Natural stocks of Japanese eel (Anguilla japonica) have decreased drastically because of overfishing, habitat destruction, and changes in the ocean environment over the past few decades. However, to date, artificial mass production of glass eels is far from reality because of the lack of appropriate feed for the eel larvae. In this study, wild glass eel, leptocephali, preleptocephali, and embryos were collected to conduct RNA-seq. Approximately 279 million reads were generated and assembled into 224,043 transcripts. The transcript levels of genes coding for digestive enzymes and nutrient transporters were investigated to estimate the capacities for nutrient digestion and absorption during early development. The results showed that the transcript levels of protein digestion enzymes were higher than those of carbohydrate and lipid digestion enzymes in the preleptocephali and leptocephali, and the transcript levels of amino acid transporters were also higher than those of glucose and fructose transporters and the cholesterol transporter. In addition, the transcript levels of glucose and fructose transporters were significantly raising in the leptocephali. Moreover, the transcript levels of protein, carbohydrate, and lipid digestion enzymes were balanced in the glass eel, but the transcript levels of amino acid transporters were higher than those of glucose and cholesterol transporters. These findings implied that preleptocephali and leptocephali prefer high-protein food, and the nutritional requirements of monosaccharides and lipids for the eel larvae vary with growth. An online database (http://molas.iis.sinica.edu.tw/jpeel/) that will provide the sequences and the annotated results of assembled transcripts was established for the eel research community.

The Japanese eel (Anguilla japonica) is the most prevalent freshwater eel species in Taiwan. However, its population has undergone a significant decline in recent decades due to factors such as overfishing, habitat destruction, and the effects of climate change. Urgent action is needed to conserve this species. Before implementing conservation measures, it is imperative to ascertain the distribution of Japanese eels in Taiwan’s rivers. This study’s primary objective was to assess the effectiveness of eDNA analysis as a method for detecting Japanese eels. To achieve this goal, we compared eDNA analysis data with results obtained from electrofishing, with the Fengshan and Shimen Rivers serving as our designated test sites. Additionally, we collected water samples from 34 other rivers across Taiwan to comprehensively assess the species’ wider distribution using eDNA analysis. Our findings demonstrated eDNA analysis’s viability for detecting Japanese eels. Of the 36 rivers tested, Japanese eel DNA was detected in samples from 21 rivers, scattered across northern, eastern, southern, and western Taiwan, with no specific concentration in any region. We also noted reduced detectability of Japanese eel DNA in highly polluted rivers, indicating that river pollution may have a potential impact on their population. In the future, expanding eDNA analysis to more rivers could identify additional rivers that Japanese eels inhabit. Subsequently, resource management and conservation efforts can be focused on these identified habitats. Furthermore, developing advanced eDNA-based methods for estimating the abundance or biomass of Japanese eels could enhance the flexibility of management and conservation measures.

Recent studies have suggested that plant‐based proteins, such as algal powder, can partially replace fishmeal used in formulated aqua feeds while maintaining the growth performance of aquaculture species. In Taiwan, the traditional pickled cabbage industry produces high‐salinity wastewater rich in nutrients and microelements essential for plant growth. Reusing this nutrient‐rich brine as a medium for microalgae cultivation offers a cost‐effective and sustainable solution. This study aimed to evaluate the feasibility of using Taiwanese pickled cabbage wastewater (TPCW) to cultivate the halotolerant microalgae ( Dunaliella salina ), and of partially replacing fishmeal in Tripneustes gratilla (TG) feed with the resulting algal powder. The experiment consisted of two phases: (1) cultivation of D. salina using seawater partially substituted with varying proportions of TPCW and (2) assessment of the effects of replacing fishmeal with different levels of algal powder on the growth, survival, and gonad index of T. gratilla (0%: TG0, 30%: TG30, 35%: TG35, 40%: TG40, 45%: TG45, and 50%: TG50). Results showed that TPCW significantly enhanced the growth of D. salina , with the TPCW100 group (100% wastewater) displaying the highest growth rate, yielding 10.07 g of algal powder with 59.6% protein. Besides, a notable CO ₂ decline in late culture stages indicated strong carbon uptake. For T. gratilla , the TG0 group exhibited the lowest weight gain and gonad index among all treatments, while TG40 showed the highest, significantly exceeding TG0 and TG30 ( p < 0.05). Moreover, higher replacement levels of fishmeal with algal powder also increased gonad redness and yellowness, suggesting greater accumulation of pigments such as astaxanthin and carotenoids. Overall, this study confirms that agricultural waste can be effectively recycled for algal cultivation, contributing to carbon reduction, and that algal protein can successfully replace fishmeal in sea urchin feed, enhancing both growth and gonad coloration.