Search

IntroductionDual-specificity phosphatases (DUSPs) are crucial regulators in many mammals, managing dephosphorylation and inactivation of mitogen-activated protein kinases (MAPKs) and playing essential roles in immune responses. However, their presence and functions in teleosts, like the yellow catfish (Pelteobagrus fulvidraco), remain unexplored.MethodsIn this study, eight pfDusp genes (pfDusp1-7 and pfDusp10) were identified in yellow catfish. We characterized their molecular features, conserved protein sequences, and chromosomal localization through genome-wide analyses, and we examined their expression patterns in immune responses.ResultsOur findings reveal two conserved motifs, Leu-Phe-Leu-Gly and Ala-Tyr-Leu-Met, within the DSPc domain of DUSP proteins. The genes were mapped across seven chromosomes without evidence of duplication. Comparative analysis showed high conservation of Dusp genes across vertebrates, with evolutionary analysis suggesting Dusp3 as a potential intermediate form. Dusp transcripts were significantly upregulated in the kidney post-A. hydrophila infection.DiscussionThese results suggest the involvement of Dusp genes in the immune response of yellow catfish to bacterial pathogens, providing insights into their evolutionary significance and potential applications in aquaculture and molecular breeding.

The yellow catfish (Pelteobagrus fulvidraco) is an economically important species in China and East Asia. However, with the development of high-density farming, bacterial diseases of yellow catfish are becoming increasingly serious. In mammals, autophagy participates in an intracellular innate defense pathway in response to bacterial and viral infections. Among these signaling pathways, stimulator of interferon genes (STING) combines with a ring diode produced by the cyclic GMP-AMP synthase (cGAS) and activates the immune response and autophagy of pathogenic microorganisms. The cGAS-STING signaling pathway in fishes remains largely unexplored. This study found that cGAS and STING exhibited both conserved gene structure and gene synteny in various species of teleosts and diverse species of vertebrates. Expression profiling revealed that the transcription levels of cGAS and STING in immune tissues were significantly up-regulated within 48 h after stimulation with Aeromonas hydrophila or Edwardsiella tarda. Our results demonstrated that the expression levels of TBK1 and IRF3 in the cGAS-STING pathway were significantly up-regulated in the liver, kidney, and spleen, suggesting that this pathway was triggered and activated within 48 h by stimulation with exogenous A. hydrophila. Analyses conducted through Transmission Electron Microscopy (TEM) and marker genes showed that autophagic hyperactivation occurred in the liver, spleen, and kidney of hybrid yellow catfish after infection with A. hydrophila or E. tarda. Taken together, the results indicate that cGAS and STING function are critical mediators of antibacterial immunity in the yellow catfish, and that the cGAS-STING signaling pathway is involved in mediating antibacterial defenses.

Exploring the effects of seasonal variation on the gut microbiota of cold-water fish plays an important role in understanding the relationship between seasonal variation and cold-water fish. Gut samples of cold-water fish and environmental samples were collected during summer and winter from the lower reaches of the Yalong River. The results of the 16S rRNA sequencing showed that significant differences were identified in the composition and diversity of gut bacteria of cold-water fish. Co-occurrence network complexity of the gut bacteria of cold-water fish was higher in summer compared to winter (Sum: nodes: 256; edges: 20,450; Win: nodes: 580; edges: 16,725). Furthermore, from summer to winter, the contribution of sediment bacteria (Sum: 5.3%; Win: 23.7%) decreased in the gut bacteria of cold-water fish, while the contribution of water bacteria (Sum: 0%; Win: 27.7%) increased. The normalized stochastic ratio (NST) and infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP) showed that deterministic processes played a more important role than stochastic processes in the microbial assembly mechanism of gut bacteria of cold-water fish. From summer to winter, the contribution of deterministic processes to gut bacteria community assembly mechanisms decreased, while the contribution of stochastic processes increased. Overall, these results demonstrated that seasonal variation influenced the gut bacteria of cold-water fish and served as a potential reference for future research to understand the adaptation of fish to varying environments.

Due to factors such as overfishing, hydropower development, and water pollution, their wild populations have drastically declined, with many species being classified as endangered or vulnerable. Understanding the driving factors behind the gut microbiota of cold-water fish holds significant implications for conservation. Therefore, to investigate the influence of different factors on the gut microbes of cold-water fish, 112 gut samples from farmed and wild habitats were collected from Schizothorax wangchiachii (herbivorous), Schizothorax kozlovi (omnivorous) and Percocypris pingi (carnivorous), in the Jinping Dahewan range of lower reaches of the Yalong River. The results of 16 S rRNA gene sequencing of the gut contents showed that habitat was the major factor influencing the gut microbes of the three cold-water fishes. In terms of microbial composition, farmed cold-water fish exhibited a dominant bacterial phylum, Proteobacteria (82 %), while those in wild environment presented multiple dominant taxa, such as Proteobacteria (38 %), Fusobacteria (30 %), Firmicutes (11 %), and Cyanobacteria (11 %). Gut microbial diversity, both α diversity and β diversity, in wild cold-water fish was significantly higher than that in farmed individuals. Network complexity of gut microbiota was notably higher in wild cold-water fish than in farmed individuals. From farmed to wild environments, the relative influence of deterministic processes in the gut microbiota assembly mechanism of cold-water fish gradually diminishes, while the contribution of stochastic processes steadily increases. The gut microbiota construction mechanism in farmed cold-water fish was primarily influenced by deterministic processes of homogeneous selection, while in wild cold-water fish, it was mainly driven by stochastic processes of homogeneous dispersal. Overall, this study is an important reference for the study of the gut microbiota of cold-water fish and the conservation of their wild populations.

