The proteasome is a highly conserved polycatalytic enzyme that is required for cellular processes and is widely present in the nucleus and cytoplasm of archaea, as well as all eukaryotes. A total of 22 members of the proteasome subunit (CiPS) gene family were identified and characterized by scanning the grass carp (Ctenopharyngodon idella) genome. These genes were classified into two subfamilies, CiPSA and CiPSB, based on phylogenetic analysis, which was consistent with the results from other species. We examined the response of this gene family to high density and saline-alkali stresses in aquaculture using publicly available transcriptome data resources. In grass carp, CiPS member transcripts were detected in all tested tissues, with the highest expression level in the head kidney and the lowest in the liver. According to transcriptome-based expression analysis, CiPS genes play a role in response to environmental stresses in grass carp, mainly in the form of negative regulation. Interestingly, a cluster of members belonging to the CiPSB subfamily on a 15 kb region on chromosome segment CI01000319, including CiPSB8, 9, 9b, and 10, showed marked responses to high density and saline-alkali stress. It appears that CiPS genes confer stress tolerance through the regulation of common genes, as well as specific genes. In summary, our genome-wide characterization, evolutionary, and transcriptomic analysis of CiPS genes in grass carp provides valuable information for characterizing the molecular functions of these genes and utilizing them to improve stress tolerance in aquaculture.

The brown frog (Rana dybowskii) exhibits a wide distribution and is extensively cultured in northeast China. This species undergoes a prolonged period of hibernation lasting from several months to half a year. The frog’s fallopian tubes are considered a valuable tonic medicine known as “Oviducts Ranae” in traditional Chinese medicine. To enhance comprehension of the molecular mechanism underlying the process of emergence from hibernation, a transcriptome-based comparative analysis was performed on differentially expressed genes (DEGs) across various organs of female frogs during hibernation and upon emergence. The organs examined encompassed the brain, liver, spleen, fallopian tube, and ovary. Subsequently, GO and KEGG enrichment analyses were performed to gain further insights into these DEGs. A total of 51,634 transcripts were identified in all five tissues. The spleen exhibited the highest number of DEGs, with 3651 members, while the liver, brain, and fallopian tube had 3182, 3115, and 3186 DEGs, respectively. The ovary had the lowest number of DEGs, with only 1661. Interestingly, only 45 genes were found to be differentially expressed in all five tissues, and GO enrichment analysis revealed distinct functional differences among the DEGs in the various tissues. Only two meaningful DEG-enriched KEGG pathways, “00310 Lysine degradation” and “05202 Transcriptional misregulation in cancer”, were present in all five tissues, and the pathway “B 09182 Protein families: genetic information processing” was significantly enriched in four tissues except the ovary, and it had the most enriched DEGs. Our findings offer insights to grasp the factors that need to be controlled in the design of overwintering sites and offer a novel perspective for the conservation and management of the overwintering population of female R. dybowskii.

Ship sturgeon (Acipenser nudiventris) is a critically endangered fish that is listed on the International Union for Conservation of Nature’s Red List of Threatened Species. Sixteen individuals from the Chinese section of the Ili River were genotyped using genome re-sequencing technology. By applying a genomic relatedness estimation with 1,527,694 genome-wide SNP markers, we found that the coancestry coefficients showed a high level of relatedness between individuals. The effective population sizes over 500 generations were estimated, and this showed that the effective population sizes began to dramatically decline from about 14,840 to 171 individuals when going back four generations from the current population. Artificial reproduction techniques guided by genomic relatedness may be a valuable approach to the conservation of this critically endangered fish species.