Spring viremia of carp virus (SVCV) poses a major threat to aquaculture industry, triggering severe economic losses and substantial damage to fish health. Effective antiviral therapeutic approaches are currently insufficient in aquaculture, highlighting an urgent demand for viable intervention strategies. This study assessed the antiviral and immunomodulatory potential of Houttuynia cordata against SVCV in common carp. Combined cellular and in vivo fish experiments demonstrated that Houttuynia cordata markedly suppresses SVCV replication, reduces viral titer, and enhances disease resistance of carp. The extract appears to suppress RARα-A, upregulate IFN-1/CXCL11, and recruit T lymphocytes via CXCL11, thereby enhancing innate and adaptive immunity against SVCV. Experimental results indicate that Houttuynia cordata alleviates hemorrhagic symptoms induced by SVCV infection. Dietary supplementation with this herb realizes dual functions of viral suppression and immune regulation for carp aquaculture. The findings provide a practical prevention and control strategy against SVCV infection and offer novel insights for research on green antiviral agents. Furthermore, this study verifies the potential value of Houttuynia cordata in improving biological safety and facilitating sustainable development of aquaculture, laying a solid foundation for the development of eco-friendly antiviral preparations.

In this study, we obtained the complete mitogenome of Lutjanus fulvus from a specimen collected in Pakistani waters (63.95 degrees E, 25.30 degrees N) by utilizing high-throughput sequencing technology, then we characterized it and downloaded the complete mitogenomes of closely related species to constructed phylogenetic trees based on 13 protein-coding genes (PCGs) using Bayesian Inference (BI) methods. The complete mitogenome of L. fulvus is a typical closed circular double-stranded DNA molecule, was 16 493 bp in length, with a relatively low G content (16.2 %) and a high AT pronounced bias (52.8 %). The genome comprises 37 genes: 22 tRNAs, two rRNAs, 13 PCGs, and one putative control region (D-loop). Among the 13 PCGs, four types of stop codons (TAA, TAG, AGA, T-) are observed, and all genes, except for COX1, which starts with GTG, begin with the ATG start codon. The BI trees exhibited consistent topologies, indicating close relationships with Lutjanus vitta and Lutjanus ophuysenii. This study provides valuable genomic insights into the mitogenome of L. fulvus, enhancing our understanding of phylogenetic relationships within the Lutjanidae family and offering a fundamental reference for further exploration of mitogenomes in the Lutjanus genus. Furthermore, these data contribute new molecular evidence and theoretical foundations for the classification, genetic diversity studies, and the conservation and management of L. fulvus.

Background: Schizothorax curvilabiatus is a commercially important freshwater fish endemic to the lower reaches of the Yarlung Zangbo River. However, its fishery resources have been severely depleted due to human activities, leading to a scarcity of data regarding its genetic characteristics. This study aims to assess the genetic diversity and population structure of this species to provide a scientific basis for its conservation. Methods: Three mitochondrial DNA markers-Cytochrome b (Cyt b), Control Region (D-loop), and Cytochrome Oxidase Subunit I (COI)-were sequenced and analyzed. A total of 100 samples were collected from three natural populations in the lower Yarlung Zangbo River: Motuo (MT), Palong (PL), and Chayu (CY). Results: High overall haplotype diversity (H-d: 0.889-0.951) but relatively low nucleotide diversity (P-i: 0.00450-0.0111) were observed. Notably, the PL population exhibited the lowest genetic diversity across all markers. Significant genetic differentiation was detected between the PL population and the other two populations (MT and CY), supported by F-ST indices, gene flow (N-m) estimates, and Analysis of Molecular Variance (AMOVA), which revealed that most variation resided within populations (>83%). Both Neighbor-Joining (NJ) phylogenetic trees and haplotype network analyses indicated a distinct geographical lineage pattern, with the PL and CY populations showing a distant genetic relationship. Discussion: Although S. curvilabiatus maintains substantial overall genetic diversity, the low diversity within specific populations (particularly PL) and the significant inter-population differentiation highlight the vulnerability of its germplasm resources. These findings provide crucial insights into the genetic background of the species and offer valuable guidance for the conservation and sustainable management of its genetic resources.