The hybrid yellow catfish exhibits advantages over pure yellow catfish in terms of fast growth, fast development, a high feeding rate, and strong immunity; additionally, it is almost sterile, thus ensuring the conservation of the genetic stock of fish populations. To investigate the sterility mechanism in hybrid yellow catfish (P. fulvidraco (♀) × P. vachelli (♂)), the mRNA and miRNA of the gonads of P. fulvidraco, P. vachelli, and a hybrid yellow catfish were analyzed to characterize the differentially expressed genes; this was carried out to help establish gene expression datasets to assist in the further determination of the mechanisms of genetic sterility in hybrid yellow catfish. In total, 1709 DEGs were identified between the hybrid and two pure yellow catfishes. A KEGG pathway analysis indicated that several genes related to reproductive functions were upregulated, including those involved in the cell cycle, progesterone-mediated oocyte maturation, and oocyte meiosis, and genes associated with ECM–receptor interaction were downregulated. The spermatogenesis-related GO genes CFAP70, RSPH6A, and TSGA10 were identified as being downregulated DEGs in the hybrid yellow catfish. Sixty-three DEmiRNAs were identified between the hybrid and the two pure yellow catfish species. The upregulated DEmiRNAs ipu-miR-194a and ipu-miR-499 were found to target the spermatogenesis-related genes CFAP70 and RSPH6A, respectively, playing a negative regulatory role, which may underscore the miRNA–mRNA regulatory mechanism of sterility in hybrid yellow catfish. The differential expression of ipu-miR-196d, ipu-miR-125b, and ipu-miR-150 and their target genes spidr, cep85, and kcnn4, implicated in reproductive processes, was verified via qRT-PCR, consistent with the transcriptome sequencing expression trends. This study provides deep insights into the mechanism of hybrid sterility in vertebrate groups, thereby contributing to achieving a better understanding and management of fish conservation related to hybrid sterility.

Abstract Background It is inevitable to change the function or expression of genes during the environmental adaption of species. Both the giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to Carnivora and have developed similar adaptations to the same dietary switch to bamboos at the morphological and genomic levels. However, the genetic adaptation at the gene expression level is unclear. Therefore, we aimed to examine the gene expression patterns of giant and red panda convergent specialized bamboo-diets. We examined differences in liver and pancreas transcriptomes between the two panda species and other non-herbivorous species. Results The clustering and PCA plots suggested that the specialized bamboo diet may drive similar expression shifts in these two species of pandas. Therefore, we focused on shared liver and pancreas DEGs (differentially expressed genes) in the giant and red panda relative to other non-herbivorous species. Genetic convergence occurred at multiple levels spanning carbohydrate metabolism, lipid metabolism, and lysine degradation. The shared adaptive convergence DEGs in both organs probably be an evolutionary response to the high carbohydrate, low lipid and lysine bamboo diet. Convergent expression of those nutrient metabolism-related genes in both pandas was an intricate process and subjected to multi-level regulation, including DNA methylation and transcription factor. A large number of lysine degradation and lipid metabolism related genes were hypermethylated in promoter regions in the red panda. Most genes related to carbohydrate metabolism had reduced DNA methylation with increased mRNA expression in giant pandas. Unlike the red panda, the core gene of the lysine degradation pathway (AASS) doesn’t exhibit hypermethylation modification in the giant panda, and dual-luciferase reporter assay showed that transcription factor, NR3C1, functions as a transcriptional activator in AASS transcription through the binding to AASS promoter region. Conclusions Our results revealed the adaptive expressions and regulations of the metabolism-related genes responding to the unique nutrients in bamboo food and provided data accumulation and research hints for the future revelation of complex mechanism of two pandas underlying convergent adaptation to a specialized bamboo diet.

Toll‐like receptor 1 (TLR1) mediates the innate immune response to a variety of microbes through recognizing cell wall components (such as bacterial lipoproteins) in mammals. However, the detailed molecular mechanism of TLR1 involved in pathogen immunity in the representative hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × P. vachelli ♂) has not been well studied. In the present study, we identified the TLR1 gene from the hybrid yellow catfish, and further comparative synteny data from multiple species confirmed that the TLR1 gene is highly conserved in teleosts. Phylogenetic analysis revealed distinguishable TLR1s in diverse taxa, suggesting consistence in evolution of the TLR1 proteins with various species. Structural prediction indicated that the three-dimensional structures of TLR1 proteins are relatively conserved among different taxa. Positive selection analysis showed that purifying selection dominated the evolutionary process of TLR1s and TLR1-TIR domain in both vertebrates and invertebrates. Expression pattern analysis based on the tissue distribution showed that TLR1 mainly transcribed in the gonad, gallbladder and kidney, and the mRNA levels of TLR1 in kidney were remarkably up-regulated after Aeromonas hydrophila stimulation, indicating that TLR1 participates in the inflammatory responses to exogenous pathogen infection in hybrid yellow catfish. Homologous sequence alignment and chromosomal location indicated that the TLR signaling pathway is very conserved in the hybrid yellow catfish. The expression patterns of TLR signaling pathway related genes (TLR1- TLR2 - MyD88 - FADD - Caspase 8) were consistent after pathogen stimulation, revealing that the TLR signaling pathway is triggered and activated after A. hydrophila infection. Our findings will lay a solid foundation for better understanding the immune roles of TLR1 in teleosts, as well as provide basic data for developing strategies to control disease outbreak in hybrid yellow catfish.

