Amur catfish is extensively distributed and cultured in Asian countries. Despite of economic importance, the genomic information of this species remains limited. A reference transcriptome of Amur ...catfish was assembled and the sex-biased gene expression in the gonads was characterized using RNA-sequencing. The assembled transcriptome of Amur catfish consisted of 74,840 transcripts. The N50, mean length and max length of transcripts are 1970, 1235 and 16,748 bp. Putative sex-specific transcripts were identified and sex-specific expression of the representative genes was verified by RT-PCR. Differential expression analysis identified 5401 ovary-biased and 5618 testis-biased genes. The ovary-biased genes were mainly enriched in pathways such as RNA transport and ribosome biogenesis in eukaryotes. The testis-biased genes were enriched in calcium signaling and cytokine-cytokine receptor interaction, etc. Our data provide a valuable genomic resource for further investigating the genetic basis of sex determination, sex differentiation and sexual dimorphism of catfish.
•Assembled a reference transcriptome of Amur catfish.•Identified and validated an array of testis-specific genes.•Compared gene expression between adult ovary and testis of Amur catfish.•Revealed the enriched pathways for the ovary- and testis-biased genes.
Chinese giant salamander Andrias davidianus is an endangered species. The success of artificial breeding provides a useful way to protect this species. However, the method to identify the sex and ...mechanism of sex determination were unclear which hinder the improvement of the artificial breeding. Detection of a sex specific marker provides an effective approach to identify genetic sex and investigate the sex determination mechanism.
We used restriction-site-associated DNA (RAD) sequencing to isolate a sex-specific genetic marker in A. davidianus to expand knowledge of the sex determination mechanism. Four male and four female specimens were subjected to RAD sequencing, which generated 934,072,989 reads containing approximately 134.4 Gb of sequences. The first round of comparison of the assembled sequence against the opposite sex raw reads revealed 19,097 female and 17,994 male unmatched sequences. Subsequently, 19,097 female sequences were subjected to a BLAST search against male genomic data, which revealed 308 sequences unmapped to the male genome. One hundred of these were randomly selected and validated by PCR in five male and five female specimens, and four putative sex-specific sequences were produced. Further validation was performed by PCR in another 24 females and 24 males, and all female individuals exhibited the expected specific bands, while the males did not. To apply the sex-specific marker, three specimens reversed from genetic female to physiological male were found in a group exposed to elevated temperature, and 13 individuals reversed from genetic male to physiological female were obtained in a 17β-estradiol exposed group.
This is the first report of a sex-specific marker in A. davidianus and may have potential for elucidation of its sex determination mechanism and, hence, its conservation.
An integrated interferometric fiber optic velocimetry sensor has been proposed and demonstrated at the central wavelength of 638 nm. The sensor is based on the principle of two laser-beams' ...interference. The light signal scattered from the particles or vapor is demodulated to measure the water surface velocity and water vapor velocity. Three velocity measurement experiments are carried out to measure the velocity, and the experimental data shows that the velocity increases linearly in the range of 4 mm·s
to 100 mm·s
, with a slope of linear fitting curve of 0.99777 and the R-Square of 1.00000. The velocity calculated from frequency shift fits well with the reference velocity. The maximum average relative error in the three velocity measurements is less than 2.5%. In addition, the maximum speed of 4.398 m·s
is confirmed in the rotating disk calibration experiment, which expands the sensor's velocity measurement range. To solve the problem that it is difficult to directly measure the velocity of small-scale water surface flow velocity, especially from the aspect of the low velocity of air-water surface, the interferometric fiber optic sensor can be applied to the measurement of water surface velocity and wind velocity on the water surface.