Background/Objectives: Schizothorax curvilabiatus, a typical highland polyploid species within the subfamily Schizothoracinae, holds economic value and ecological research significance. Currently, there are no related genomic studies. To obtain its genetic information and lay the foundation for subsequent whole-genome map construction, this study conducted a genome survey analysis, preliminary genome assembly, microsatellite identification, repeat sequence annotation, mitochondrial genome characterization, and phylogenetic relationship research. Methods: DNA was sequenced on a DNBSEQ-T7 platform to obtain paired-end genomic data. The genome was analyzed using GCE, and the draft genome was assembled with SOAPdenovo. Microsatellites were identified using MISA, and the mitochondrial genome was assembled with NOVOPlasty. Genome features were analyzed, and phylogenetic trees were constructed using PhyloSuite and MEGA. Results: The genome size was estimated at 2.53 Gb, with a heterozygosity of 6.55% and 47.66% repeat sequences. A 1.324 Gb preliminary genome draft was obtained, with repeat sequences comprising 47.17%, the majority being DNA transposons (24.64%). Dinucleotide repeats were most abundant (46.91%), followed by mononucleotide repeats (38.31%), with A/T and AC/GT being the most frequent. A complete mitochondrial genome of 16,589 bp was assembled, and a 939 bp D-loop was annotated. Phylogenetic relationships among genera in the Schizothoracinae subfamily were also clarified. Conclusions: This study provides the latest molecular data for analysis of the S. curvilabiatus genome and its related populations, and for the first time offers genomic resources for research on genomic adaptive evolution and polyploidization in high-altitude environments.

The Chinese herring (Ilisha elongata) is a commercially and scientifically significant fish species. In this study, we conducted high-precision whole-genome sequencing using two high-throughput platforms: second-generation MGI and third-generation PacBio. Hi-C technology assisted in assembling the contig sequences onto 24 chromosomes, resulting in a high-quality chromosome-level genome map with excellent continuity and coverage. The completed genome size was approximately 815 Mb, with a contig N50 of 4.82 Mb, scaffold N50 of 32.61 Mb, and a chromosome mounting rate of 95.32%. SNP and InDel purity rates were 0.003% and 0.012%, respectively, and the genome assembly completeness was 96.68%, assessed by BUSCO. Repetitive sequences were annotated via ab initio and homology predictions, identifying 295.7 Mb of repetitive sequences, constituting 35.08% of the genome. A total of 26,381 protein-coding genes were predicted, with 24,596 functionally annotated.

Aquatic biodiversity of the Yarlung Zangbo River is both unique and fragile, with its ecological environment currently under significant pressure. However, comprehensive studies on the biological characteristics and resource status of fish in its tributaries remain insufficient. In this study, we analyzed the population structure, growth characteristics, and resource dynamics of 2058 specimens of Schizopygopsis younghusbandi that were collected from four major tributaries in the middle reaches of the Yarlung Zangbo River (Duoxiong Zangbo, Lhasa River, Niyang River, and Nianchu River) between 2023 and 2024. Population parameters were estimated using the Von Bertalanffy growth equation, revealing asymptotic body lengths (L∞) between 387.877 and 414.535 mm and growth coefficients (k) ranging from 0.154 to 0.174. Notably, the k values exhibited a gradual decline in growth rate with increasing altitude. Based on calculations from FiSAT II software, the exploitation rate (E) revealed that the Duoxiong Zangbo population remained within a safe range (E < 0.5), whereas the Nianchu, Lhasa, and Niyang River populations were overexploited (E > 0.5), with their population structures showing signs of under-ageing and miniaturization. To ensure stable population continuity, the minimum catchable body lengths were estimated as 248 mm, 240 mm, 233 mm, and 236 mm for the Duoxiong Zangbo, Nianchu, Lhasa, and Niyang Rivers, respectively, with slight variations among tributaries. These findings suggest that S. younghusbandi populations in the Yarlung Zangbo River tributaries are adversely affected by external pressures and face a decline, necessitating effective conservation and restoration strategies.

