Transcriptome analysis of the Japanese eel (Anguilla japonica) during larval metamorphosis.

BACKGROUND: Anguillid eels spend their larval period as leptocephalus larvae that have a unique and specialized body form with leaf-like and transparent features, and they undergo drastic metamorphosis to juvenile glass eels. Less is known about the transition of leptocephali to the glass eel stage, because it is difficult to catch the metamorphosing larvae in the open ocean. However, recent advances in rearing techniques for the Japanese eel have made it possible to study the larval metamorphosis of anguillid eels. In the present study, we investigated the dynamics of gene expression during the metamorphosis of Japanese eel leptocephali using RNA sequencing. RESULTS: During metamorphosis, Japanese eels were classified into 7 developmental stages according to their morphological characteristics, and RNA sequencing was used to collect gene expression data from each stage. A total of 354.8 million clean reads were generated from the body and 365.5 million from the head, after the processing of raw reads. For filtering of genes that characterize developmental stages, a classification model created by a Random Forest algorithm was built. Using the importance of explanatory variables feature obtained from the created model, we identified 46 genes selected in the body and 169 genes selected in the head that were defined as the "most characteristic genes" during eel metamorphosis. Next, network analysis and subsequently gene clustering were conducted using the most characteristic genes and their correlated genes, and then 6 clusters in the body and 5 clusters in the head were constructed. Then, the characteristics of the clusters were revealed by Gene Ontology (GO) enrichment analysis. The expression patterns and GO terms of each stage were consistent with previous observations and experiments during the larval metamorphosis of the Japanese eel. CONCLUSION: Genome and transcriptome resources have been generated for metamorphosing Japanese eels. Genes that characterized metamorphosis of the Japanese eel were identified through statistical modeling by a Random Forest algorithm. The functions of these genes were consistent with previous observations and experiments during the metamorphosis of anguillid eels.

Aureispira anguillae sp. nov., isolated from Japanese eel Anguilla japonica leptocephali.

A novel filamentous eel-leptocephalus pathogenic marine bacterium, designated strain EL160426T, was isolated from Japanese eel, Anguilla japonica, leptocephali reared at a laboratory in Mie, Japan. In experimental infection studies on eel larvae, the strain EL160426T caused massive larval mortality and was reisolated from moribund leptocephali. Characteristically, observations of infected larvae found that EL160426T forms columnar colonies on the cranial surface of larvae. The novel isolate exhibited growth at 15-30 °C, pH 7-9, and seawater concentrations of 60-150% (W/V). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain EL160426T was most closely related to Aureispira maritima 59SAT with 97.7% sequence similarity. The whole genome sequence analysis of the strain EL160426T showed that the strain maintained a circular chromosome with a size of approximately 7.58 Mbp and the DNA G + C content was 36.2%. The major respiratory quinone was MK-7 and the predominant cellular fatty acids were 16:0, 20:4 w6c (arachidonic acid), 17:0 iso and 16:0 N alcohol. DNA relatedness between the closest phylogenetic neighbor strain EL160426T and A. maritima (JCM23207T) was less than 13%. On the basis of the polyphasic taxonomic data, the strain represents a novel species of the genus Aureispira, for which the name Aureispira anguillae sp. nov. is proposed. The type strain is EL160426T (= JCM 35024 T = TSD-286 T).

Effects of the short-term fasting and refeeding on growth-related genes in Japanese eel (Anguilla japonica) larvae.

The Japanese eel (Anguilla japonica) spends a long period as the leptocephalus larval form under current rearing conditions. The duration of the larval stage until metamorphosis is influenced by body size and growth; however, little knowledge exists of the regulatory mechanism of growth in eel larvae. The present study focused on growth hormone (GH), insulin-like growth factors (IGFs), and IGF binding protein (IGFBP) as the central regulators of growth in teleost fishes and transforming growth factor-beta 3 (TGF-ß3) as a possible key modulator of muscle growth and body component synthesis. Japanese eel IGFBP-1a and TGF-ß3, comprising 264 and 411 amino acids, respectively, were cloned. Short-term (5-day) fasting and refeeding experiments were performed to understand changes in growth-related genes affected by nutritional status. The relative expression of gh increased with fasting and subsequently decreased with refeeding to the basal levels of the fed control. Relative igf-1 and igf-2 expression levels were high in the fasted group. Relative igf-1 was reduced after 2-day refeeding, whereas igf-2 decreased to the basal level after 1-day refeeding, suggesting that IGF-1 and IGF-2 might be regulated independently and contribute to postnatal growth in eel larvae. Relative igfbp-1a expression was sharply increased by fasting, whereas tgf-ß3 showed high and low values in the fed and fasted groups, respectively. Relative igfbp-1a and tgf-ß3 levels were negatively and positively correlated with body size, respectively. These results suggest that igfbp-1a and tgf-ß3 are potential indices of growth for exploring optimal rearing conditions to shorten the larval stage in Japanese eels.

