Transcriptome characterization of HPG axis from Chinese sea perch Lateolabrax maculatus

Transcriptomics-based analysis of neurotoxic and reproductive effects in turbot (Scophthalmus maximus) after exposure to tris (2-chloroethyl) phosphate (TCEP)

BACKGROUND

Tris (2-chloroethyl) phosphate (TCEP), a widely used flame retardant, is widespread in the environment and potentially harmful to organisms. However, the specific mechanisms of TCEP-induced neurological and reproductive toxicity in fish are largely unknown. Turbot (Scophthalmus maximus) is cultivated on a large scale, and the emergence of pollutants with endocrine disrupting effects seriously affects its economic benefits. This study aimed to investigate the toxic effects of TCEP on turbot by integrating physio-biochemical and transcriptomic analyses.

RESULTS

TCEP exposure induced severe neuroendocrine disrupting effects in turbot. Firstly, the hormone levels of luteinizing hormone (LH), follicle-stimulating hormone (FSH), estradiol (E2), and 11-ketotestosterone (11-KT) were significantly decreased under prolonged TCEP stress, which may have a negative impact on normal reproductive function. We identified and summarized representative differentially expressed genes (DEGs) and their functions, such as endocrine system and oxidative stress. Pathway enrichment showed that the toxicological characteristics of TCEP on turbot were neuroendocrine regulation disorders, including oxidative phosphorylation, apoptosis, steroid biosynthesis, GnRH signaling pathway and so on. Weighted gene co-expression network analysis (WGCNA) also revealed key genes involved in these pathways. Among these genes, those encoding the components of the electron transport chain presented an initial increase in expression followed by a decrease, indicating that TCEP stress might affect mitochondrial function and lead to cell damage. This finding was also supported by the upregulation of apoptosis-related gene expression. Moreover, acute exposure to TCEP regulated MAPK-mediated transduction and regulation of GnRH signaling, thereby altering the expression of hypothalamic-pituitary-gonadal (HPG) axis-related genes.

CONCLUSIONS

These findings revealed the endocrine disrupting effects of TCEP on turbot and identified biomarkers related to reproductive toxicity, providing early warning for the monitoring of healthy aquaculture.

Chronic low salinity stress rescued masculinization effect in farmed Cynoglossus semilaevis population

Salinity, being an indispensable abiotic factor crucial for the survival of marine organisms, has demonstrated diverse alterations globally in response to the current trend of global warming. In this study, the effect of chronic low salinity stress on teleosts' sex differentiation was investigated using Cynoglossus semilaevis, an economically important fish with both genetic and environmental sex determination system. The cultivation experiment was conducted employing artificially simulated seawater of 20 ppt and ambient sea water of 30 ppt to rear juveniles C. semilaevis. Throughout the experiment, the growth performance was assessed and the histology of gonadal development was examined, a significantly lower masculinization rate was observed in LS group. To gain further insights, transcriptome analysis was conducted using raw reads obtained from 53 libraries derived from gonads of 55 days post fertilization (dpf) and 100 dpf juveniles in both LS and CT groups. GO/KEGG enrichment were further proceeded, Terms and pathways involved in reproduction ability, germ cell proliferation, immune function, steroid metabolism etc., were illuminated and a possible crosstalk between HPI and HPG axis was proposed. WGCNA was conducted and two hub genes, hspb8-like and Histone H2A.V were exhibited to be of great significance in the changes of masculinization rate. Our findings provided solid reference for sex differentiation study of GSD + ESD species in a constantly changing ocean environment, as well as practice guiding significance for the environmental management for the culture of C. semilaevis.

Transcriptome characterization of BPG axis and expression profiles of ovarian steroidogenesis-related genes in the Japanese sardine

Background

The clupeoid fishes are ecologically and commercially important fish species worldwide that exhibit a high level of population fluctuation, accompanied by alteration of reproductive traits. However, knowledge about their reproductive physiology in order to understand mechanisms underlying such population dynamics is limited. The endocrine system along with the brain–pituitary–gonadal (BPG) axis is critical for regulating reproduction. The aims of this study were to provide transcript data and genes related to the BPG axis, and to characterize the expression profiles of ovarian steroidogenesis-related genes in the Japanese sardine (Sardinops melanostictus, Clupeidae).

