Wei Song

Background: The visual system plays critical roles in fish feeding, predator avoidance, and reproduction, with the phototransduction pathway serving as the core molecular mechanism of visual signal transduction. This study represents the first systematic analysis of phototransduction-related genes in large yellow croaker (Larimichthys crocea). Methods: Bioinformatics, transcriptomic analysis, and RT-qPCR were used to identify phototransduction-related genes in large yellow croaker and analyze their developmental expression patterns and responses to different light spectra. Results: Thirty phototransduction-related genes were identified, including genes involved in light perception, signal amplification, and signal termination and recovery. Structural analyses indicated that these genes were highly conserved in teleosts. Most genes showed low expression during 1–7 days post-hatching (dph), increased expression during 7–24 dph, and stable expression during 24–35 dph. Collectively, these results identify 15–24 dph as a critical developmental window for visual system maturation in large yellow croaker larvae. Under different spectral treatments at 15 dph, phototransduction-related genes exhibited wavelength-dependent expression patterns. Under the present experimental conditions, relatively higher expression levels of most phototransduction-related genes were observed under blue- and green-light treatments, whereas relatively lower expression levels were observed under the red-light treatment. Key downstream genes, including gucy2f, guca1d, calml4a, and rgs9b, were significantly affected by different light spectra. Conclusions: This study revealed the developmental dynamics and spectral response characteristics of phototransduction-related genes in the large yellow croaker. These findings provide new insights into teleost visual development and light adaptation and provide a molecular basis for future studies aimed at optimizing light conditions during larval rearing in large yellow croaker aquaculture.

Emerging evidence shows that N6-methyladenosine (m6A) is a post-transcriptional RNA modification that plays a vital role in regulation of gene expression, fundamental biological processes, and physiological functions. To explore the effect of starvation on m6A methylation modification in the liver of Larimichthys crocea (L. crocea) under low temperatures, the livers of L. crocea from cold and cold + fasting groups were subjected to MeRIP-seq and RNA-seq using the NovaSeq 6000 platform. Compared to the cryogenic group, the expression of RNA methyltransferases mettl3 and mettl14 was upregulated, whereas that of demethylase fto and alkbh5 was downregulated in the starved cryogenic group. A Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that the differentially m6A-modified genes were mainly enriched in steroid biosynthesis, DNA replication, ribosome biogenesis in eukaryotes, PPAR, ECM-receptor interaction, lysine degradation, phosphatidylinositol, and the MAPK signaling pathway, suggesting that L. crocea responds to starvation under low-temperature stress through m6A methylation modification-mediated cell growth, proliferation, innate immunity, and the maintenance of lipid homeostasis. This study advances understanding of the physiological response mechanism exerted by m6A methylation modification in starved L. crocea at low temperatures.

Background: The Antarctic krill, Euphausia superba (E. superba), is a key organism in the Antarctic marine ecosystem and has been widely studied. However, there is a lack of transcriptome data focusing on temperature responses. Methods: In this study, we performed transcriptome sequencing of E. superba samples exposed to three different temperatures: −1.19 °C (low temperature, LT), − 0.37 °C (medium temperature, MT), and 3 °C (high temperature, HT). Results: Illumina sequencing generated 772,109,224 clean reads from the three temperature groups. In total, 1,623, 142, and 842 genes were differentially expressed in MT versus LT, HT versus LT, and HT versus MT, respectively. Moreover, Kyoto Encyclopedia of Genes and Genomes analysis revealed that these differentially expressed genes were mainly involved in the Hippo signaling pathway, MAPK signaling pathway, and Toll−like receptor signaling pathway. Quantitative reverse-transcription PCR revealed that ESG037073 expression was significantly upregulated in the MT group compared with the LT group, and ESG037998 expression was significantly higher in the HT group than in the LT group. Conclusions: This is the first transcriptome analysis of E. superba exposed to three different temperatures. Our results provide valuable resources for further studies on the molecular mechanisms underlying temperature adaptation in E. superba.

