Bin Zhu

Genomic resources for Tor species are currently limited, and their molecular systematics remain poorly resolved. In this study, we report the first chromosome-level genome assembly of Tor sinensis, generated using PacBio long-read sequencing and Hi-C scaffolding. The final genome assembly spans approximately 1.80 Gb and consists of 228 contigs, with a contig N50 of 31.67 Mb. A total of 97 contigs were successfully anchored and ordered into 50 chromosomes, covering 96.57% of the genome. Chromosome lengths range from 23.67 Mb to 62.88 Mb. Repeat analysis identified 807.40 Mb of repetitive sequences, representing 44.84% of the genome. In addition, 3,794 rRNA genes and 11,264 tRNA genes were annotated, along with 379 snRNAs and 35 snoRNAs. The average length of tRNA genes was 72 bp. A total of 62,000 protein-coding genes were predicted, yielding 263,453 protein sequences. This high-quality reference genome provides a valuable foundation for future studies and facilitate comparative genomic analyses across the Tor genus and support biodiversity conservation efforts in the Lancang-Mekong River basin.

Introduction: The Han River Basin, a critical water source for the South-to-North Water Diversion Project, faces escalating eutrophication pressures due to intensive anthropogenic activities. This study aims to systematically evaluate the ecological responses of phytoplankton and bacterial communities to eutrophication gradients, and to elucidate their interactions for guiding ecosystem restoration. Methods: Water samples were collected from 15 sites across the Han River Basin in July 2023. Phytoplankton composition was identified microscopically (6 phyla, 33 genera), and bacterial communities were characterized via high-throughput sequencing of the 16S rRNA gene. Trophic states were assessed using a modified Carlson’s Trophic State Index (TSI). Relationships between environmental variables (TN, TP, Chl-a, COD, etc.) and community structures were analyzed via Monte Carlo tests, redundancy analysis (RDA), and co-occurrence network analysis. Results: Eutrophication Status: 75% of sites were eutrophic (TSI: 42.5–66.0), with significant spatial variations in TN (1.10–6.00 mg/L), TP (0.010–0.29 mg/L), and Chl-a (0.86–70.00 μg/L). Community Shifts: Phytoplankton dominance transitioned from Bacillariophyta in low-TSI areas to Cyanophyta in high-TSI regions. Bacterial communities were dominated by Proteobacteria (>60% abundance), with diversity declining as eutrophication intensified. Environmental Drivers: Monte Carlo tests indicated Chl-a and COD as key drivers for bacteria ( p < 0.05), while TN primarily influenced phytoplankton ( r = 0.39, p < 0.01). Network Interactions: Co-occurrence networks revealed increased negative correlations (0.32% to 0.61%) and reduced modularity (0.641 to 0.558) under eutrophic conditions, suggesting intensified competition. Conclusion: Eutrophication filters species adaptability, leading to deterministic succession in phytoplankton and homogenization of bacterial communities. The rise in negative correlations underscores escalating resource competition, potentially destabilizing ecosystem functions. Our findings emphasize the urgency of nutrient load reduction and adaptive management. Future studies should prioritize leveraging phytoplankton-bacterial synergism for bioremediation and resilience enhancement.

Human activities have altered rivers worldwide, but how their combined effects shape fish assemblages remains unclear. We therefore surveyed fish and habitats seasonally along the middle and lower reaches of the Han River, China, during 2022, specifically in June–August (wet season) and October–November (dry season). This study analyzed the spatial distribution pattern of fish diversity, explored the effects of natural factors (e.g., hydrology, water quality) and human stressors (e.g., dam, land use) on the spatial pattern of fish diversity, and identified the key driving factors. Cluster analysis and Non-metric Multidimensional Scaling (NMDS) showed that the fish communities could be divided into three groups: the Danjiangkou reservoir area (DRA), the middle reaches (MR), and the lower reaches (LR). For α-diversity, the LR had the highest value, followed by the DRA, with the MR being the lowest. For β-diversity, the MR had the highest value, followed by the LR, with the DRA being the lowest. Random Forest model showed that fish diversity was mainly affected by natural factors; among these factors, the key drivers of α-diversity were hydrological factors such as the water level (3.56–5.97%) and river width (4.53–4.69%), while for β-diversity, the key drivers were water quality factors, including the dissolved oxygen (10.08–12.36%), total nitrogen (6.49–9.31%), and chlorophyll a (8.26–8.40%). Structural Equation Modeling further revealed that natural factors affected β-diversity mainly through direct pathways, while human stressors affected β-diversity mainly through indirect pathways. The results revealed the differential roles of natural factors and human stressors in driving the patterns of fish α-diversity and β-diversity in human-disturbed rivers, which will provide a scientific basis for the conservation of fish diversity in the Han River.