One novel catfish (Chinese called it ‘Gou nian’) widely cultured in China shares the same name with Ictalurus punctatus introduced from America, but is morphologically closed to genus Silurus. For years, the novel catfish was speculated to be an artificial hybrid of S. asotus and S. meridionalis. Therefore, we investigated the correct taxonomic status and origin of the novel catfish by means of morphological and molecular approaches. First, the novel ‘Gou nian’ could not be distinguished from S. asotus and S. meridionalis through anatomical observation, however, it was morphologically similar to S. asotus. Then, the novel ‘Gou nian’ was found not a hybrid of S. asotus and S. meridionalis based on the identification of ITS-2 and RAG-2, moreover, the analysis of COI barcoding found it more likely to be S. asotus. The phylogenic and population genetic analysis of Cyt b showed that the novel ‘Gou nian’ belonged to a taxonomic branch of S. asotus from the Liao River. The results convincingly indicated that the novel catfish is S. asotus and may originate from Northern China. The findings also provided useful implications for aquaculture management of the species.

The Datong and Xiaotong rivers are karst tributaries in the upper Yangtze River drainage and represent considerable habitat diversity that contributes to high fish diversity and rich fishery resources in the two rivers. During the few decades, fish resources have abruptly declined due to overfishing, water pollution and habitat degradation. In order to further strengthen conservation and restoration of fish resources and provide scientific support for fishery management in these rivers, the temporal and spatial dynamics of fish assemblage in the Datong and Xiaotong rivers were investigated in the present study. A total of 45 species were captured at 30 sample sites during four surveys conducted from March 2016 to January 2017. Species diversity and richness both increased from upstream to downstream in the two rivers. The fish assemblages significantly differed between river reaches, while did not differ in significantly between 4 months. The spatial variations in the abundance of Rhynchocypris oxycephalus, Zacco platypus, Triplophysa bleekeri, Sinogastromyzon szechuanensis, Platysmacheilus nudiventris, Sinibrama taeniatus, Saurogobio gymnocheilus, Pseudorasbora parva, Pseudobagrus truncates and Opsariichthys bidens were considered to contribute most to the spatial pattern of fish assemblages. The lack of a temporal pattern of the fish assemblage in the rivers might be attributed to ecological habits of short-distance migration and diversified mesohabitats with riffles and pools for fish spawning, feeding or overwintering within a very short river range. Our results suggest the spatio-temporal dynamics of fish assemblages is highly adapted to the habitat characteristics in the two karst rivers. We recommend that fish conservation of these tributaries be focused on the mesohabitats, particularly the many pools and riffles.

Abstract Background Microsatellite repeats are ubiquitous in organism genomes and play an important role in the chromatin organization, regulation of gene activity, recombination and DNA replication. Although microsatellite distribution patterns have been studied in most phylogenetic lineages, they are unclear in fish species. Results Here, we present the first systematic examination of microsatellite distribution in coding and non-coding regions of 14 fish genomes. Our study showed that the number and type of microsatellites displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation and DNA replication slippage theories alone were insufficient to explain the distribution patterns. Our results showed that microsatellites are dominant in non-coding regions. The total number of microsatellites ranged from 78,378 to 1,012,084, and the relative density varied from 4925.76 bp/Mb to 25,401.97 bp/Mb. Overall, (A + T)-rich repeats were dominant. The dependence of repeat abundance on the length of the repeated unit (1–6 nt) showed a great similarity decrease, whereas more tri-nucleotide repeats were found in exonic regions than tetra-nucleotide repeats of most species. Moreover, the incidence of different repeated types appeared species- and genomic-specific. These results highlight potential mechanisms for maintaining microsatellite distribution, such as selective forces and mismatch repair systems. Conclusions Our data could be beneficial for the studies of genome evolution and microsatellite DNA evolutionary dynamics, and facilitate the exploration of microsatellites structural, function, composition mode and molecular markers development in these species.

