FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research.

We launched the initial version of FishTEDB in 2018, which aimed to establish an open-source, user-friendly, data-rich transposable element (TE) database. Over the past 5 years, FishTEDB 1.0 has gained approximately 10 000 users, accumulating more than 450 000 interactions.

Adaptive evolution of mitochondrial genomes in Triplophysa cavefishes.

Extreme conditions in caves pose survival challenges for cave dwellers, who gradually develop adaptive survival features. Cavefishes are one of the most successful animals among cave dwellers. Triplophysa cavefishes are an important group of cavefishes, and they show remarkable adaptability to the extreme environments of caves.

A study on the mechanism of Indium phosphide/zinc sulfide core/shell quantum dots influencing embryo incubation of rare minnow (Gobiocypris rarus).

Quantum dots (QDs) inhibit fish hatching, but the mechanism is still unclear. In this study, the effect of Indium phosphide/zinc sulfide quantum dots (InP/ZnS QDs) on the embryo incubation of rare minnow was investigated. Five experimental concentration groups were set up according to the preliminary experimental results, which were 0, 50, 100, 200 and 400 nM.

Molecular evolution of the hemoglobin gene family across vertebrates.

Adaptation to various altitudes and oxygen levels is a major aspect of vertebrate evolution. Hemoglobin is an erythrocyte protein belonging to the globin superfamily, and the α-, β-globin genes of jawed vertebrates encode tetrameric ((αβ) hemoglobin, which contributes to aerobic metabolism by delivering oxygen from the respiratory exchange surfaces into cells. However, there are various gaps in knowledge regarding hemoglobin gene evolution, including patterns in cartilaginous fish and the roles of gene conversion in various taxa.

Exposure to acute waterborne cadmium caused severe damage on lipid metabolism of freshwater fish, revealed by nuclear lipid droplet deposition in hepatocytes of rare minnow.

Cadmium (Cd) is a widely distributed aquatic toxic heavy metal with the potential to disrupt fish metabolism; however, more research is needed to clarify the underlying mechanisms. In the present study, rare minnows (Gobiocypris rarus) were used to detect the effects of cadmium on freshwater fish lipid metabolism and its underlying mechanism by histopathological observation, measurement of serum and liver biochemical indexes, and analysis of gene expression in terms of lipid oxidation, synthesis and transport. Here, severe damage, such as cytoplasmic lipid droplet (LD) accumulation, ectopic deposition of LDs, and the appearance of nuclear LDs (nLDs), was detected after exposure to 2.

Sympatric or micro-allopatric speciation in a glacial lake? Genomic islands support neither.

Apparent cases of sympatric speciation may actually be due to micro-allopatric or micro-parapatric speciation. One way to distinguish between these models is to examine the existence and nature of genomic islands of divergence, wherein divergent DNA segments are interspersed with low-divergence segments. Such islands should be rare or absent under micro-allopatric speciation but common in cases of speciation with gene flow.

InP/ZnS quantum dots cause liver damage in rare minnow (Gobiocypris rarus) larvae.

InP/ZnS quantum dots (QDs) are widely used in biomedical imaging and light-emitting component manufacturing industries, but there are few studies on their biological toxicity. In this study, we conducted experiments with rare minnow larvae and found that InP/ZnS QDs can cause liver damage. InP/ZnS QDs appeared only in the intestine of larvae and were not enriched in other parts of the larvae.

Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes.

All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome-wide evolutionary signatures of cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole-genome assembly of the Chinese cavefish Triplophysa rosa.

Reproductive toxicity of InP/ZnS QDs in male rare minnow (Gobiocypris rarus).

InP/ZnS quantum dots (QDs) stand out among cadmium-free alternatives for higher exciton Bohr radius and strong quantum confined effect. In this study, the reproductive toxicity and mechanism of InP/ZnS QDs at different concentrations in male Chinese rare minnows (Gobiocypris rarus) were investigated. The results showed that QDs in 800 nmol/L concentration group could enter the testes after 1 d of exposure and caused changes in the structure of the testes, including the scattered distribution of seminal vesicles, reduction in germ cells and vacuolation in some areas of interstitial cells.

Parental exposure to CdSe/ZnS QDs affects cartilage development in rare minnow (Gobiocypris rarus) offspring.

Cartilage development is a sensitive process that is easily disturbed by environmental toxins. In this study, the toxicity of CdSe/ZnS quantum dots on the skeleton of the next generation (F1) was evaluated using rare minnows (Gobiocypris rarus) as model animals. Four-month-old sexually mature parental rare minnows (F0) were selected and treated with 0, 100, 200, 400 and 800 nmol/L CdSe/ZnS quantum dots for 4 days.

Molecular Evolution of clock Genes in Vertebrates.

