the profiles of thyroid hormone receptors (TRs) in Japanese eels (Anguilla japonica) during development from hatched larvae to juveniles. Two TRαs (TRαA and TRαB) and one TRβ (TRβA) cDNA clones were generated by RACE. The TRαA, TRαB and TRβA cDNAs encoded 416, 407 and 397 amino acid proteins with much higher homologies to the Japanese conger eel (Conger myriaster) TRs than to other fish TRs. In a transiently transfected Japanese eel cell line, Hepa-E1, the TRs showed thyroid hormone (TH)-dependent activation of transcription from the TH-responsive promoter. Four TR cDNA clones, including TRβB reported in a previous study, were analyzed by real-time RT-PCR. The TR mRNA levels in hatched larvae were determined. The two TRβ mRNAs were present at low levels but there was a peak in the TRαs during the larval stage before metamorphosis. During metamorphosis, the two TRαs both exhibited peaks and expression of the two TRβs was higher than during the early growth stage. This expression pattern is similar to that of the Japanese conger eel. It is possible that thyroid hormones control the early development of Japanese eels and Japanese conger eels through TRs. This is the first analysis of the expression sequence of TRs during early larval stages of Anguilliformes.

Intestinal expression of peptide transporter 1 (PEPT1) at different life stages of Japanese eel, Anguilla japonica

The expression of peptide transporter 1 (PEPT1) was investigated at the different life stages of Japanese eel, Anguilla japonica. The cDNA encoding Japanese eel PEPT1 was cloned and sequenced. The hydrophilicity plot analysis of its deduced amino acid sequence showed high similarities with topological features of known PEPT1 molecules in other species. Tissue distribution analysis confirmed that PEPT1 mRNA was detected specifically in the anterior and posterior intestines of adult eel. In eel larvae at 13days post hatching (dph), PEPT1 mRNA expression was mainly detected in the intestinal tract regions. The trypsinogen mRNA was only detected in the gastric region including the pancreas. Intense immunoreaction for PEPT1 was observed in the apical membrane of the intestinal epithelial cells of both larval and adult eel. These results indicated that PEPT1 was an intestine-specific transporter, which was localized at the luminal side of the epithelial cells, suggesting that di/tri-peptide absorption via PEPT1 takes place in the eel intestine. According to the ontogenetic analyses by quantitative PCR, PEPT1 and trypsinogen mRNA expressions were simultaneously increased at 5-7 dph. It is thus assumed that nutrient absorption systems in the intestinal tracts of larvae become functional at this age.

Epigenetic modifications during sex change repress gonadotropin stimulation of cyp19a1a in a teleost ricefield eel (Monopterus albus)

In vertebrates, cytochrome P450 aromatase, encoded by cyp19a1, converts androgens to estrogens and plays important roles in gonadal differentiation and development. The present study examines whether epigenetic mechanisms are involved in cyp19a1a expression and subsequent gonadal development in the hermaphroditic ricefield eel. The expression of the ricefield eel cyp19a1a was stimulated by gonadotropin via the cAMP pathway in the ovary but not the ovotestis or testis. The CpG within the cAMP response element (CRE) of the cyp19a1a promoter was hypermethylated in the ovotestis and testis compared with the ovary. The methylation levels of CpG sites around CRE in the distal region (region II) and around steroidogenic factor 1/adrenal 4 binding protein sites and TATA box in the proximal region (region I) were inversely correlated with cyp19a1a expression during the natural sex change from female to male. In vitro DNA methylation decreased the basal and forskolin-induced activities of cyp19a1a promoter. Chromatin immunoprecipitation assays indicated that histone 3 (Lys9) in both regions I and II of the cyp19a1a promoter were deacetylated and trimethylated in the testis, and in contrast to the ovary, phosphorylated CRE-binding protein failed to bind to these regions. Lastly, the DNA methylation inhibitor 5-aza-2'-deoxycytidine reversed the natural sex change of ricefield eels. These results suggested that epigenetic mechanisms involving DNA methylation and histone deacetylation and methylation may abrogate the stimulation of cyp19a1a by gonadotropins in a male-specific fashion. This may be a mechanism widely used to drive natural sex change in teleosts as well as gonadal differentiation in other vertebrates.

Experimental and computational study of inter- and intra- species specificity of gonadotropins for various gonadotropin receptors

The gonadotropins follicle-stimulating hormone (FSH) and luteinizing hormone (LH) and their receptors play critical roles in vertebrate reproduction. In order to study intra- and interspecies ligand promiscuity of gonadotropins, COS-7 cells were transiently transfected with one of the gonadotropin receptor genes, FSHR or LHR, and tested for activation by gonadotropins from representative fish orders: Aquilliformes (eel; e), Salmoniformes (trout; tr), and Perciformes (tilapia; ta), and of mammalian origin: porcine (p), bovine (b) and human (h). The study reveals complex relations between the gonadotropin hormones and their receptors. Each gonadotropin activated its own cognate receptor. However, taLHR was also activated by hCG and eLHR was activated by hFSH, hCG, and trFSH. For FSHR, the only cross-reactivity detected was for hFSHR, which was activated by pFSH and bFSH. These findings are of great interest and applicability in the context of activation of various GTHRs by their ligands and by ligands from other vertebrates. Analysis of the three-dimensional models of the structures highlights the importance of residues outside of the currently established hormone-receptor interface region. In addition, the interface residues in taFSHR and the effect of exon duplication, which causes an insert in the LRR domain, are suggested to affect the interaction and binding of taFSH.

