Sillago sihama has high economic value and is one of the most attractive aquaculture species in China. Despite its economic importance, studies of its genome have barely been performed. In this study, we conducted a first genomic survey of S. sihama using next-generation sequencing (NGS). In total, 45.063 Gb of high-quality sequence data were obtained. For the 17-mer frequency distribution, the genome size was estimated to be 508.50 Mb. The sequence repeat ratio was calculated to be 21.25%, and the heterozygosity ratio was 0.92%. Reads were assembled into 1,009,363 contigs, with a N50 length of 1362 bp, and then into 814,219 scaffolds, with a N50 length of 2173 bp. The average Guanine and Cytosine (GC) content was 45.04%. Dinucleotide repeats (56.55%) were the dominant form of simple sequence repeats (SSR).

The spotted scat (Scatophagus argus) is an economically important cultured marine fish that exhibits a typical sexual size dimorphism (SSD). SSD has captivated considerable curiosity for farmed fish production; however, up till now the exact underlying mechanism remains largely unclear. As an important digestive and metabolic organ, the liver plays key roles in the regulation of fish growth. It is necessary to elucidate its significance as a downstream component of the hypothalamic-pituitary-liver axis in the formation of SSD. In this study, the liver physiological differences between the sexes were evaluated in S. argus, and the activity of several digestive and metabolic enzymes were affected by sex. Females had higher amylase, protease, and glucose-6-phosphate dehydrogenase activities, while males exhibited markedly higher hepatic lipase and antioxidant enzymes activities. A comparative transcriptomics was then performed to characterize the responsive genes. Illumina sequencing generated 272.6 million clean reads, which were assembled into 79,115 unigenes. A total of 259 differentially expressed genes were identified and a few growth-controlling genes such as igf1 and igfbp1 exhibited female-biased expression. Further analyses showed that several GO terms and pathways associated with metabolic process, particularly lipid and energy metabolisms, were significantly enriched. The male liver showed a more active mitochondrial energy metabolism, implicating an increased energy expenditure associated with reproduction. Collectively, the female-biased growth dimorphism of S. argus may be partially attributed to sexually dimorphic metabolism in the liver. These findings would facilitate further understanding of the nature of SSD in teleost fish.

Diodon hystrix is a new and emerging aquaculture species in south China. However, due to the lack of understanding of reproductive regulation, the management of breeding and reproduction under captivity remains a barrier for the commercial aquaculture of D. hystrix. More genetic information is needed to identify genes critical for gonadal development. Here, the first gonadal transcriptomes of D. hystrix were analyzed and 151.89 million clean reads were generated. All reads were assembled into 57,077 unigenes, and 24,574 could be annotated. By comparing the gonad transcriptomes, 11,487 differentially expressed genes were obtained, of which 4599 were upregulated and 6888 were downregulated in the ovaries. Using enrichment analyses, many functional pathways were found to be associated with reproduction regulation. A set of sex-biased genes putatively involved in gonad development and gametogenesis were identified and their sexually dimorphic expression patterns were characterized. The detailed transcriptomic data provide a useful resource for further research on D. hystrix reproductive manipulation.

Neuropeptide Y (Npy) is an intricate neuropeptide regulating numerous physiological processes. It is a highly conserved peptide known to improve feed intake in many vertebrates, including fishes. To enlighten the mechanism of Npy in spotted scat feed intake control, we cloned and identified the Npy cDNA sequence. We further examined its expression in some tissues and explored its expression effects at different time frames (hours and days). Here, we discovered that spotted scat Npy comprised a 300 bp open reading frame (ORF) and a 99 amino acid sequence. Npy was identified to be expressed in all tissues examined. Using in situ hybridization examination, we proved that npy has a wide expression in the brain of the spotted scat. Furthermore, the expression of npy in the hypothalamus significantly increased one hour after feeding (p < 0.05). Further, it was revealed that npy expression significantly increased in fish that were fasted for up to 5 days and significantly increased after refeeding from the 8th to the 10th day. This suggests that Npy is an orexigenic peptide, and hence, it increases food intake and growth in the spotted scat. Additionally, results from in vitro and in vivo experiments revealed that Npy locally interacts with other appetite-regulating peptides in the spotted scat hypothalamus. This research aimed to set a fundamental study in developing the feed intake regulation, improving growth and reproduction, which is significant to the aquaculture industry of the spotted scat.

The wild populations of the commercially valuable ornamental fish species, Betta splendens, and its germplasm resources have long been threatened by habitat degradation and contamination with artificially bred fish. Because of the lack of effective marker resources, population genetics research projects are severely hampered. To generate genetic data for developing polymorphic simple sequence repeat (SSR) markers and identifying functional genes, transcriptomic analysis was performed. Illumina paired-end sequencing yielded 105,505,486 clean reads, which were then de novo assembled into 69,836 unigenes. Of these, 35,751 were annotated in the non-redundant, EuKaryotic Orthologous Group, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology databases. A total of 12,751 SSR loci were identified from the transcripts and 7970 primer pairs were designed. One hundred primer pairs were randomly selected for PCR validation and 53 successfully generated target amplification products. Further validation demonstrated that 36% (n = 19) of the 53 amplified loci were polymorphic. These data could not only enrich the genetic information for the identification of functional genes but also effectively facilitate the development of SSR markers. Such knowledge would accelerate further studies on the genetic variation and evolution, comparative genomics, linkage mapping and molecular breeding in B. splendens.

Grass carp is an economically important cultured species in China. Triploid embryo production is widely applied in aquaculture to achieve reproductive sterility, improve somatic growth, and reduce ecological risks associated with uncontrolled breeding. In this study, a simple cold shock method for inducing triploid grass carp was developed. The triploid induction rate of 71.73 ± 5.00% was achieved by applying a cold treatment at 4 °C for 12 min, starting 2 min after artificial fertilization. Flow cytometry and karyotype analysis revealed that triploid individuals exhibited a 1.5-fold increase in DNA content compared to diploid counterparts, with a chromosomal composition of 3n = 72 (33m + 36sm + 3st). Additionally, embryonic transcriptome analysis demonstrated that, in the cold shock-induced embryos, genes associated with abnormal mesoderm and dorsal–ventral axis formation, zygotic genome activation (ZGA), and anti-apoptosis were downregulated, whereas pro-apoptotic genes were upregulated, which may contribute to the higher abnormal mortality observed during embryonic development. Overall, this study demonstrates optimized conditions for inducing triploidy in grass carp via cold shock and provides insights into the transcriptomic changes that take place in cold shock-induced embryos, which could inform future grass carp genetic breeding programs.