Circadian rhythms not only influence the overall daily routine of organisms but also directly affect life activities to varying degrees. Circadian locomotor output cycle kaput (Clock), the most critical gene in the circadian rhythm feedback system, plays an important role in the regulation of biological rhythms. Here, we aimed to elucidate the evolutionary history of the clock gene family in a taxonomically diverse set of vertebrates, providing novel insights into the evolution of the clock gene family based on 102 vertebrate genomes.

Toxic effects of ZnSe/ZnS quantum dots on the reproduction and genotoxiticy of rare minnow (Gobiocypris rarus).

ZnSe/ZnS quantum dots (QDs) have excellent optical properties, but researchers have not clearly determined whether they cause harm to organisms. In the present study, the effect of ZnSe/ZnS QDs on the parents and offspring of rare minnow were evaluated for the first time. Exposure to ZnSe/ZnS QDs altered the testicular structure, caused sperm DNA damage and decreased sperm motility in males.

, a new species of cave-dwelling loach (Teleostei, Nemacheilidae) from Chongqing, Southwest China.

We describe a new species of cave-dwelling loach, , based on specimens collected in a subterranean pool in a cave in Wulong County, Chongqing, Southwest China. The pool is connected to the Wujiang River drainage. differs from its congeners by the following combination of characters: eyes present, caudal fin with 18 branched rays; posterior chamber of the air bladder degenerate; stomach U-shaped; intestine without bends or loops immediately posterior to stomach; body smooth and scaleless, and lateral line complete.

Morphometric and population genomic evidence for species divergence in the Chimarrichthys fish complex of the Tibetan Plateau.

The uplift of the Tibetan Plateau altered the environmental conditions of the local area substantially. Here, we conducted a comprehensive investigation based on morphometrics, population genomics, and climatic factors to evaluate phenotypic and genome-level variations in a radiation of Chimarrichthys catfish endemic to the Plateau. Discriminant function analysis showed phenotypic differences of Chimarrichthys between rivers with respect to elevation.

Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis).

Background: The western mosquitofish (Gambusia affinis) is a sexually dimorphic poeciliid fish known for its worldwide biological invasion and therefore an important research model for studying invasion biology. This organism may also be used as a suitable model to explore sex chromosome evolution and reproductive development in terms of differentiation of ZW sex chromosomes, ovoviviparity, and specialization of reproductive organs. However, there is a lack of high-quality genomic data for the female G.

Standards for Methods Utilizing Environmental DNA for Detection of Fish Species.

Environmental DNA (eDNA) techniques are gaining attention as cost-effective, non-invasive strategies for acquiring information on fish and other aquatic organisms from water samples. Currently, eDNA approaches are used to detect specific fish species and determine fish community diversity. Various protocols used with eDNA methods for aquatic organism detection have been reported in different eDNA studies, but there are no general recommendations for fish detection.

Characterization of Myxidium spinibarba sp. nov. (Cnidaria, Myxosporea, Myxidiidae) from Spinibarbus sinensis (Bleeker, 1871) in Chongqing China.

In the present study, we described a new species of Myxidium Bütschli, 1882, obtained from the gallbladder of Spinibarbus sinensis (Bleeker, 1871) from the Jialing River in Chongqing, China. Myxidium spinibarba sp. nov.

Comparative Transcriptome Profiling of the Loaches and Reveals Potential Mechanisms of Eye Degeneration.

Eye degeneration is one of the most obvious characteristics of organisms restricted to subterranean habitats. In cavefish, eye degeneration has evolved independently numerous times and each process is associated with different genetic mechanisms. To gain a better understanding of these mechanisms, we compared the eyes of adult individuals of the cave loach and surface loach .

Triplophysa sanduensis, a new loach species of nemacheilid (Teleostei: Cypriniformes) from South China.

A new species of Nemacheilidae, Triplophysa sanduensis sp. nov., is described here based on specimens collected from a small cave in Dengguang Village, Zhonghe Town, Sandu County, Guizhou Province, China.

Evolution and diversity of transposable elements in fish genomes.

Transposable elements (TEs) are genomic sequences that can move, multiply, and often form sizable fractions of vertebrate genomes. Fish belong to a unique group of vertebrates, since their karyotypes and genome sizes are more diverse and complex, with probably higher diversity and evolution specificity of TE. To investigate the characteristics of fish TEs, we compared the mobilomes of 39 species, and observed significant variation of TE content in fish (from 5% in pufferfish to 56% in zebrafish), along with a positive correlation between fish genome size and TE content.

Highly Resolved Phylogenetic Relationships within Order Acipenseriformes According to Novel Nuclear Markers.

Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called "living fossil" species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear genetic data, leaving questions as to their phylogenetic relationships. This study aimed to utilize a bioinformatics approach to screen for candidate single-copy nuclear genes, using transcriptomic data from sturgeon species and genomic data from the spotted gar, .