PIWI-interacting RNAs (piRNAs) are an emerging class of small RNAs which protect the animal germline genome against deleterious transposable elements. Nevertheless, the characteristics and sex-related expression patterns of piRNA in Collichthys lucidus remain unknown. In this study, we first performed systematic next-generation high-throughput sequencing in C. lucidus ovaries and testes. We identified 3,027,834 piRNAs across six gonad libraries. Of these, 2225 piRNAs were differently expressed between testes and ovaries; 1195 were upregulated and 1030 downregulated in the testes. Interestingly, the potential target genes of 208 differentially expressed piRNAs had sex-related functions, including germ cell development, gonad development, ovarian follicle development, gamete generation, spermatid development, and spermatogenesis. Moreover, these target genes are involved in the TGF-β, Wnt, MAPK, mTOR, VEGF, and PI3K-Akt pathways. Further, 10 piRNAs were derived from Nectin2 and Mea1, which play important roles in sexual reproduction, male gamete generation, and germ cell development. We also identified 5482 piRNA clusters across the gonads, among which 139 piRNA clusters were uniquely expressed in the testes and 98 in the ovaries. The expression of core sex-related piRNA was validated by real-time PCR. Overall, our findings provide significant insights into C. lucidus’ sex-related piRNAs.

The world-famous Antarctic krill (Euphausia superba) plays a fundamental role in the Antarctic food chain. It resides in cold environments with the most abundant biomass to support the Antarctic ecology and fisheries. Here, we performed the first genome survey of the Antarctic krill, with genomic evidence for its estimated genome size of 42.1 gigabases (Gb). Such a large genome, however, is beyond our present capability to obtain a good assembly, although our sequencing data are a valuable genetic resource for subsequent polar biomedical research. We extracted 13 typical protein-coding gene sequences of the mitochondrial genome and analyzed simple sequence repeats (SSRs), which are useful for species identification and origin determination. Meanwhile, we conducted a high-throughput comparative identification of putative antimicrobial peptides (AMPs) and antihypertensive peptides (AHTPs) from whole-body transcriptomes of the Antarctic krill and its well-known counterpart, the whiteleg shrimp (Penaeus vannamei; resident in warm waters). Related data revealed that AMPs/AMP precursors and AHTPs were generally conserved, with interesting variations between the two crustacean species. In summary, as the first report of estimated genome size of the Antarctic krill, our present genome survey data provide a foundation for further biological research into this polar species. Our preliminary investigations on bioactive peptides will bring a new perspective for the in-depth development of novel marine drugs.

The complete mitochondrial genome DNA sequence of Cryodraco antarcticus was 17,857 bp in size. It consists of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and one control region. Among 22 tRNA genes, 8 tRNAs were encoded on the L-strand. The overall base composition of the genome is 26.45% for A, 25.96% for T, 29.78% for C, and 17.81% for G. The phylogenetic tree suggested C. antarcticus was genetically closest to some species in family Channichthyidae. This study could provide valuable information for further studies on population structure, conservation genetics and molecular evolution of C. antarcticus.

In this study, the complete mitochondrial genome of Pagetopsis macropterus was obtained, which was 17,342 bp including 2 ribosomal RNAs, 13 protein-coding genes, 22 transfer RNAs, and one control region. Of the 37 genes, 28 were encoded on the heavy strand, while 9 were encoded on light strand. The overall nucleotide composition of mitogenome is 27.08% for A, 25.75% for T, 29.78% for C, 17.39% for G, respectively, in accordance with structural characteristics of AT rich. Further, the phylogenetic tree based on complete mtDNA sequences revealed that the P. macropterus was closest to some species of Channichthyidae. This study could provide some valuable information for the studies on evolution for low-temperature adaptability, stock evaluation, and population genetics of P. macropterus.