Production of recombinant Japanese eel (Anguilla japonica) growth hormones and their effects on early-stage larvae.

Growth hormone (Gh) regulates somatic growth in fishes, particularly through the Gh - insulin-like growth factor-I (Igf-I) axis. In this study, recombinant Japanese eel Ghs with or without C-terminal peptides of human chorionic gonadotropin (CTP), which are known to prolong the half-life, were produced using the HEK 293 and CHO expression system. The effect of recombinant Gh administration to eel larvae on their somatic growth was investigated in short-term feeding experiments, and it was found that three types of recombinant Ghs with CTP (CTP-reGh, reGh-CTP and reGh-CTP × 2) were more effective in promoting somatic growth in eel larvae than recombinant Ghs without CTP. Among the three recombinant Ghs with CTP, reGh-CTP × 2 had the highest growth-promoting effects, however only when provided in the short term. After long-term administration of reGh-CTP × 2, there was no difference in growth between the Gh administrated group and the control group. The survival rate of eel larvae were not affected by recombinant Ghs. In addition, the mRNA expression of gh, Gh receptors, Igf-I and IGF-II were measured by quantitative real-time PCR, and significant reductions in the expression of gh, Gh receptors and Igf-I were observed. These findings provide useful tools to study the mechanisms of somatic growth and increase understanding of Gh regulation in anguillid eel larvae.

Developmental features of Japanese eels, Anguilla japonica, from the late leptocephalus to the yellow eel stages: an early metamorphosis to the eel-like form and a prolonged transition to the juvenile.

Organogenesis of Japanese eels (Anguilla japonica) was investigated histologically from the late leptocephalus to the yellow eel stages. Early organogenesis, such as the formation of inner ears and the appearance of round blood cells that might be larval erythrocytes, had already begun at the late leptocephalus stage. During the first developmental phase (M1-M3 stages) of metamorphosing into early glass eels (G1 stage), the formation of gills and lateral muscles progressed conspicuously with a drastic body shape change from leaf-like to eel-like. In contrast, obvious regression in oesophageal muscle and pancreas occurred during metamorphosis. Formation of lateral line canals advanced continuously until the yellow eel stage. When the second developmental phase was initiated at the G1 stage, cone photoreceptor cells appeared, and the formation of oesophageal, stomach and intestinal muscles was initiated. Differentiation of gastric glands began at 1 week after metamorphosis. Erythrocytes increased continuously in density in glass eels and elvers (G1-E2 stages), and the morphological features of cone cells and olfactory epidermal cells became clearer with stage progression. In early elvers (E1 stage), the swimbladder initiated inflation, the stomach fully expanded and the rectal longitudinal fold changed to a circle. Swimbladder gas glands appeared in late elvers (E2 stage). In the yellow eels (juvenile stage), almost all organ structures were formed. These observations indicate that the organogenesis of A. japonica is ongoing after metamorphosis into glass eels, and the M1-E2 stages are considered to be a homologous phase to first metamorphosis, which is a transformation from the larval to the juvenile stages in other teleosts. In comparison to conger eels, the completion of the body shape change to eel-like occurs at the G1 stage, when organogenesis is still in progress, being followed by a prolonged duration of the G1-E2 stages before reaching the yellow eel juvenile stage, which may be a unique characteristic that is related to the early migratory life history of A. japonica.

Genetic parameters and quantitative trait loci analysis associated with body size and timing at metamorphosis into glass eels in captive-bred Japanese eels (Anguilla japonica).

