Yanfeng Zhou

Neosalanx taihuensis is a fish species endemic to China, primarily distributed in the middle and lower reaches of the Yangtze and Huaihe rivers and their affiliated lakes. To assess its resource status and facilitate targeted conservation of genetic diversity, we analyzed genetic differences among populations in the lower Yangtze River. Samples were collected from four natural river populations (JJ, AQ, NJ, and TZ) and one lacustrine population (THL). Whole genome resequencing was performed to characterize genetic diversity, population structure, and selection signatures across the five populations. The results showed no obvious genetic divergence among the natural river populations, whereas all natural river populations were distinctly separated from the THL population. The natural river populations harbored higher genetic diversity than the THL population. Gene flow analysis suggested that historical gene exchange might have occurred between TZ and THL, as well as between TZ and NJ. Selective sweep analysis identified Chr01, Chr04, Chr09, and Chr15 as candidate genomic regions potentially carrying adaptive selection signatures. In summary, conservation efforts should prioritize the genetic diversity of both natural river populations and the THL population, facilitate gene flow among populations, and adopt differentiated management strategies for each group.

A small cold-water teleost endemic to Northeast Asia, Hypomesus nipponensis possesses a short lifecycle, high fecundity, and rapid population growth, with extensive introductions for aquacultural purposes across East Asia. In this study, we generated a gap-free, telomere-to-telomere (T2T) genome assembly of H. nipponensis using a combined sequencing strategy, incorporating MGI short reads, PacBio High-Fidelity (HiFi) reads, Oxford Nanopore Technologies (ONT) ultra-long reads, and Hi-C data. The final assembly spans 526.31 Mb with a contig N50 of 20.23 Mb, and all genomic sequences were successfully anchored to 28 pseudochromosomes. BUSCO assessment (Actinopterygii_odb10) confirms 98.19% completeness, including 3,548 single-copy and 26 duplicated orthologs out of 3,640 conserved genes. Repeat elements account for 39.17% (206.18 Mb) of the genome, and 31,310 protein-coding genes are annotated. This gap-free T2T assembly resolves previously uncharacterized genomic regions, providing a high-quality reference for molecular breeding, evolutionary analyses of the Hypomesus genus, and functional investigations into adaptive traits of cold-water fishes.

Protosalanx chinensis is a suitable particular species for genetic studies on nearly scaleless skin, transparency and high sensitivity to hypoxia stress. Here, we generated a high-quality chromosome-level de novo assembly of P. chinensis. The final de novo assembly yielded 379.47 Mb with 28 pseudo-chromosomes and a scaffold N50 length of 14.52 Mb. In total, 21,074 protein-coding genes were predicted. P. chinensis, Esox lucius and Hypomesus transpacificus had formed a clade, which diverged about 115.5 million years ago. In the air exposure stress experiment, we found that some genes play an essential role during P. chinensis hypoxia, such as bhlh, Cry1, Clock, Arntl and Rorb in the circadian rhythm pathway. These genomic data offer a crucial foundation for P. chinensis ecology and adaptation studies, as well as a deeper understanding of the response to air exposure stress.

Air exposure is a common stress for Corbicula fluminea, an economically important freshwater shellfish consumed in China, during aquaculture and transportation. However, little is known about its molecular responses to air exposure. Therefore, this study used a combination of PacBio full-length and Illumina transcriptomes to investigate its molecular responses to air exposure. A total of 36,772 transcripts were obtained using PacBio sequencing. Structural analysis identified 32,069 coding sequences, 1906 transcription factors, 8873 simple sequence repeats, and 17,815 long non-coding RNAs. Subcellular localization analysis showed that most transcripts were located in the cytoplasm and nucleus. After 96-h of air exposure, 210 differentially expressed genes (DEGs) in the gill were obtained via Illumina sequencing. Among these DEGs, most of the genes related to glycolysis, tricarboxylic acid cycle, lipid metabolism, and amino acid metabolism were upregulated. Additionally, many DEGs associated with immunity, cytoskeleton reorganization, autophagy, and ferroptosis were identified. These findings indicated that metabolic strategy change, immune response, cytoskeleton reconstruction, autophagy, and ferroptosis might be the important mechanisms that C. fluminea use to cope with air exposure. This study will enrich the gene resources of C. fluminea and provide valuable data for studying the molecular mechanisms coping with air exposure in C. fluminea and other freshwater mollusks.

Using systemic, periodic surveys from 2015 to 2019, population distribution, speculated age and habitat preference were analyzed to assess the living status for the Silver Carp (Hypophthalmichthys molitrix) in the lower Yangtze River. Small Silver Carps became more temporarily abundant in spring and autumn, and the catch per unit effort (CPUE) fluctuated yearly. Spatially, going from Anqing (AQ) to Changshu (CS), Silver Carps in the 200 mm standard length(SL) group became less abundant, whereas those in the 400–600 mm and >600 mm SL groups steadily increased. According to the Von Bertalanffy growth equation, the Silver Carp exhibits isometric growth, and the inflection point of SL and body weight (BW) were 564.01mm and 2948.31g, respectively, with a growth characteristic index (φ) of 5.0655. The fish dominant age range was 0+ to 5 years, reflecting the young age composition of the fish. Furthermore, the habitat survey findings revealed that the Silver Carp has the different preference on habitat selection in different life history. Juvenile Silver Carps were comparatively staying in the lower Yangtze River, where there exists a relatively stable bifurcated river. Adult fishes were mostly found in the CS and Nantong(NT) section where the river is wide and the food is rich. When compared with the historical survey data, it was found that the Silver Carp live in the AQ through NT section. The living status and perspective of the Silver Carp in the lower reach of the Yangtze River were clarified, and future work should be more concerned with the strengthening of conservation and the restoration of adequate habitat.

