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.

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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.

An inverse relation exists between the maturation stage at the start of the oceanic reproductive migration and the migration distance to the spawning grounds for the various eel species. The European eel Anguilla anguilla migrates up to 5-6,000 km and leaves in a previtellogenic state.The shortfinned eel A. australis migrates 2-4,000 km and leaves in an early vitellogenic state.In this study, we compared the early pubertal events in European silver eels with those in silver shortfinned eels to gain insights into the initiation of vitellogenesis. Immediately after being caught, yellow and silver eels of both species were measured and sampled for blood and tissues.Eye index (EI), gonadosomatic index (GSI) and hepatosomatic index (HSI) were calculated.Plasma 11-ketotestosterone (11-KT) and 17β-estradiol (E2) levels were measured by radioimmunoassay. Pituitary, liver and ovaries were dissected for quantitative real-time PCR analyses (pituitary dopamine 2b receptor d2br, gonadotropin-releasing hormone receptors 1 and 2 gnrhr1 and gnrhr2, growth hormone gh and follicle-stimulating hormone-β fshb; liver estrogen receptor 1 esr1; gonad follicle-stimulating hormone receptor fshr, androgen receptors α and β ara and arb, vitellogenin receptor vtgr and P450 aromatase cyp19). Silver eels of both species showed a drop in pituitary gh expression, progressing gonadal development (GSI of ~1.5 in European eels and ~3.0 in shortfinned eels) and steroid level increases. In shortfinned eels, but not European eels, expression of fshb, gnrhr1 and gnrhr2, and d2br in the pituitary was up-regulated in the silver-stage as compared to yellow-stage females, as was expression of fshr, ara and arb in the ovaries. Expression of esr1 in European eels remained low while esr1 expression was up-regulated over 100-fold in silver shortfinned eels. The mechanistic model for anguillid vitellogenesis that we present suggests a first step that involves a drop in Gh and a second step that involves Fsh increase when switching in the life history trade-off from growth to reproduction. The drop in Gh is associated with gonadal development and plasma steroid increase but precedes brain-pituitary-gonad axis (BPG) activation. The Fsh increase marks BPG activation and increased sensitivity of the liver to estrogenic stimulation, but also an increase in D2br-mediated dopaminergic signaling to the pituitary.

In eels, large variations in larval mortality exist, which would impede the viable production of juvenile glass eels in captivity. The transcriptome of European eel larvae was investigated to identify physiological pathways and genes that show differential regulation between non-viable vs. viable larvae. Expression of genes involved in inflammation and host protection was higher, suggesting that non-viable larvae suffered from microbial infection. Expression of genes involved in osmoregulation was also higher, implying that non-viable larvae tried to maintain homeostasis by strong osmoregulatory adaptation. Expression of genes involved in myogenesis, neural, and sensory development was reduced in the non-viable larvae. Expression of the major histocompatibility complex class-I (mhc1) gene, M-protein (myom2), the dopamine 2B receptor (d2br), the melatonin receptor (mtr1), and heat-shock protein beta-1 (hspb1) showed strong differential regulation and was therefore studied in 1, 8, and 15 days post-hatch (dph) larvae by RT-PCR to comprehend the roles of these genes during ontogeny. Expression patterning of these genes indicated the start of active swimming (8 dph) and feed searching behavior (15 dph) and confirmed immunocompetence immediately after hatching. This study revealed useful insights for improving larval survival by microbial control and salinity reduction.