The Japanese eel (Anguilla japonica) is among the most important aquaculture fish species in Eastern Asia. The present study aimed to identify the genetic parameters underlying body size and the timing at metamorphosis from leptocephali to glass eels in captive-bred Japanese eels, with the intent to foster sustainable development. Larvae from a partly factorial cross (14 sires × 11 dams) were reared until the point of metamorphosis into glass eels. In these organisms, we observed moderate heritability and mild genetic correlations among traits related to body size (h2 = 0.16-0.33) and timing at metamorphosis (h2 = 0.36-0.41). In an F1 full-sib family, quantitative trait loci (QTL) mapping for these traits identified one significant (genome-wide P < 0.05) and five suggestive QTLs (chromosome-wide P < 0.05). These results suggest that in the Japanese eel, metamorphic traits exhibit a polygenic genetic structure comprising many QTLs with small effects. In addition, we updated the genetic linkage map for the Japanese eel and integrated it with our newly constructed de novo genome assembly. The information and tools generated from this study will contribute to the development of freshwater eel genetics and genomics.

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.

Effective de novo assembly of fish genome using haploid larvae.

Recent improvements in next-generation sequencing technology have made it possible to do whole genome sequencing, on even non-model eukaryote species with no available reference genomes. However, de novo assembly of diploid genomes is still a big challenge because of allelic variation. The aim of this study was to determine the feasibility of utilizing the genome of haploid fish larvae for de novo assembly of whole-genome sequences. We compared the efficiency of assembly using the haploid genome of yellowtail (Seriola quinqueradiata) with that using the diploid genome obtained from the dam. De novo assembly from the haploid and the diploid sequence reads (100 million reads per each datasets) generated by the Ion Proton sequencer (200 bp) was done under two different assembly algorithms, namely overlap-layout-consensus (OLC) and de Bruijn graph (DBG). This revealed that the assembly of the haploid genome significantly reduced (approximately 22% for OLC, 9% for DBG) the total number of contigs (with longer average and N50 contig lengths) when compared to the diploid genome assembly. The haploid assembly also improved the quality of the scaffolds by reducing the number of regions with unassigned nucleotides (Ns) (total length of Ns; 45,331,916 bp for haploids and 67,724,360 bp for diploids) in OLC-based assemblies. It appears clear that the haploid genome assembly is better because the allelic variation in the diploid genome disrupts the extension of contigs during the assembly process. Our results indicate that utilizing the genome of haploid larvae leads to a significant improvement in the de novo assembly process, thus providing a novel strategy for the construction of reference genomes from non-model diploid organisms such as fish.

Growth promoting effect of hyaluronan synthesis promoting substances on Japanese eel leptocephali.

Hyaluronans (HAs) are glycosaminoglycans produced in the bodies of Anguilliform and Elopiform leptocephali, and play a role in metabolic energy. In mammals, HA synthesis-promoting substances (HASPS) up-regulate the expression of HA synthase (HAS) and increase the amount of HA in the body. In this study, Japanese eel leptocephali were fed a HASPS containing diet. We analyzed HAS1s and HAS2 expression, HA content, and their influence on growth. HASPS extracted from Grifola frondosa promoted HAS1s and HAS2 mRNA and HA content. Other than mammals, these results are first reported in vertebrate. Moreover, HASPS extracted from G. frondosa promoted leptocephalus growth. The relationship between growth and HA in the leptocephali is not yet clear. However, based on our results we hypothesize that HA is involved in the storage of energy, which is metabolized to sugars when needed for metabolic energy.

A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication.

BACKGROUND: Recent advancements in next-generation sequencing technology have enabled cost-effective sequencing of whole or partial genomes, permitting the discovery and characterization of molecular polymorphisms. Double-digest restriction-site associated DNA sequencing (ddRAD-seq) is a powerful and inexpensive approach to developing numerous single nucleotide polymorphism (SNP) markers and constructing a high-density genetic map. To enrich genomic resources for Japanese eel (Anguilla japonica), we constructed a ddRAD-based genetic map using an Ion Torrent Personal Genome Machine and anchored scaffolds of the current genome assembly to 19 linkage groups of the Japanese eel. Furthermore, we compared the Japanese eel genome with genomes of model fishes to infer the history of genome evolution after the teleost-specific genome duplication. RESULTS: We generated the ddRAD-based linkage map of the Japanese eel, where the maps for female and male spanned 1748.8 cM and 1294.5 cM, respectively, and were arranged into 19 linkage groups. A total of 2,672 SNP markers and 115 Simple Sequence Repeat markers provide anchor points to 1,252 scaffolds covering 151 Mb (13%) of the current genome assembly of the Japanese eel. Comparisons among the Japanese eel, medaka, zebrafish and spotted gar genomes showed highly conserved synteny among teleosts and revealed part of the eight major chromosomal rearrangement events that occurred soon after the teleost-specific genome duplication. CONCLUSIONS: The ddRAD-seq approach combined with the Ion Torrent Personal Genome Machine sequencing allowed us to conduct efficient and flexible SNP genotyping. The integration of the genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits and for investigating comparative genomics of the Japanese eel.