The fish gut microbiome plays an important role in nutrition absorption and energy metabolism. Studying the gut microbes of cold-water fish is important to understand the dietary adaptation strategies in extreme environments. In this study, the gut samples of Schizothorax wangchiachii (SW, herbivorous), Schizothorax kozlovi (SK, omnivorous), and Percocypris pingi (PP, carnivorous) in the upper Yangtze River were collected, and we sequenced 16S rRNA amplicon to study the potential relationship between gut microbes and host species. The results showed that gut microbial composition and diversity were significantly different between the three cold-water fishes. These fishes had different key taxa in their gut microbes, including bacteria involved in the breakdown of food (e.g., Cetobacterium, Aeromonas, and Clostridium sensu stricto 10). The highest alpha diversity indices (e.g., Chao 1 index) were identified in the herbivore (SW), followed by the carnivore (PP), and the lowest in the omnivore (SK). Non-metric multidimensional scaling (NMDS) results revealed that the gut microbial community of these species was different between host species. The neutral community model (NCM) showed that the microbial community structure of SW was shaped by stochastic processes, and the highest species dispersal was found in SW, followed by PP, and the lowest in SK. The results of niche breadth agreed with these findings. Our results demonstrated that host species influenced the gut microbiome composition, diversity, and microbial community assembly processes of the three cold-water fishes. These findings implied that the variation of gut microbiome composition and function plays a key role in digesting and absorbing nutrients from different foods in cold-water fish.

The Hengduan Mountains region is known for its river capture and drainage reversal events during the tectonic upheaval of the Qinghai-Tibetan Plateau. However, little is known of the geomorphological processes at fine scales such as in the upper and middle Yalong River. Here, we investigated whether the phylogeography of Schizopygopsis malacanthus reflected the palaeodrainage changes using the mitochondrial DNA control region and 12 microsatellite markers. A wide-range sampling of fish (439 individuals) was collected across the upper and middle Yalong River (14 populations: 5 in mainstream and 9 in seven major tributaries). Phylogenetic trees, hierarchical AMOVA, STRUCTURE and gene flow confirmed a river capture event in the upper mainstream of Yalong River and Xianshui River during the middle and late Pleistocene, provided evidence for historical drainage connection between the Jiulong and Liqiu rivers before the Gonghe Movement, and revealed a potential secondary contact event in upper reaches of the Litang and Huoqu rivers during the last interglacial period. Our results indicated that the current phylogeographic structure of S. malacanthus was impacted by the geological events and climatic fluctuations during the middle and late Pleistocene. The study provides insights into the historical drainage evolution across the upper and middle Yalong River in the Hengduan Mountains region.

Salmonids are composed of anadromous and freshwater fishes, which is an important model for studying adaptive evolution. Herein, 49 salmonid complete mitochondrial genomes and those of two outgroups were used to infer a robust phylogeny for the family Salmonidae. The BI and RAxML phylogenetic trees based on 13 concatenated mitochondrial protein-coding genes showed well-supported nodes, and topologies were highly congruent. The concatenated 13 mitochondrial protein-coding genes, ND2, ND3, and ND5 genes were shown to have significantly larger dN/dS ratios in anadromous species than in freshwater species of Salmonidae, but the CYTB gene had significantly smaller dN/dS in anadromous species. The FEL analysis identified positively selected sites and negatively selected sites in each mitochondrial protein-coding gene separately. The RELAX program revealed that the ATP8 and CYTB genes supported intensified selection of the anadromous lineages. Our results demonstrated the phylogeny of Salmonidae and explored the mitochondrial DNA evolution pattern between anadromous and freshwater salmonids.

As a major mediator of cellular response to viral infection in mammals, Toll-like receptor 3 (TLR3) was proved to respond to double-stranded RNA (dsRNA). However, the molecular mechanism by which TLR3 functions in the viral infection response in teleosts remains to be investigated. In this study, the Toll-like receptor 3 gene of the hybrid yellow catfish was identified and characterized by comparative genomics. Furthermore, multiple sequence alignment, genomic synteny and phylogenetic analysis suggested that the homologous TLR3 genes were unique to teleosts. Gene structure analysis showed that five exons and four introns were common components of TLR3s in the 12 examined species, and interestingly the third exon in teleosts was the same length of 194 bp. Genomic synteny analysis indicated that TLR3s were highly conserved in various teleosts, with similar organizations of gene arrangement. De novo predictions showed that TLR3s were horseshoe-shaped in multiple taxa except for avian (with a round-shaped structure). Phylogenetic topology showed that the evolution of TLR3 was consistent with the evolution of the studied species. Selection analysis showed that the evolution rates of TLR3 proteins were usually higher than those of TLR3-TIR domains, indicating that the latter were more conserved. Tissue distribution analysis showed that TLR3s were widely distributed in the 12 tested tissues, with the highest transcriptions in liver and intestine. In addition, the transcription levels of TLR3 were significantly increased in immune-related tissues after infection of exogenous Aeromonas hydrophila and poly (I:C). Molecular docking showed that TLR3 in teleosts forms a complex with poly (I:C). In summary, our present results suggest that TLR3 is a pattern recognition receptor (PRR) gene in the immune response to pathogen infections in hybrid yellow catfish.