The Qinghai-Tibet Plateau is renowned for its rich yet fragile biodiversity, attracting global conservation attention. The aquatic biodiversity in the Yarlung Zangbo River's core area faces significant pressures, yet our understanding of fish community structures in its tributaries remains limited. To address this gap, we surveyed fishery resources and analyzed six Schizothoracinae species (Oxygymnocypris stewarti, Ptychobarbus dipogon, Schizothorax oconnori, Schizothorax macropogon, Schizothorax waltoni, and Schizopygopsis younghusbandi) across four major tributaries of the middle Yarlung Zangbo River (Dogxung Zangbo, Niangchu River, Lhasa River, and Niyang River). Results indicated that S. younghusbandi was the dominant species across all tributaries, while other species' dominance varied spatially. Notably, O. stewarti showed the lowest catch per unit effort (CPUE) in three tributaries (Lhasa, Niyang, and Niangchu Rivers), whereas S. waltoni had the lowest CPUE in Dogxung Zangbo. Fish diversity and evenness were significantly higher in Dogxung Zangbo and Niangchu River compared to Niyang and Lhasa Rivers, with the latter two exhibiting lower community complexity and greater anthropogenic disturbance. Abundance-biomass comparison curves revealed all communities experienced substantial disturbance, with Dogxung Zangbo being least affected. Cluster analysis and NMDS grouped the tributaries into two distinct clusters: Niyang and Lhasa Rivers, and Niangchu River and Dogxung Zangbo, reflecting high within-group community similarity. Using a priority protection assessment, S. macropogon emerged as the top conservation priority in Dogxung Zangbo, while O. stewarti ranked highest among the other three tributaries. These findings elucidate current fish community statuses, disturbance levels, and conservation challenges, offering critical insights for developing targeted protection strategies.

Saline lakes are extreme habitats that host unique microbial communities with high biotechnological potential. In this study, a novel strain, designated Q87T, was isolated from Gaxiukule Lake, a high-altitude magnesium sulfate-type saline lake in the Qaidam Basin, China. A polyphasic taxonomic approach, including morphological, physiological, chemotaxonomic, phylogenetic, and genomic analyses, was applied to characterize the isolate. Strain Q87T is a Gram-stain-negative, non-motile, rod-shaped bacterium showing high tolerance to salinity (0-15.0 %, w/v; optimum 5.0 %) and alkalinity (pH 6.0-10.5; optimum pH 7.0), with a temperature range for growth of 10-40 °C (optimum 32 °C). Phylogenetic and genomic analyses confirmed its affiliation with the genus Gracilimonas and revealed it as a distinct species. The genome of strain Q87T (3.3 Mb, G + C 41.5 %) encodes diverse functional genes associated with nitrogen and sulfur metabolism, stress adaptation, and biosynthesis of secondary metabolites, including terpenoids and polyketides. Comparative analyses with reference Gracilimonas strains demonstrated its unique genomic features and ecological adaptability. Structural modeling confirmed functional conservation of key enzymes involved in nitrogen detoxification and sulfide oxidation. Pangenome analysis highlighted the genetic diversity and open nature of the species of the genus Gracilimonas. Biogeographic assessments suggest a wide distribution of the genus in saline environments, especially in sediments. This study expands our understanding of the genus Gracilimonas taxonomy, physiology, and ecological potential, and underscores the importance of extremophilic bacteria as promising resources for environmental and industrial biotechnology.

A halophilic bacterium, named Halomonas sp. NEC-1 was isolated from the Nyer Co Salt Lake on the Xizang Plateau, SW China. The strain exhibited a broad pH tolerance range of 5–11, distinguishing it from Halomonas alkaliphila despite a 99

