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The light spectrum is a vital environmental factor for the culture of fish, and the welfare of farmed fish is a crucial issue in aquaculture. In this study, Nile tilapia (Oreochromis niloticus, GIFT strain) juveniles were exposed to full-spectrum (LW), red (LR), yellow (LY), or blue (LB) light. After the 45-day experiment, growth performance, stress responses, and aggressive behaviors were evaluated, and transcriptomic analysis was carried out. The results revealed that LW and LR positively affected growth performance. At the same time, LY and LB had a negative effect. Light spectrum induced stress responses of juvenile fish exposed to LY, under which the total antioxidant capacity (T-AOC) and cortisol (COR) contents were the highest. The activities of α-amylase (AMS), protease (PES), and lipase (LPS) in the digestive tract showed a similar tendency, indicating that the light spectra altered the digestive enzyme activities and then affected growth. Behavioral analyses showed increased chase and bite activities of tilapia juveniles exposed to LW and LY. The affected functions included the nervous system, muscle morphogenesis, and immune system-related regulation. Enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways include the tryptophan metabolism signaling pathway, protein digestion and absorption signaling pathway, Jak-STAT signaling pathway, arachidonic acid metabolism signaling pathway, and alpha-linolenic acid metabolism signaling pathway. Overall, light spectra influenced the welfare of farmed tilapia juveniles in terms of growth, stress, and behavior. Our results suggested that LR should be used in juvenile tilapia culture.

The Mozambique tilapia (Oreochromis mossambicus) is a fascinating taxon for evolutionary and ecological research. It is an important food fish and one of the most widely distributed tilapias. Because males grow faster than females, genetically male tilapia are preferred in aquaculture. However, studies of sex determination and sex control in O. mossambicus have been hindered by the limited characterization of the genome. To address this gap, we assembled a high-quality genome of O. mossambicus, using a combination of high coverage of Illumina and Nanopore reads, coupled with Hi-C and RNA-Seq data. Our genome assembly spans 1,007 Mb with a scaffold N50 of 11.38 Mb. We successfully anchored and oriented 98.6% of the genome on 22 linkage groups (LGs). Based on re-sequencing data for male and female fishes from three families, O. mossambicus segregates both an XY system on LG14 and a ZW system on LG3. The sex-patterned SNPs shared by two XY families narrowed the sex determining regions to ∼3 Mb on LG14. The shared sex-patterned SNPs included two deleterious missense mutations in ahnak and rhbdd1, indicating the possible roles of these two genes in sex determination. This annotated chromosome-level genome assembly and identification of sex determining regions represents a valuable resource to help understand the evolution of genetic sex determination in tilapias.

The dojo loach Misgurnus anguillicaudatus is an important economic species in Asia because of its nutritional value and broad environmental adaptability. Despite its economic importance, genomic data from M. anguillicaudatus was unavailable. In the present study, we conducted a genome survey of M. anguillicaudatus using next-generation sequencing technology. Its genome size was estimated to be 1105.97 Mb by using K-mer analysis, and its heterozygosity ratio, repeat sequence content, GC content were 1.45%, 58.98%, and 38.03%, respectively. A total of 376,357 microsatellite motifs were identified and mononucleotides, with a frequency of 42.57%, were the most frequently repeated motifs, followed by 40.83% dinucleotide, 7.49% trinucleotide, 8.09% tetranucleotide, and 0.91% pentanucleotide motifs. The AC/GT, AAT/ATT, and ACAG/CTGT repeats were the most abundant motifs among dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. Besides, a complete mitochondrial genome was sequenced. Based on the maximum likelihood and Bayesian inference analyses, M. anguillicaudatus in this study was the “introgressed” mitochondrial type. Furthermore, a total of 376,357 SSR motifs were detected from the genome survey assembly. Seventy microsatellite loci were randomly selected from these SSR loci to test polymorphic, of which, twenty microsatellite loci were assessed in 30 individuals from a wild population. The number of alleles (Na), observed heterozygosity (Ho), and expected heterozygosity (He) per locus ranged from 7 to 19, 0.400 to 0.933, and 0.752 to 0.938, respectively. All twenty loci were highly informative (PIC > 0.700). Eight loci deviated from Hardy–Weinberg equilibrium after Bonferroni correction (P M. anguillicaudatus, and genome information, mitochondrial genome, and microsatellite markers will be valuable for further studies on population genetic analysis, natural resource conservation, and molecular marker-assisted selective breeding.