Elongate loach (Leptobotia elongata) is an endemic fish distributed in middle and upper reaches of the Yangtze River in China. The genetic diversity and population structure of twelve populations of the species collected before (2008) and after dam constructions (2014–2015) on lower reaches of the Jinsha River were investigated using mtDNA control region and nuclear microsatellite DNA markers. The allelic richness (Ar) within populations varied from 11.06 to 15.25. Average polymorphic information content (PIC) ranged from 0.796 to 0.863. Haplotype diversities (h) ranged from 0.873 to 0.902, nucleotide diversity (π) ranged from 0.0030 to 0.0047. No significant differences of genetic diversities were identified between populations collected in 2008 and 2014–2015. The genetic differentiations (Fst) among the five populations (LUA, CQ, PZH, BX and NX) collected in 2008 were all insignificant, while that among some populations (JPD and CQ or GC, and GLP and NX or WS) collected in 2014–2015 were significant based on microsatellites. Negative correlations between the genetic diversities and geographical elevations for the seven populations collected in 2014–2015 indicated that the populations of L. elongata in high elevation regions were more vulnerable than that in low elevation regions. The results in the present study showed that no decline of genetic diversity occurred in L. elongata after dam constructions on lower reaches of the Jinsha River, while genetic structure of the populations between upstream and downstream of the dams tended to be formed. Translocating wild individuals of the populations between dams is suggested to enhance the gene flow and prevent potential genetic declines and isolations in L. elongata.

The releasing program of Chinese sucker (Myxocyprinus asiaticus) has been conducted for years in China. To prevent loss of genetic variation in wild populations, it is important to assess and monitor genetic diversity of broodstocks before release of offspring. Three broodstocks (Pixian Base of Sichuan Fisheries Research Institute, China (PBS), Yibin Base of Sichuan Fisheries Research Institute, China (YBS) and Yibin Rare Aquatic Animal Research Institute, China (YRA)) were investigated using mitochondrial control region and 12 microsatellites. The relatively low genetic diversities of these broodstocks were detected (PBS, haplotype diversity (h) = 0.877, observed heterozygosity (Ho) = 0.416; YBS, h = 0.812, Ho = 0.392; YRA, h = 0.818, Ho = 0.365). PBS showed higher Ho than YBS and YRA (P < 0.05). Genetic divergence (FST) based on microsatellites between PBS and YRA was significant (FST = 0.1270, P < 0.05), the same situation happened between YBS and YRA (FST = 0.1319, P < 0.05). However, divergence between PBS and YBS was not significant (FST = 0.0029, P > 0.05). Structure analysis revealed that YRA were distinct from PBS and YBS. Based on these results, it is important to propose some suggestions of genetic management for artificial propagation of Chinese sucker, such as broodstock exchange among hatcheries and broodstock supplement from wild.

The complete mitochondrial genome of the Hainan Glass Lizard (Dopasia hainanensis) from its type locality (Diaoluo Mountain in Hainan Island, China) was determined using next-generation sequencing. The mitogenome was 17,000 bp in length and comprised the standard set of 1 control region, 2 rRNAs, 22 tRNAs, plus 13 protein-coding genes (PCGs). The PCGs were used to perform Bayesian phylogenetic analysis together with other Anguidae and Helodermatidae as well as Shinisauridae lizards with mitogenome in GenBank. The resulting phylogenetic tree recovered D. hainanensis as the sister-taxon to Dopasia harti. The mitogenome of D. hainanensis will provide a valuable resource for various study areas such as species delimitation, molecular evolution, and phylogenetic inference.

The viviparous Tartar sand boa, Eryx tataricus, is a widespread species in arid Central Asia. A complete mitochondrial genome of one individual from Junggar Basin in Northwest China was determined by next-generation sequencing. The mitogenome is 17,537 bp in size, comprising 2 ribosomal RNA genes, 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 control regions. The order and structure of the genes are similar to those of other Henophidia snakes. Phylogenetic analysis based on 13 concatenated PCGs recovered the monophyly of Boidae and indicated that E. tataricus is closely related to Boa constrictor plus Eunectes notaeus.

Schizothorax wangchiachii is a key fish species in the stock enhancement program of the Yalong River hydropower project, China. Alizarin red S (ARS) was used to mark large numbers of juvenile S. wangchiachii in the Jinping Hatchery and later used to evaluate stock enhancement in the Jinping area of the Yalong River. In a small-scale pilot study, 7,000 juveniles of the 2014 cohort were successfully marked by immersion in ARS solution, and no mortality was recorded during the marking process. The ARS mark in the fish otoliths remained visible 20 months later. In the large-scale marking study, approximately 600,000 juveniles of the 2015 cohort were successfully marked. Mortalities of both marked and unmarked juveniles were very low and did not differ significantly. Total length, wet mass and condition factor did not differ significantly between unmarked and marked individuals after three months. On 24 July 2015, about 840,000 Jinping Hatchery-produced young S. wangchiachii, including 400,000 marked individuals, were released at two sites in the Jinping area. Recapture surveys showed that (1) marked and unmarked S. wangchiachii did not differ significantly in total length, wet mass and condition factor; (2) stocked individuals became an important part of recruitment of the 2015 cohort; (3) instantaneous growth rate of marked individuals tended to slightly increase; and (4) most stocked individuals were distributed along a 10–15 km stretch near the release sites. These results suggest that the ARS method is a cost-efficient way to mass mark juvenile S. wangchiachii and that releasing juveniles is an effective means of stock recruitment.