The Yarlung Zangbo River (With a total length of 2057 km, the river forms part of the Ganges–Brahmaputra River system), located in the core region of the Tibetan Plateau, hosts a unique yet fragile aquatic ecosystem. Fish populations inhabiting this ecosystem have been significantly impacted by external factors, leading to declining resources. This decline is particularly evident in local tributaries, including the DuoXiong Zangbo River—a main tributary where scientific research remains scarce due to its geographic remoteness. Consequently, the status of schizothoracinae in this river remains poorly understood, necessitating research on their population structure, growth characteristics, and resource dynamics, as well as the extent of external disturbances. During the 2023–2024 season, fishery surveys were conducted during two sampling periods: summer (June–July) and autumn (September–October). This study focuses on the Duoxiong Zangbo River, a tributary of the Yarlung Zangbo River, targeting three schizothoracinae fish species: Schizothorax o’connori, Oxygymnocypris stewartii, and Ptychobarbus dipogon. The results show that their body lengths ranged from 23.02 to 440.00 mm, 23.02 to 460.00 mm, and 45.18 to 418.00 mm, with body weights ranging from 0.30 to 1394.30 g, 0.20 to 1013.00 g, and 1.20 to 814.30 g. Age distributions spanned 0–14, 0–16, and 0–13 years, respectively, indicating a trend toward younger and smaller individuals. Von Bertalanffy growth modeling revealed asymptotic body lengths (L∞) of 591.233 mm, 507.557 mm, and 515.292 mm, with growth coefficients (k) of 0.098, 0.122, and 0.118, respectively. These parameters suggest that the populations are exhibiting accelerated growth strategies in response to fishing pressure. Using FiSAT II, exploitation rates (E) were calculated as 0.547, 0.758, and 0.711 for the three species, with predicted maximum sustainable exploitation rates of 0.579, 0.882, and 0.884, respectively. These findings indicate that the three schizothoracinae species have approached the threshold of overexploitation and are facing threats of overexploitation. In summary, this study demonstrates that schizothoracinae in the DuoXiong Zangbo River are experiencing adverse effects from external pressures, with populations at risk of decline. These results underscore the urgent need for targeted conservation and management strategies.

Tidal flats are vital coastal ecosystems that play a significant role in organic carbon accumulation and biogeochemical cycles. Members of the family Flavobacteriaceae is known for its ability to degrade complex organic matter, including polysaccharides. However, the ecological roles and metabolic capabilities of Flavobacteriaceae in tidal flat environments remain underexplored. In this study, we isolated and characterized a novel bacterium, strain NBU2967T, from the tidal flats of Meishan Island in the East China Sea. Phylogenetic and genomic analyses identified this strain as a new genus and species within the family Flavobacteriaceae, for which we propose the name Meishania litoralis gen. nov., sp. nov. Comprehensive polyphasic characterization, including morphological, physiological, chemotaxonomic, and genomic analyses, confirmed its distinct taxonomic status. Genomic analysis revealed a diverse set of carbohydrate-active enzymes (CAZymes), along with multiple metabolic pathways associated with carbon and sulfur cycling, highlighting the strain's potential adaptation to organic-rich marine environments. Comparative genomic and pangenome analyses further demonstrated significant genetic divergence from related taxa. Environmental distribution data revealed that the newly proposed genus Meishania is widely distributed across global marine ecosystems. We isolated and characterized a novel bacterium, designated NBU2967T (= KCTC 82912 T = MCCC 1K06391T), for which we propose the name Meishania litoralis gen. nov., sp. nov. This strain is classified as a new genus within the family Flavobacteriaceae. The strain’s ability to process both carbon and sulfur compounds underscores its ecological significance in marine ecosystems. These findings provide novel insights into the ecological functions of the family Flavobacteriaceae in coastal tidal flats environments and enhance our understanding of microbial-mediated degradation and transformation of chemical compounds in dynamic coastal ecosystems.

The nine endemic species of the genus Schizothorax from the Yarlung Zangbo River, Tibet comprise a putative cyprinid species flock. In this study, the effectiveness of the COI DNA barcode for Schizothoracinae species identification was verified by using 45 COI sequences covering nine species in four genera of Schizothoracinae fishes. The average Kimura two parameter (K2P) genetic distances within and among species were 0.13% and 8.57%, respectively. The results revealed that most of the species were clearly discriminated by their estimated genetic distances and monophyletic clustering in a maximum likelihood tree. However, insignificant genetic distances were noticed in two reportedly valid species: Schizothorax molesworthi and S. integrilabiatus (0.1%), and the monophyly of S. macropogon could not be recovered in the schizothoracine group. The fishes of S.curilabiatus living in the lower course of Yalung Zangbo River were clustered together with three species from the upper course, which is inconsistent with the geographical distribution of the populations.

