Konosirus punctatus is an important species for the structure of marine ecosystems. Meanwhile, it is a native species in the northwest Pacific Ocean and supports important commercial fishery. In the present study, we generated the whole transcriptome of K. punctatus from combined tissues (muscle, liver, gill, heart, kidney, swim bladder and sexual gland) using Illumina RNA-seq technology and a total of 46087110 clean reads were obtained, corresponding to 6531521430 nucleotides. Meanwhile, 10000 clean reads were randomly selected and compared with NT database to examine the possible contamination. Results showed that 6754 clean reads were distributed among some species closely related with K. punctatus, indicating no-pollution. De novo assembly was performed and all clean reads were assembled to produce 71610 longest unigenes with an N50 of 906 bp. Among all the unigenes, 43974 unigenes were annotated in at least one database and 3172 unigenes were annotated in all databases. All unigenes were further analyzed to predict the gene structure and we have obtained a total of 54864 coding sequences (CDSs) and 17326 simple sequence repeats (SSRs). Saturation analyses were applied to evaluate the accuracy of gene expression and we hypothesized that the detection of gene expression might be effective. Finally, single-copy orthologous genes were applied to construct the phylogenetic relationship of K. punctatus. Results showed that K. punctatus diverged from the common ancestor with Alosa alosa, Alosa pseudoharengus and Sardina pilchardus at approx. 61.16–92.52 MYA. The present study will provide a foundational molecular information for the biological research of K. punctatus.

Environmental DNA (eDNA) has the potential for quantitative biomass estimation, but its application in open marine cages remains challenging due to biological variability and seawater current conditions. Here, we evaluated an eDNA-based framework for estimating biomass of cage-cultured Thamnaconus modestus by integrating controlled experiments with field calibration under different current conditions. Under controlled conditions, eDNA concentration increased with total fish biomass, whereas eDNA signals per unit biomass showed patterns associated with individual body size and population size structure. Based on five field calibration observations, pond-to-cage conversion coefficients showed a positive association with model-derived instantaneous seawater current speed. This relationship was preliminarily evaluated using three temporally separated observations from a single cage site (site B), resulting in absolute percentage errors of 11.6%, 23.2%, and 26.8% and an overall mean absolute percentage error (MAPE) of 20.5%. These preliminary results suggest that combining size-matched biological references with current-dependent calibration may provide a potential approach for improving eDNA-based biomass estimation in marine cages.