The salangid Neosalanx taihuensis (Salangidae) is a commercially important economical fish endemic to China and restricted to large freshwater systems with a wide-ranging distribution. This fish species has continuous distribution ranges and a long-introduced aquaculture history in Chinese basins. However, the research on its population genetic differentiation within and between basins is very limited. In this regard, 197 individuals were sampled from 11 populations in the Nenjiang River Basin (A1–A4), Songhua River Basin (B1), Yellow River Basin (C1–C2), Yangtze River Basin (D1), Lanchang River Basin (E1–E2) and Huaihe River Basin (F1). Based on the COI sequence, the N.taihuensis population’s genetic difference within and between river basins was investigated. The haplotypes and their frequency distributions were strongly skewed, with most haplotypes (n = 13) represented only in single samples each and thus restricted to a single population. The most common haplotype (H4, 67/197) was found in all individuals. The analysis of molecular variance (AMOVA) revealed a random pattern in the distribution of genetic diversity, which is inconsistent with contemporary hydrological structure. The mismatch between the distribution and neutrality tests supported the evidence of a population expansion, which occurred during the late Pleistocene (0.041–0.051 million years ago). Significant levels of genetic subdivision were detected among populations within basins rather than between the six basins. Population history dynamics showed that N. taihuensis experienced an expansion during the glacial period in the late Pleistocene. Therefore, different populations should be considered as different management units to achieve effective conservation and management purposes. These results have great significance for the evaluation and exploitation of the germplasm resources of N. taihuensis.

Due to its ability to collect and remove aquaculture waste, an in-pond raceway system (IPRS) has been used to decrease the uncontrolled waste discharge in the traditional cage aquaculture method in large water bodies. However, when applied to large water bodies, its environmental performance is still lacking. This study focused on analyzing the microbial characteristics and the interaction between largemouth bass (gill and gut) microbiota and the environment (water and sediment) microbiota of an IPRS. Further, it revealed the primary relationship from the perspective of microbiota in the IPRS. The results show that (1) the alpha diversity of microbiota in the water is significantly lower than that of fish and sediment. The relationship between water microbiota and fish microbiota is limited. (2) The water microbiota inside and outside the tank showed high similarity and were not significantly affected by environmental factors. (3) The SourceTrack analysis showed that fish microbiota is one of the primary sources of sediment microbiota, and more than 15% of the sediment microbiota come from fish. Microbes such as Faecalibacterium, Escherichia-Shigella, and Bacteroides can significantly enrich the sediment. Our study revealed the characteristics and preliminary interaction of fish and environmental microbiota in the IPRS. It provided a reference for evaluating microbial health status in the application of IPRS in large water bodies’ aquaculture.

Early development, when many important developmental events occur, is a critical period for fish. However, research on the early development of clearhead icefish is very limited, especially in molecular research. In this study, we aimed to explore the dynamic changes in the biological functions of five key periods in clearhead icefish early development, namely the YL (embryonic), PM (first day after hatching), KK (fourth day after hatching), LC (seventh day after hatching), and SL (tenth day after hatching) stages, through transcriptome sequencing and different analysis strategies. A trend expression analysis and an enrichment analysis revealed that the expression ofgenes encoding G protein-coupled receptors and their ligands, i.e., prss1_2_3, pomc, npy, npb, sst, rln3, crh, gh, and prl that are associated with digestion and feeding regulation gradually increased during early development. In addition, a weighted gene co-expression network analysis (WGCNA) showed that eleven modules were significantly associated with early development, among which nine modules were significantly positively correlated. Through the enrichment analysis and hub gene identification results of these nine modules, it was found that the pathways related to eye, bone, and heart development were significantly enriched in the YL stage, and the ccnd2, seh1l, kdm6a, arf4, and ankrd28 genes that are associated with cell proliferation and differentiation played important roles in these developmental processes; the pak3, dlx3, dgat2, and tas1r1 genes that are associated with jaw and tooth development, TG (triacylglycerol) synthesis, and umami amino acid receptors were identified as hub genes for the PM stage; the pathways associated with aerobic metabolism and unsaturated fatty acid synthesis were significantly enriched in the KK stage, with the foxk, slc13a2_3_5, ndufa5, and lsc2 genes playing important roles; the pathways related to visual perception were significantly enriched in the LC stage; and the bile acid biosynthetic and serine-type peptidase activity pathways were significantly enriched in the SL stage. These results provide a more detailed understanding of the processes of early development of clearhead icefish.