The family Sisoridae is one of the largest and most diverse Asiatic catfish families, with most species occurring in the water systems of the Qinhai-Tibetan Plateau and East Himalayas. At present, the phylogenetic relationship of the Sisoridae is relatively chaotic. In this study, the mitochondrial genomes (mitogenomes) of three species Creteuchiloglanis kamengensis, Glaridoglanis andersonii, and Exostoma sp. were systematically investigated, the phylogenetic relationships of the family were reconstructed and to determine the phylogenetic position of Exostoma sp. within Sisoridae. The lengths of the mitogenomes’ sequences of C. kamengensis, G. andersonii, and Exostoma sp. were 16,589 bp, 16,531 bp, and 16,529 bp, respectively. They all contained one identical control region (D-loop), two ribosomal RNAs (rRNAs), 13 protein-coding genes (PCGs) and 22 transfer RNA (tRNA) genes. We applied two approaches, Bayesian Inference (BI) and Maximum Likelihood (ML), to construct phylogenetic trees. Our findings revealed that the topological structure of both ML and BI trees exhibited significant congruence. Specifically, the phylogenetic tree strongly supports the monophyly of Sisorinae and Glyptosternoids and provides new molecular biological data to support the reconstruction of phylogenetic relationships with Sisoridae. This study is of great scientific value for phylogenetic and genetic variation studies of the Sisoridae.

Species resilience to diversified environments largely depends on their genetic diversity. Disentangling the respective roles of multiple landscape factors on population genetic variation could help us interpret the adaptive mechanism of species to environments, which is a central issue in evolutionary biology and biodiversity conservation. Herein, a typical Tibetan loach Triplophysa stenura was selected as study object to perform landscape genetics analyses inferred from mitochondrial cytochrome b gene sequences. Based on extensive sample collection, a total of 377 individuals from 20 sites in the Yarlung Tsangpo River were included in the analyses and results of genetic diversity assessment demonstrated relatively high haplotype diversity and low nucleotide diversity for most geographic populations. Genetic diversity pattern analysis proved that both haplotype and nucleotide diversity were greater in higher, colder and drier areas, which was consistent with the central-marginal hypothesis for this plateau hinterland-originated species. Degree of genetic differentiation among geographic populations varied from low level to extremely high level, with genetic variation coming mainly from within populations. Elevational and climatic divergences were detected to be principally responsible for the formation of population genetic structure of this species, coinciding with the isolation-by-environment model. On this basis, we put forward some applicable proposals that the marginal populations with relatively low elevations deserved more attentions in designing conservation scheme and those genetically differentiated populations should be treated as separate conservation units. In the context of global climate change and intensifying human activity, a sound genetic resources monitoring along elevational or climatic gradient is pivotal to develop future conservation interventions.

A facultative anaerobic, Gram-strain-negative, rod-shaped bacterium (strain NBU2970T) was isolated by using modified ichip in situ cultivation from a marine sediment sample collected from Meishan Island in the East China Sea. Strain NBU2970T grew optimally at 37 °C, with a NaCl concentration of 2.0 % (w/v) and at pH 7.0. The 16S rRNA gene sequence analyses revealed that strain NBU2970T represents a novel species with the genus Muricauda, sharing highest sequence identities with Muricauda beolgyonensis BB-My12T (96.1 %), Muricauda alvinocaridis SCR12T (96.0 %), Muricauda taeanensis 105T (96.0 %) and Muricauda ruestringensis B1T (95.6 %). Phylogenetic analyses also indicated that strain NBU2970T clustered with the genus Muricauda and was closely related to M. beolgyonensis BB-My12T and M. ruestringensis B1T. The draft genome sequence of strain NBU2970T was composed of six contigs with a size of 3.2 Mbp, containing 3045 protein-coding genes and 38 RNA genes. The DNA G+C content was 43.8 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain NBU2970T and related species of the genus Muricauda were well below the threshold limit for prokaryotic species delineation. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The only respiratory quinone was MK-6. The major polar lipid was phosphatidylethanolamine. Based on its phenotypic, chemotaxonomic and genotypic data, strain NBU2970T is considered to be a representative of a novel species in the genus Muricauda, for which the name Muricauda meishanensis sp. nov. is proposed. The type strain is NBU2970T (=KCTC 82915T=MCCC 1K06394T).