Properly regulated transcriptional responses to environmental perturbations are critical for the fitness of fish. Although gene expression profiles in the tissues of common carp upon cold stress were ...previously characterized, the transcriptional programs underlying cold acclimation are still not well known. In this study, the ability of three common carp strains including Hebao red carp (HB), Songpu mirror carp (SPM) and Yellow river carp (YR) to establish cold resistance after acclimation to a mild hypothermia stress at 18°C for 24 h was confirmed by measurements of the critical thermal minimums (CTMin). The gene expression profiles of the brain and the heart from these strains under both control and cold-acclimated conditions were characterized with RNA-sequencing. The data of the three common carp strains with different genetic background were combined in the differential gene expression analyses to balance the effects of genetic diversity on gene expression. Marked effects of tissue origins on the cold-induced transcriptional responses were revealed by comparing the differentially expressed gene (DEG) lists of the two tissues. Functional categories including spliceosome and RNA splicing were highly enriched in the DEGs of both tissues. However, steroid biosynthesis was specifically enriched in DEGs of the brain and response to unfolded protein was solely enriched in DEGs of the heart. Consistent with the up-regulation of the genes involved in cholesterol biosynthesis, total cholesterol content of the brain was significantly increased upon cold stress. Moreover, cold-induced alternative splicing (AS) events were explored and AS of the
rbmx
(RNA-binding motif protein, X chromosome) gene was confirmed by real-time quantitative PCR. Finally, a core set of cold responsive genes (CRGs) were defined by comparative transcriptomic analyses. Our data provide insights into the transcriptional programs underlying cold acclimation of common carp and offer valuable clues for further investigating the genetic determinants for cold resistance of farmed fish.
Chinese giant salamander
has strong tolerance to starvation. Fasting triggers a complex array of adaptive metabolic responses, a process in which the liver plays a central role. Here, a ...high-throughput proteomic analysis was carried out on liver samples obtained from adult
after 3, 7, and 11 months of fasting. As a result, the expression levels of 364 proteins were significantly changed in the fasted liver. Functional analysis demonstrated that the expression levels of key proteins involved in fatty acid oxidation, tricarboxylic acid cycle, gluconeogenesis, ketogenesis, amino acid oxidation, urea cycle, and antioxidant systems were increased in the fasted liver, especially at 7 and 11 months after fasting. In contrast, the expression levels of vital proteins involved in pentose phosphate pathway and protein synthesis were decreased after fasting. We also found that fasting not only activated fatty acid oxidation and ketogenesis-related transcription factors PPARA and PPARGC1A, but also activated gluconeogenesis-related transcription factors FOXO1, HNF4A, and KLF15. This study confirms the central role of lipid and acetyl-CoA metabolism in
liver in response to fasting at the protein level and provides insights into the molecular mechanisms underlying the metabolic response of
liver to fasting.
To provide the theoretical basis for researching growth, development, and molecular marker-assisted breeding of the economically important Yellow River carp (
) using dynamic quantitative trait locus ...(QTL) mapping, we constructed three genetic linkage maps from 207 progeny using a new modified genotyping-by-sequencing method. The three maps contained 16,886, 16,548, and 7482 single nucleotide polymorphism markers, respectively, with an average interval of 0.36 cM, 0.45 cM, and 1.00 cM. We identified 148 QTLs related to four growth traits that were located on 25 chromosomes from three growth stages of Yellow River carp. A total of 32, 36, 43, and 37 QTLs were associated with body length, height, width, and weight, respectively. Among them, 47 QTLs were detected for only one growth trait in one stage, but all of the other QTLs were co-localized. Of the 14 main QTLs, 13 were located on chromosome 12, which suggests the presence of growth-related genes on this chromosome. We then detected 17 candidate genes within 50 K upstream and downstream of the 14 main QTLs. This is the first report of the dynamic QTL mapping of growth traits of Yellow River carp, and the results can be used in future studies of growth, development, and molecular-assisted breeding of this species.
The identification and expression of germ cells are important for studying sex-related mechanisms in fish. The vasa gene, encoding an ATP-dependent RNA helicase, is recognized as a molecular marker ...of germ cells and plays a crucial role in germ cell development. Silurus asotus , an important freshwater economic fish species in China, shows significant sex dimorphism with the female growing faster than the male. However, the molecular mechanisms underlying these sex differences especially involving in the vasa gene in this fish remain poorly understood. In this work, the vasa gene sequence of S. asotus (named as Savasa ) was obtained through RT-PCR and rapid amplification of cDNA end (RACE), and its expression in embryos and tissues was analyzed using qRT-PCR and an in situ hybridization method. Letrozole (LT) treatment on the larvae fish was also conducted to investigate its influence on the gene. The results revealed that the open reading frame (ORF) of Savasa was 1989 bp, encoding 662 amino acids. The SaVasa protein contains 10 conserved domains unique to the DEAD-box protein family, showing the highest sequence identity of 95.92% with that of Silurus meridionalis . In embryos, Savasa is highly expressed from the two-cell stage to the blastula stage in early embryos, with a gradually decreasing trend from the gastrula stage to the heart-beating stage. Furthermore, Savasa was initially detected at the end of the cleavage furrow during the two-cell stage, later condensing into four symmetrical cell clusters with embryonic development. At the gastrula stage, Savasa -positive cells increased and began to migrate towards the dorsal side of the embryo. In tissues, Savasa is predominantly expressed in the ovaries, with almost no or lower expression in other detected tissues. Moreover, Savasa was expressed in phase I–V oocytes in the ovaries, as well as in spermatogonia and spermatocytes in the testis, implying a specific expression pattern of germ cells. In addition, LT significantly upregulated the expression of Savasa in a concentration-dependent manner during the key gonadal differentiation period of the fish. Notably, at 120 dph after LT treatment, Savasa expression was the lowest in the testis and ovary of the high concentration group. Collectively, findings from gene structure, protein sequence, phylogenetic analysis, RNA expression patterns, and response to LT suggest that Savasa is maternally inherited with conserved features, serving as a potential marker gene for germ cells in S.asotus , and might participate in LT-induced early embryonic development and gonadal development processes of the fish. This would provide a basis for further research on the application of germ cell markers and the molecular mechanisms of sex differences in S. asotus .