This study examines the genetic diversity and population structure of silver carp (Hypophthalmichthys molitrix), an ecologically and economically important freshwater species. Samples were collected from 17 sites along the Yangtze River, including LCH, LCS, LJHK, and LXZX, as well as one population from the United States (SV). Restriction-site associated DNA sequencing (RAD-seq) generated 759,453 high-quality single-nucleotide polymorphisms (SNPs) for population genomic analyses, including genetic differentiation (F_ST), population structure, and linkage disequilibrium (LD) decay. Genetic variation was primarily found within populations (78.05%), with 21.94% among populations. Most sites exhibited low genetic differentiation (F_ST < 0.05), suggesting high admixture along the river, although a few sites displayed elevated values (F_ST > 0.15). Rapid LD decay in LCH, LCS, and LJZ indicated frequent recombination and moderate to large effective population sizes. These patterns reflect the influence of geographic and ecological factors on population structure. Conservation strategies should maintain genetic connectivity while protecting distinct genetic resources. Populations with high differentiation, such as LXZX and LWZ, warrant targeted management to preserve unique genetic diversity.

The Bighead carp (Hypophthalmichthys nobilis), a primary freshwater aquaculture species in China, faces challenges due to over-exploitation and environmental changes. We leveraged RAD-seq to perform a comprehensive population genetic analysis on 14 H. nobilis populations sampled from the Yangtze River (13 populations) and the Marseilles Reach of the Illinois River (one population). Analysis of genetic diversity showed that different parameters demonstrated varied inferences, and notably, Zhongxian (ZX2), Wanhzou (WZ2), Yangzhou hatchery (YZYZ), Yangzhou (YZ), and Taihu (TH) populations showed apparent heterozygote deficiency. Linkage disequilibrium (LD) analysis exhibited a trend of higher linkage disequilibrium in populations from the upper reaches of the Yangtze River, followed by those from the middle reaches and then those from the lower reaches. Additionally, the reconstructed polygenetic tree and PCA plot clustered all populations into 2 major subgroups, while the results of structure analysis indicated 4 ancestors. The pairwise F_ST values ranged from 0 to 0.5530. Among these, high F_ST values (0.1931–0.5530) were only observed between populations WZ2, YZ, YZYZ, and the remaining 11 populations. Furthermore, genetic bottlenecks were observed in all populations 20–30 thousand years ago. Overall, the research offers insights essential for genetic management practices for sustainable aquaculture and biodiversity conservation of bighead carp.

Underwater noise pollution caused by human activities may affect freshwater cetaceans to different degrees. To analyze the impacts of water intake pontoons on Yangtze finless porpoises (Neophocaena asiaeorientalis), this study collected underwater noise data from such a pontoon in a nature reserve, plotted the power spectral density of acoustic signals, and calculated the root mean square sound pressure levels and the magnitude of sound source levels. The 1/3-octave sound pressure level root mean square values at the transient holding pens were <18.0 kHz, 39.5−60.0 kHz, which were slightly higher than the Yangtze finless porpoise hearing threshold curve values and therefore could be perceived. However, the results indicated that the porpoises would not develop a temporary hearing threshold shift. Meanwhile, pontoon noise did not interfere with the porpoises’ high-frequency acoustic signal nor did it affect their echolocation; it significantly interfered with their low-frequency acoustic signal, however, and the mother–child communication of the finless porpoises was affected, but this effect was quickly compensated due to the limited space range of the holding pens. Through this study of Yangtze finless porpoises, this paper provides a reference for assessing whether human facilities have impacts on freshwater cetaceans.

Seasonal water-level fluctuations may lead to changes in river nutrients, which causes corresponding changes in the trophic structure of an aquatic food web, and finally affects the whole ecosystem. In this study, we focused on the Ganjing River, a tributary of the Yangtze River, China. Common organisms were sampled and measured for carbon and nitrogen stable isotopes in the wet and dry seasons, respectively, and the relative contributions of different food sources were combined to construct the food web, so as to realize the influence of water-level fluctuation on aquatic food web. Our results showed that basal food sources for fish consumers were endogenous carbon sources such as POM, zooplankton and zoobenthos in the dry season, while high water level exposed fish to more diverse and abundant food sources, and the contribution proportions of exogenous carbon sources (e.g., terrestrial detritus) to consumers increased in the wet season. In parallel, the abundance and species diversity of fish were higher than those in the dry season. Most fish species had relatively higher trophic levels in the dry season compared to the wet season, because the increase in fish densities led to an increase in piscivores fish. The food web was composed of planktonic and benthic food chains in the dry season. During the wet season, the planktonic food chain was dominant, followed by the herbivorous food chain, and the benthic food chain was relatively less important. Therefore, water-level fluctuation may alter the trophic linkages within fish communities, which contributed to a more complex and interconnected food web. Moreover, as we expect, the stable isotope analysis food web was broadly in line with the gut content analysis food web.

Triplophysa anterodorsalis is an endemic fish in the upper stream of the Yangtze River, Jinsha River and its tributaries. However, wild populations of T. anterodorsalis declined sharply due to cascade hydropower stations constructed successively in the Jinsha River during the past decades. In the present study, the complete mitochondrial DNA genome sequence of T. anterodorsalis was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial genome sequence of T. anterodorsalis is a circular molecule of 16,567 bp in size. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene nucleotide composition of T. anterodorsalis is 27.37% A, 25.68% C, 18.37% G, and 28.57% T, with a relatively a relatively high A + T content (55.94%). The results could provide useful data for studies on genetic structure and diversity and rational resource conservation in T. anterodorsalis.