Abstract Brine shrimp Artemia is the crucial live food in fish and crustacean larviculture. With the decrease of Artemia resources and the increase in aquaculture demand, it is necessary to conduct Artemia population genetics and to manage this important resource efficiently. In this study, the genetic diversity and distribution pattern of Artemia populations originated from ten inland salt lakes in central-west China were studied using a large number of single nucleotide polymorphisms (SNPs) obtained by high-throughput sequencing. The results showed that Tibetan populations had the highest level of genetic diversity, while Shanxi population had the lowest value. Genetic structure and principal component analysis further revealed these populations can be classified into four geographically and genetically distinct groups, and Tibetan populations were further divided into two subgroups and showed a trend of higher in the west and lower in the east at the level of genetic diversity. In addition, a certain amount of gene flow was observed among these 10 populations, and A. sinica had a unidirectional gene flow to all populations in the eastern Nagri region. Finally, species distribution models indicated that Bio1, Bio4, and Bio12 were the main environmental factors affecting the distribution of Artemia, and climate fluctuations had a strong influence on the distribution of Artemia. The findings revealed Tibetan populations will be further reduced in the future, and it is necessary to adopt a series of measures to strengthen Artemia protection and promote rational exploitation and utilization of this natural resources. This study further improves our understanding of the genetic structure of Artemia in central-west China, and provides certain guidance for the protection of Artemia germplasm resources.

Understanding the evolutionary history of the highly diverse ray-finned fishes has been challenging, and the development of more universal primers for phylogenetic analyses may help overcoming these challenges. We developed FishPIE, a nested PCR primer set of 82 phylogenetically informative exon markers, and tested it on 203 species from 31 orders of Actinopterygii. We combined orthologous sequences of the FishPIE markers obtained from published genomes and transcriptomes and constructed the phylogeny of 710 species belonging to 190 families and 60 orders. The resulting phylogenies had topologies comparable to previous phylogenomic studies. We demonstrated that the FishPIE markers could address phylogenetic questions across broad taxonomic levels. By incorporating the newly sequenced taxa, we were able to shed new light on the phylogeny of the highly diverse Cypriniformes. Thus, FishPIE holds great promise for generating genetic data for broad taxonomic groups and accelerating our understanding of the fish tree of life.

In the study, we report the complete mitochondrial genome of Artemia persimilis Piccinelli and Prosdocimi, 1968 for the first time. The mitochondrial genome of A. persimilis is 15,436 bp in length, with the typical structure of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and 2 ribosomal RNA genes, and a non-coding control region (CR). Phylogenetic analysis showed that A. persimilis was at the basal position among the bisexual Artemia species, which revealed that A. persimilis is likely to be an ancestral clade. The present study could provide effective resources for population genetics study, as well as germplasm conservation in Artemia.

Complete mitochondrial genomes (mitogenomes) can provide valuable information for phylogenetic relationships, gene rearrangement, and molecular evolution. Here, we report the mitochondrial whole genomes of three Garra species and explore the mechanisms of rearrangements that occur in their mitochondrial genomes. The lengths of the mitogenomes' sequences of Garra dengba, Garra tibetana, and Garra yajiangensis were 16,876, 16,861, and 16,835, respectively. They contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genomes of three Garra species were rearranged compared to other fish mitochondrial genomes. The tRNA-Thr, tRNA-Pro and CR (T-P-CR) genes undergo replication followed by random loss of the tRNA-Thr and tRNA-Pro genes to form tRNA-Thr, CR1, tRNA-Pro and CR2 (T-CR-P-CR). Tandem duplication and random loss best explain this mitochondrial gene rearrangement. These results provide a foundation for future characterization of the mitochondrial gene arrangement of Labeoninae and further phylogenetic studies.