The largemouth bass (
), an economically important freshwater fish species widely farmed in China, is traditionally cultured using a diet of forage fish. However, given the global decline in forage ...fish fisheries and increasing rates of waterbody pollution and disease outbreaks during traditional culturing, there is a growing trend of replacing forage fish with formulated feed in the largemouth bass breeding industry. The specific molecular mechanisms associated with such dietary transition in this fish are, nevertheless, poorly understood.
To identify single nucleotide polymorphisms (SNPs) related to food habit domestication traits and growth traits in largemouth bass fry, we initially genotyped fry using eight candidate SNPs based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, with genetic parameters being determined using Popgen32 and Cervus 3.0. Subsequently, we assessed the associations between food habit domestication traits of largemouth bass fry and these SNPs using the Chi-square test or Fisher's exact test. Furthermore, we used a general linear model to assess the relationships between the growth traits of largemouth bass fry and these SNPs. The Pearson correlation coefficient between growth traits and the SNPs was also determined using bivariate correlation analysis in IBM SPSS Statistics 22. Finally, the phenotypic variation explained (PVE) by the SNPs was calculated by regression analysis in Microsoft Excel.
The genotyping results obtained based on PCR-RFLP analysis were consistent with those of direct sequencing. Five SNPs (SNP01, SNP02, SNP04, SNP05, and SNP06) were found to be significantly correlated with the food habit domestication traits of fry (
< 0.05); SNP01 (
= 0.0011) and SNP04 (
= 0.0055) particularly, had showed highly significant associations. With respect to growth traits, we detected significant correlations with the two SNPs (SNP01 and SNP07) (
< 0.05), with SNP01 being significantly correlated with body length, and height (
< 0.05), and SNP07 being significantly correlated with body height only (
< 0.05).
Our findings indicated that the PCR-RFLP can be used as a low-cost genotyping method to identify SNPs related to food habit domestication and growth traits in largemouth bass, and that these trait-related SNPs might provide a molecular basis for the future breeding of new varieties of largemouth bass.
To screen the quantitative trait loci (QTL) and genes related to the growth of Yellow River carp (Cyprinus carpio haematopterus) after removing the maternal effect, we established a family of these ...carps. Four growth-related traits (body length, height, thickness, and weight) of the family at 5 and 17 months after hatching (MAH) were measured. Analysis of QTL mapping for the four growth-related traits was conducted using the genetic linkage map constructed in our laboratory. We identified 47 QTL that were related to the four growth traits and three consensus QTL (cQTL). A total of 10, 14, 10, and 13 QTL were associated with body length, height, thickness, and weight, respectively; cQTL-1, cQTL-2, and cQTL-3 contained 11, 2, and 2 QTL, respectively. We detected 17 growth-related candidate genes within 50 Kb upstream and downstream of the five main-effect QTL (phenotypic variation explained > 10%, logarithm of odds > 5.5). Two genes (cbfa2t2 and neca1) that may be affected by maternal effects were identified by comparing the main-effect QTL at 17 and 5–17 MAH. This study was the first attempt to eliminate growth-related QTL and genes affected by maternal effects in Yellow River carp. These results can be used in molecular marker-assisted breeding and provide valuable genomic resources for the genetic mechanisms underlying growth in Yellow River carp.
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