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.

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.

Developing an optimal larval diet for Japanese eel ( Anguilla japonica ) remains a major bottleneck in artificial seedling production due to the limited efficacy of conventional heuristic formulation methods. We implemented a data-driven, human-in-the-loop optimization framework based on Bayesian optimization (BO) and Gaussian process regression (GPR) to systematically refine shark egg yolk-free diets. Across eight sequential feeding trials, the ingredient ratios of seven key components were iteratively adjusted, guided by empirical expert insight. Survival rate and total length (TL) were measured from 6 to 100 days post-hatch (dph). Multi-objective optimization targeted simultaneous improvement in survival and growth during the early (6–40 dph) and late (41–80 dph) periods. The optimized diet formulations achieved survival rates up to 74.9% versus 30.7% in controls and mean TL of 40.1 mm versus 35.2 mm ( p < 0.05) at 100 dph. These results were consistently reproduced in independent validation trials. Mechanistic modeling via Random Forest and SHapley Additive exPlanations (SHAP) revealed that stage‑specific balancing of yeast extract-derived nutrients and other macronutrient components were critical drivers of improved survival and growth. To our knowledge, this is the first reported application of BO to larval feed optimization in Japanese eel. Our framework integrates probabilistic modeling with expert input to reduce experimental burden and accelerate development of superior larval diet formulations. This approach offers a practical, broadly applicable template for feed innovation across aquaculture species.

Heterochrony is a major mode of vertebrate body plan evolution, yet its molecular and cellular basis remains poorly characterized. Here, we show that axis segmentation in Anguilla japonica —a species that forms 120 vertebrae—is driven by the temporal extension of somitogenesis. This is achieved through the prolonged maintenance of axial progenitors in the tail beyond the hatching stage, coupled to an extreme segment scaling regime that operates under the constraint of minimal axis growth. We identify delayed Hox13 activation and sustained Oct4 expression as molecular signatures of the prolonged segmentation program. Furthermore, we describe two spatially distinct axial progenitor pools that expand stemness in the tail. These findings reveal how the modulation of stemness in time and space drives extreme morphological evolution in vertebrates. One-Sentence Summary: Spatiotemporal modulation of stemness drives extreme axis segmentation in the Japanese eel.

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