Percocypris pingi is a near threatened cyprinid species, which has suffered a dramatic decline due to anthropogenic factors. As one response to this decline, hatchery release for P. pingi has been conducted in the lower reaches of the Yalong River since 2012. To understand the conservation status of this species and the potential impact of the release of hatchery-reared fish, we studied the genetic diversity and population structure of wild and hatchery populations of P. pingi. Two hatchery populations (Jinping [JPH] and Ya'an [YAH]) and two wild populations (Muli [MLW] and Woluo [WLW]) of P. pingi were analyzed based on microsatellite markers and the mitochondrial DNA control region. The results showed that P. pingi possesses moderate levels of genetic diversity, with observed heterozygosities ranging from 0.657 to 0.770 and nucleotide diversities ranging from 0.00212 to 0.00491. Our results also suggested WLW harbors considerable proportions of genetic diversity in this species and serves as a refuge for P. pingi during anthropogenic disturbance, thus playing an important role for the conservation of P. pingi populations. Microsatellite and mitochondrial markers both indicated close genetic relationships between YAH and MLW, JPH and WLW, respectively. The results to some extent reflected the geographical provenances for original broodstocks of the two hatchery populations, which provide some practical guidance for hatchery release of P. pingi. The existence of remarkable genetic divergence distributed along limited geographical range (approximately 10 kilometers) suggests the two wild populations should be regarded at least as two distinct evolutionary significant units (ESUs) and management units (MUs). Considering reduced intra-population genetic variation in hatchery population for release and significant genetic compositions of the two hatchery populations, some appropriate breeding strategies were proposed to benefit conservation of P. pingi.

Transcriptome profiles provide a practical and inexpensive alternative to explore genomic data in non-model organisms, particularly in amphibians where the genomes are very large and complex. The odorous frog Odorranamargaretae (Anura: Ranidae) is a dominant species in the mountain stream ecosystem of western China. Limited knowledge of its genetic background has hindered research on this species, despite its importance in the ecosystem and as biological resources. Here we report the transcriptome of O. margaretae in order to establish the foundation for genetic research. Using an Illumina sequencing platform, 62,321,166 raw reads were acquired. After a de novo assembly, 37,906 transcripts were obtained, and 18,933 transcripts were annotated to 14,628 genes. We functionally classified these transcripts by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). A total of 11,457 unique transcripts were assigned to 52 GO terms, and 1,438 transcripts were assigned to 128 KEGG pathways. Furthermore, we identified 27 potential antimicrobial peptides (AMPs), 50,351 single nucleotide polymorphism (SNP) sites, and 2,574 microsatellite DNA loci. The transcriptome profile of this species will shed more light on its genetic background and provide useful tools for future studies of this species, as well as other species in the genus Odorrana. It will also contribute to the accumulation of amphibian genomic data.

In the present study, the genetic variability and relationships of the domestic populations of channel catfish (Ictalurus punctatus) in Sichuan Province, China were studied to determine their genetic background and provide essential data for its artificial breeding. Eight microsatellite markers were used to analyze genetic characteristics of eight channel catfish populations (POPA, POPB, POPC, POPD, POPE, POPF, POPG, and POPH). The average polymorphic information content (PIC) ranged from 0.525 (POPD) to 0.733 (POPA) indicating high polymorphism (PIC > 0.5). The average observed heterozygosity (Ho) and expected heterozygosity (He) in the eight populations ranged from 0.504 (POPH) to 0.767 (POPG) and from 0.6 (POPD) to 0.781 (POPA), respectively. The results showed that the eight populations possess considerable genetic diversity. The largest genetic differentiation (FST) among the eight populations was 0.233 (between POPB and POPD) and the lowest FST was 0.04 (between POPA and POPE). Furthermore, population structure analysis and UPGMA dendrogram suggested that there were close genetic relationships between POPA and POPE, POPA and POPG, and POPF and POPH, respectively. POPH showed serious inbreeding based on FIS analysis. [ABSTRACT FROM AUTHOR]

Triplophysa fishes are the primary component of the fish fauna on the Tibetan Plateau and are well adapted to the high-altitude environment. Despite the importance of Triplophysa fishes on the plateau, the geneticmechanisms of the adaptations of these fishes to this high-altitude environment remain poorly understood. In this study, we generated the transcriptome sequences for three Triplophysa fishes, that is, Triplophysa siluroides, Triplophysa scleroptera, andTriplophysa dalaica, and used these and the previously available transcriptome and genome sequences from fishes living at low altitudes to identify potential genetic mechanisms for the high-altitude adaptations in Triplophysa fishes. An analysis of 2,269 orthologous genes among cave fish (Astyanax mexicanus), zebrafish (Danio rerio), large-scale loach (Paramisgurnus dabryanus), and Triplophysa fishes revealed that each of the terminal branches of the Triplophysa fishes had a significantly higher ratio of nonsynonymous to synonymous substitutions than that of the branches of the fishes from low altitudes, which provided consistent evidence for genome-wide rapid evolution in the Triplophysa genus. Many of theGO (GeneOntology) categories associated with energymetabolism and hypoxia response exhibited accelerated evolution in the Triplophysa fishes compared with the large-scale loach. The genes that exhibited signs of positive selection and rapid evolution in the Triplophysa fishes were also significantly enriched in energy metabolism and hypoxia response categories. Our analysis identified widespread Triplophysa-specific nonsynonymous mutations in the fast evolving genes and positively selected genes. Moreover, we detected significant evidence of positive selection in the HIF (hypoxia-inducible factor)-1A and HIF-2B genes in Triplophysa fishes and found that the Triplophysa-specific nonsynonymous mutations in the HIF-1A and HIF-2B genes were associated with functional changes. Overall, our study provides new insights into the adaptations and evolution of fishes in the high-altitude environment of the Tibetan Plateau and complements previous findings on the adaptations of mammals and birds to high altitudes. [ABSTRACT FROM AUTHOR]