Genomics in eels--towards aquaculture and biology

Freshwater eels (genus Anguilla), especially the species inhabiting the temperate areas such as the European, American and Japanese eels, are important aquaculture species. Although artificial reproduction has been attempted since the 1930s and large numbers of studies have been conducted, it has not yet fully succeeded. Problems in eel artificial breeding are highly diverse, for instance, lack of basic information about reproduction in nature, no appropriate food for larvae, high mortality, and high individual variation in adults in response to maturation induction. Over the last decade, genomic data have been obtained for a variety of aquatic organisms. Recent technological advances in sequencing and computation now enable the accumulation of genomic information even for non-model species. The draft genome of the European eel Anguilla anguilla has been recently determined using Illumina technology and transcriptomic data based on next generation sequencing have been emerging. Extensive genomic information will facilitate many aspects of the artificial reproduction of eels. Here, we review the progress in genome-wide studies of eels, including additional analysis of the European eel genome data, and discuss future directions and implications of genomic data for aquaculture.

Primitive duplicate Hox clusters in the European eel's genome

The enigmatic life cycle and elongated body of the European eel (Anguilla anguilla L., 1758) have long motivated scientific enquiry. Recently, eel research has gained in urgency, as the population has dwindled to the point of critical endangerment. We have assembled a draft genome in order to facilitate advances in all provinces of eel biology. Here, we use the genome to investigate the eel's complement of the Hox developmental transcription factors. We show that unlike any other teleost fish, the eel retains fully populated, duplicate Hox clusters, which originated at the teleost-specific genome duplication. Using mRNA-sequencing and in situ hybridizations, we demonstrate that all copies are expressed in early embryos. Theories of vertebrate evolution predict that the retention of functional, duplicate Hox genes can give rise to additional developmental complexity, which is not immediately apparent in the adult. However, the key morphological innovation elsewhere in the eel's life history coincides with the evolutionary origin of its Hox repertoire.

The alloherpesviral counterparts of interleukin 10 in European eel and common carp

Viral interleukin 10 (IL-10) like open reading frames have been identified in several pox- and herpesviruses, including the fish herpesviruses Anguillid herpesvirus 1 (AngHV-1) and Cyprinid herpesvirus 3 (CyHV-3). European eel (Anguilla anguilla) IL-10 was sequenced, in order to compare European eel and common carp (Cyprinus carpio) IL-10 with their alloherpesviral counterparts. Homology between the virus and host IL-10 amino acid sequences is low, which is confirmed by phylogenetic analysis. However, the three dimensional structures of the fish and alloherpesviral IL-10 proteins as predicted by modeling are highly similar to human IL-10. Closely related AngHV-1 and CyHV-3 are expected to have obtained their viral IL-10 genes independently in the course of coexistence with their respective hosts. The presence and structural conservation of these alloherpesviral IL-10 genes suggest that they might play an important role in the evolution of pathogenesis.

Localization of diversified relaxin gene transcripts in the brain of eels

Relaxin 3 (RLN3) is a newly-discovered member of the insulin superfamily. We isolated three RLN3-like cDNAs from the brain of the Japanese eel (Anguilla japonica). The deduced amino acid sequences of the RLN3-like cDNAs contained the two-chain structure common to relaxin including a RXXXRXXI/V motif in the B-chain. Phylogenetic analysis assigned the two prepropeptides into teleost/mammalian RLN3 group, which are a pair of duplicates generated by the teleost-specific third-round whole genome duplication, and the other one into teleost RLN group. Therefore, they have been named eel rln3a, rln3b and rln. rln3a transcripts were abundant in the middle-posterior region of the brain and detected at lower levels in the gills, head kidney and kidney. rln3b transcripts were also detected in the middle-posterior region of the brain, but the expression levels were lower than those of rln3a. Low levels of rln transcripts were detected in all brain areas, pituitary, digestive tract and gonad. Quantitative PCR analysis did not detect differences in expression of any rln3 or rln gene between freshwater- and seawater-acclimated eels. In situ hybridization showed that rln3a was expressed in neurons of the lateral lemniscus of the midbrain and of the griseum centrale (GC) of the hindbrain, while low amounts of rln transcripts were found in neurons of the periventricular nucleus of the posterior tuberculum of the diencephalon and the GC. These results suggest that the multiple RLN3-like peptides may play regulatory roles in the brain of euryhaline fish.