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 TRß (TRßA) cDNA clones were generated by RACE. The TRαA, TRαB and TRßA 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 TRßB reported in a previous study, were analyzed by real-time RT-PCR. The TR mRNA levels in hatched larvae were determined. The two TRß 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 TRßs 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.

Partial characterization and ontogenetic development of pancreatic digestive enzymes in Japanese eel Anguilla japonica larvae.

The pancreatic digestive enzymes, trypsin, chymotrypsin, lipase and amylase were partially characterized, and changes in their activities were examined during the initial ontogeny of Japanese eel Anguilla japonica larvae from 5 to 34 days post-hatching (dph). The pH optima of the eel larval enzymes were narrower than those other fish species; trypsin activity was highest at pH 9, chymotrypsin and amylase activities were highest at pH 7 and 8, and lipase activity was highest at pH 8 and 9. In an analysis of thermal profiles, the larval pancreatic enzymes had a high optimal temperature and high thermal stability, which are typical of fish from the tropics. At 12 and 13 dph, lipase activity and gene expression levels of trypsin (-a and -b), lipase and amylase decreased markedly, suggesting a marked change in larval metabolism at that time. These data could be useful in the development of artificial larval diets in Japanese eel.

The mechanism for primordial germ-cell migration is conserved between Japanese eel and zebrafish.

Primordial germ cells (PGCs) are segregated and specified from somatic cells during early development. These cells arise elsewhere and have to migrate across the embryo to reach developing gonadal precursors. Several molecules associated with PGC migration (i.e. dead-end, nanos1, and cxcr4) are highly conserved across phylum boundaries. However, since cell migration is a complicated process that is regulated spatially and temporally by multiple adaptors and signal effectors, the process is unlikely to be explained by these known genes only. Indeed, it has been shown that there are variations in PGC migration pattern during development among teleost species. However, it is still unclear whether the actual mechanism of PGC migration is conserved among species. In this study, we studied the migration of PGCs in Japanese eel (Anguilla japonica) embryos and tested the migration mechanism between Japanese eel and zebrafish (Danio rerio) for conservation, by transplanting eel PGCs into zebrafish embryos. The experiments showed that eel PGCs can migrate toward the gonadal region of zebrafish embryos along with endogenous PGCs, even though the migration patterns, behaviors, and settlements of PGCs are somewhat different between these species. Our results demonstrate that the migration mechanism of PGCs during embryonic development is highly conserved between these two distantly related species (belonging to different teleost orders).

Distribution of pepsinogen- and ghrelin-producing cells in the digestive tract of Japanese eel (Anguilla japonica) during metamorphosis and the adult stage.

Pepsinogen is the precursor form of the gastric-specific digestive enzyme, pepsin. Ghrelin is a representative gastric hormone with multiple functions in vertebrates, including the regulation of growth hormone release, stimulation of food intake and gastrointestinal motility function. We investigated chronological changes in the distribution of pepsinogen-expressing cells by in situ hybridization and ghrelin-immunoreactive cells by immunohistochemistry in the Japanese eel (Anguilla japonica) during metamorphosis from the leptocephalus sage to the elver stage. The ghrelin-producing cells first appeared in the gastric cecum and pyloric portion of the stomach in the late phase of metamorphosing leptocephali, whereas the pepsinogen-producing cells were first detected in the early phase of the glass-eel stage. These suggest that endocrine cells differentiated earlier than exocrine cells in the eel stomach. Accompanying eel development, the distribution of ghrelin-producing cells spread to the esophagus and other regions of the stomach, but not to the intestine. These results may be related to the changes in dietary habits during metamorphosis in the Japanese eel.

Oceanic spawning ecology of freshwater eels in the western North Pacific.

The natural reproductive ecology of freshwater eels remained a mystery even after some of their offshore spawning areas were discovered approximately 100 years ago. In this study, we investigate the spawning ecology of freshwater eels for the first time using collections of eggs, larvae and spawning-condition adults of two species in their shared spawning area in the Pacific. Ovaries of female Japanese eel and giant mottled eel adults were polycyclic, suggesting that freshwater eels can spawn more than once during a spawning season. The first collection of Japanese eel eggs near the West Mariana Ridge where adults and newly hatched larvae were also caught shows that spawning occurs during new moon periods throughout the spawning season. The depths where adults and newly hatched larvae were captured indicate that spawning occurs in shallower layers of 150-200 m and not at great depths. This type of spawning may reduce predation and facilitate reproductive success.