Thirty microsatellite markers were developed from Leptobotia elongata through 454 sequencing and 27 were polymorphic among 24 individuals, with an average of 9.67 alleles per locus, and the mean observed and expected heterozygosities were 0.81 and 0.79, respectively. Polymorphism information content (PIC) ranged from 0 416 to 0.933. In addition, cross-species amplification was tested for all 30 loci in four other loaches of Cobitidae (Leptobotia microphthalma, Botia superciliaris), and Nemacheilidae (Oreias dabryi, Triplophysa stenura) The results showed a significant high level of transferability (63%-97%), which means the possibility of these markers applying to other related species. The microsatellite loci described here would be useful in conservation of L elongata and possibly some other species. [ABSTRACT FROM AUTHOR]

Ten tetranucleotide microsatellite loci were isolated from GATA-enriched library of rock carp ( Procypris rabaudi). The loci were tested in 25 individuals from four populations. The number of alleles per locus ranged from 3 to 6. Polymorphism information content (PIC) ranged from 0.460 to 0.788. Observed and expected heterozygosities ranged from 0.375 to 0.739 and from 0.531 to 0.833, respectively. These microsatellites will facilitate the study of population genetics of rock carp. [ABSTRACT FROM AUTHOR]

As a subspecies of Schizopygopsis chengi (Fang), Schizopygopsis chengi baoxingensis (Fu, Ding et Ye) occurs as a single population endemic to the Baoxing River in China. The influences from the construction of hydropower dams in its distribution area might result in its extinction in the future due to its very narrow habitat and small population size. In this study, we sequenced the mitochondrial DNA control region of 81 individuals to analyze the genetic variability of the subspecies, hoping to acquire basic genetic information. The results revealed a limited genetic diversity of the population. Total samples could only be defined as seven haplotypes based on nucleotide variations. The nucleotide diversity (0.0008), haplotype diversity (0.534), and overall mean genetic distance among individuals (0.00080 ± 0.00053) were very low. Therefore, it is very necessary and urgent to conserve the population of this subspecies, avoiding further genetic loss, or even extinction. [ABSTRACT FROM AUTHOR]

Abstract  Rock carp, Procypris rabaudi (Tchang), is an endemic fish species in China. We sequenced the complete mitochondrial genome of it by high-fidelity polymerase chain reaction with conserved primers and primer walking sequencing method. The complete mitochondrial genome of rock carp is 16595 bp in length and contains 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region, with an identical order to that of most other vertebrates. The origin of L-strand replication (OL) in rock carp mitochondrion is located in a cluster of five tRNA genes (WANCY region) with 35 nucleotides in length. The control region is located between the tRNA-Pro and tRNA-Phe genes and is 943 bp in length. Three conserved sequence blocks (CSB), an extended termination associated sequence (ETAS), an AT-repeat microsatellite sequence and a putative promoter sequence for H-strand transcription (HSP) were identified within this region. The microsatellite sequence has a very low variation, with only one repeat alteration in 50 checked individuals (from 12 to 13 repeats). The phylogenetic analysis for rock carp was performed with Bayesian and Maximum likelihood (ML) methods based on the concatenated nucleotide sequence of 12 protein-coding genes on the heavy strand. The result suggested that traditional taxonomic barbines possibly originated more early than cyprininaes; rock carp was placed at the position between barbines and cyprininaes, while has a closer relationship with cyprininaes than barbines. [ABSTRACT FROM AUTHOR]

Effects of water temperature, starvation and photoperiod on otolith increment formation in larval Chinese sucker, Myxocyprinus asiaticus, were examined in this study. The results demonstrated that otolith increments of larvae reared under diel temperature fluctuations were very clear and appeared with a high contrast, while those of larvae raised under constant water temperatures were vague or hard to identify. The increment deposition rates were less than 1.0/day in later stage of starvation period. Also, increment deposition was affected by cyclic regimes of water temperature fluctuations, the number of increments corresponded to the cycle times rather than the exact days larvae experienced. However, varying of feeding frequency and photoperiod did not result in any alterations of daily increment formation. Increment width increased obviously with higher rearing temperatures till several days after yolk absorption. However, the width presented an ontogenetic decline during period of endogenous nutrition and the first several days of exogenous nutrition stage. Starvation decoupled the relationship between somatic growth and otolith growth; otolith kept growing, and increment width of starved larvae was similar to those in fed individuals before 9–20 days old; the divergence of increment width from the fed larvae occurred in later stage of starvation period. It can be concluded that temperature regimes and food levels are the major factors affecting increment formation in terms of clarity, deposition rate and width, while photoperiod and feeding frequency have less influence on it. [ABSTRACT FROM AUTHOR]