A close relationship between androgen levels and eumelanogenesis in the teleost red seabream (Pagrus major): Quantitative analysis of its seasonal variation and effects of oral treatment with methyl-testosterone.

Male and female teleost seabream (Pagrus major) were examined for seasonal variation of eumelanin, pheomelanin, 11-ketotestosterone (11KT, fish androgen), lightness (L* value) and Gonad Somatic Index (GSI: gonad mass/body massx100). In males, levels of pyrrole-2,3,5-tricarboxylic acid (a marker of eumelanin), 11KT and the GSI increased sharply from September and plateaued in March and April when the fish are sexually mature. These results are consistent with the lightness of their body color. Using the data from males, a high correlation was observed for all combinations of those four variables (PTCA, 11KT, lightness and GSI). In females, little change was observed in those variables except for the GSI. 4-Amino-3-hydroxyphenylalanine (a marker of pheomelanin) was also analyzed, but it was below the detection limit at all times. Oral treatment of juvenile red seabream with synthetic androgen methyl-testosterone for 2 months induced eumelanin accumulation about 3 times higher than the control. These data show that there is a close relationship between androgen levels and eumelanin accumulation in teleosts. This is the first report that androgen affects melanin accumulation in a dose-dependent manner.

Feeding restriction alters expression of some ATP related genes more sensitively than the RNA/DNA ratio in zebrafish, Danio rerio.

The growth rate of fish shows extensive plasticity in response to various environments. Metabolic responses of fish to excessive nutritional shortages such as starvation have been reported, but the effects of moderate nutrient shortage remain unclear. We examined expression levels of some genes related to ATP metabolism and to myogenesis, the RNA/DNA ratio, and the protein/DNA ratio of fish under different feeding conditions: a diet of 212-432% (frequent feeding, FR) or 32-82% (restricted feeding, RE) of initial body weight per week was supplied. The expression levels of nucleoside diphosphate kinase (NDK)-Z2, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and myogenin genes of RE fish were higher than those of FR fish, although the RNA/DNA ratio and the protein/DNA ratio were unaffected by the feeding amount. Moreover, expression levels of NDK-Z2 and GAPDH were upregulated to a greater extent than those for myogenin and myostatin 1 under restricted feeding. Together, our results show that gene expression is more sensitive to nutrient conditions of fish than traditional indicators such as the RNA/DNA ratio. The ATP metabolic system is more sensitive to moderate nutrient shortages than the myogenic system.

Metabolism of a Glycosaminoglycan during Metamorphosis in the Japanese Conger eel, Conger myriaster.

Hyaluronan (HA) is a linear polysaccharide of high molecular weight that exists as a component of the extracellular matrix. The larvae (leptocephali) of the Japanese conger eel (Anguilliformes: Conger myriaster) have high levels of hyaluronan (HA) which is thought to help control body water content. We isolated glycosaminoglycans (GAGs) from Japanese conger eel leptocephali and measured the changes in tissue HA content during metamorphosis. HA content decreased during metamorphosis. In contrast, neutral sugar content increased during metamorphosis. We hypothesize that the leptocephali utilize a metabolic pathway that converts HA to glucose during metamorphosis. Glucose may then be metabolized to glycogen and stored in the juvenile life-history stage.

The first success of glass eel production in the world: basic biology on fish reproduction advances new applied technology in aquaculture.

The eel has long been esteemed as an important food fish in the world, especially in Japan, and has been used as an experimental fish for many fields of fish physiology. However, the decreases in eel resources have been a serious concern in recent years. The catches of glass eels as seedlings for aquaculture have shown a long-term decrease in both Europe and East Asia. To increase eel resources, the development of techniques for artificial induction of maturation and spawning and rearing their larvae have been eagerly desired. Recent progress of reproductive physiology of fish, especially mechanisms of oocyte maturation and ovulation in female and of spermatozoa maturation in male, facilitate to establish techniques for hormonal induction of maturation and spawning in sexually immature eels. With persistent effort to development of rearing techniques of larvae, we have first succeeded to produce glass eel. These applied techniques are may contribute to understand the basic reproductive physiology of the eel.