Otolith development was observed and the formation of daily growth increments in otoliths of Chinese sucker, Myxocyprinus asiaticus, was validated by monitoring known-age larvae and juveniles in the laboratory from 2003 to 2005. Otolith shape changed with larval and juvenile development, and there was an exponential relationship until a body length of 16 mm or so, and a linear relationship after a body length of 16 mm between otolith size and fish size. The first increment was identified in larvae 1 day after hatching. The regressed equations between daily age (D) and increment number in otoliths (N) were N = −0.64 + 0.96D in lapillus, and N = −0.31 + 0.98D in sagitta. The slopes were not significantly different than 1.0. This demonstrated that otolith increments in this species were formed daily and can be used for daily age determination. [ABSTRACT FROM AUTHOR]

Otolith thermal marking was conducted in larval Chinese sucker, Myxocyprinus asiaticus, by exposing the larvae to water with different temperature regimes ranging from heated water (28°C) to chilled water (16°C) at different time intervals. The results showed that increment patterns differed among groups; the control of duration in the heated water could produce some increments much narrower or wider than those deposited in the natural diel water temperature fluctuation; there was a significantly positive relation between increment width and the duration reared in heated water in each cycle of water temperature fluctuation. These increments with abnormal widths were thermal marks in otoliths, and would be used as bar codes to track the released individuals, and discriminate them from the wild populations in the future. The thermal marking is suitable to mass-mark the Chinese sucker larvae. [ABSTRACT FROM AUTHOR]

Prenant's schizothoracin, Schizothorax prenanti, an endemic fish to China, has undergone a dramatic decline in numbers due to human impacts. We studied its genetic diversity in three tributaries of the Yangtze River: the Qingyi River, which has many hydropower dams, and the Dadu River and Muli River where many hydropower dams are being proposed. Using amplified fragment length polymorphism (AFLP), 621 loci were amplified with seven AFLP primer combinations in 45 individuals. The loci were highly polymorphic and heterozygous (87% polymorphism, 30% heterozygosity). The genetic distances within populations were large. The analysis of molecular variance demonstrated that most variation occurred within populations. The estimated fixation index (Φst) value averaged over all polymorphic loci across the three rivers was 0.0837, indicating a moderate genetic differentiation. The differentiations between populations were significant, and population structure was strong. The results suggested that China had wild populations of Prenant's schizothoracin with considerable genetic diversity in the Muli, Dadu and Qingyi rivers. The proposals to dam these rivers should take into account the importance of conserving their genetic quality. [ABSTRACT FROM AUTHOR]

Nine highly polymorphic microsatellite loci were isolated from AC- and GATA-repeat microsatellite enrichment DNA libraries in the rock carp, Procypris rabaudi (Tchang). The number of alleles for these loci ranged from eight to 18 in tested individuals. Polymorphism information content ranged from 0.712 to 0.908 with an average of 0.837. Average observed and expected heterozygosities were 0.719 and 0.870, respectively. These molecular markers will be useful for the assessment of genetic diversity and analysis of population structure in wild rock carp. [ABSTRACT FROM AUTHOR]

The article presents a description of the endangered fish, Cyprinus qionghaiensis Liu, which belongs to the family Cyprinidae. It is commonly known as Qionghai carp and is listed in endangered list in the China Species Red List. Its features include a large head and a laterally compressed body, with a pair of short barbells at corners, thin lips and large eyes. The fish is endemic only in the Qionghai Lake of Sichuan Province in China. Its habitat is the bottom of the lake with clear water, and it mainly feeds on plankton, hydrophytes, benthos and organic debris.

The article features the Zacco chengtui, in the family Cyprinidae, known as Chengdu chub and one of the endangered species of fish in the world. It notes the detailed physical description of Chengdu chub and its distinction from other Zacco species. It also suggests the endemic distribution of the Chengdu chub in Jianjiang River in China.

The article offers information on the fish called Catfish-like loach. The said fish is listed on the China Red Data Book of Endangered Animals, and China Species Red List. It has a scaleless body but densely covered with wart-like epidermal tubercles. Irregular cloud-like bars present on the trunk in large individuals, while eight to 15 regular bars in small ones.

Rock carp (Procypris rabaudi (Tchang)) is an endemic species in the upper Yangtze River drainage. The genetic variability and population structure of eight populations (Mudong (MD), Hejiang (HJ), Wanzhou (WZ), Xishui (XS), Nantan (NT), Cangxi (CX), Tongjiang (TJ) and Wulong (WL)) were investigated based on mitochondrial DNA control region. According to the river dimensions, MD, HJ, WZ, WL and CX were defined as large river populations, while TJ, XS and NT were defined as small. The total genetic diversity level of rock carp was moderate (h = 0.858, p = 0.0079). Genetic differentiations among populations in small rivers were greater than those among populations in large rivers, and small rivers showed significant differentiation from large rivers. Analysis from the coalescent-based method showed that there were asymmetric gene flows among four large river populations (CX, HJ, MD and WZ). Demographic analyses suggested that the species as a whole and the WZ population experienced population expansion, while the HJ, NT, and MD populations experienced bottlenecks. The analysis of genetic diversity and population structure suggested that the WL, TJ, CX, NT and XS populations should be protected and managed separately, and that the HJ, MD and WZ populations should be considered as a genetic management unit. [ABSTRACT FROM AUTHOR]