Results

RNA sequencing was performed using the sardine brain, pituitary, and gonad in both sexes. A total of 290,119 contigs were obtained and 115,173 non-redundant ORFs were annotated. The genes differentially expressed between ovary and testis were strongly associated with GO terms related to gamete production. The tissue-specific profile of the abundance of transcripts was characterized for the major regulators in the BPG axis, such as gonadotropin-releasing hormone, gonadotropin, and steroidogenic enzyme. By comparing between ovary and testis, out of eight different 17β-hydroxysteroid dehydrogenase (Hsd17b) genes identified, higher hsd17b7 expression was found in testis, whereas higher expression of hsd17b8, hsd17b10, hsd17b12a, and hsd17b12b was found in ovary. The cDNAs encoding key endocrine factors in the ovarian steroidogenic pathway were cloned, sequenced, and quantitatively assayed. In the pituitary, follicle-stimulating hormone beta peaked during vitellogenesis, while luteinizing hormone beta peaked at the completion of vitellogenesis. In the ovary, follicle-stimulating hormone receptor and luteinizing hormone receptor were upregulated from mid- to late phase of vitellogenesis. Furthermore, three steroidogenic enzyme genes (cyp11a1, cyp17a1, and cyp19a1a) gradually increased their expression during ovarian development, accompanying a rise in serum estradiol-17β, while 3β-hydroxysteroid dehydrogenase and steroidogenic acute regulatory protein did not change significantly.

Conclusions

This is the first report of deep RNA sequencing analysis of Japanese sardine, in which many key genes involved in the BPG axis were identified. Expression profiles of ovarian steroidogenesis-related genes provide a molecular basis of the physiological processes underlying ovarian development in the sardine. Our study will be a valuable resource for clarifying the molecular biology of clupeoid fishes.

De novo transcriptome assembly of four organs of Collichthys lucidus and identification of genes involved in sex determination and reproduction

The spinyhead croaker (Collichthys lucidus) is a commercially important fish species, which is mainly distributed in the coastal regions of China. However, little is known about the molecular regulatory mechanism underlying reproduction in C. lucidus. A de novo transcriptome assembly in brain, liver, ovary and testis tissues of C. lucidus was performed. Illumina sequencing generated 60,322,004, 57,044,284, 60,867,978 and 57,087,688 clean reads from brain, liver, ovary and testis tissues of C. lucidus, respectively. Totally, 131,168 unigenes with an average length of 644 bp and an N50 value of 1033 bp were assembled. In addition, 1288 genes were differentially expressed between ovary and testis, including 442 up-regulated and 846 down-regulated in ovary. Functional analysis revealed that the differentially expressed genes between ovary and testis were mainly involved in the function of sexual reproduction, sex differentiation, development of primary male sexual characteristics, female gamete generation, and male sex differentiation. A number of genes which might be involved in the regulation of reproduction and sex determination were found, including HYAL and SYCP3 and BMP15. Furthermore, 35,476 simple sequence repeats (SSRs) were identified in this transcriptome dataset, which would contribute to further genetic and mechanism researches. De novo transcriptome sequencing analysis of four organs of C. lucidus provides rich resources for understanding the mechanism of reproductive development of C. lucidus and further investigation of the molecular regulation of sex determination and reproduction of C. lucidus.

Genome-wide identification and characterization of glucose transporter (glut) genes in spotted sea bass (Lateolabrax maculatus) and their regulated hepatic expression during short-term starvation

The glucose transporters (GLUTs) are well known for their essential roles in moving the key metabolites, glucose, galactose, fructose and a number of other important substrates in and out of cells. In this study, we identified a total of 21 glut genes in spotted sea bass (Lateolabrax maculatus) through extensive data mining of existing genomic and transcriptomic databases. Glut genes of spotted sea bass were classified into three subfamilies (Class I, Class II and Class III) according to the phylogenetic analysis. Glut genes of spotted sea bass were distributed in 15 out of 24 chromosomes. Deduced gene structure analysis including the secondary structure and the three-dimensional structures, as well as the syntenic analysis further supported their annotations and orthologies. Expression profile in healthy tissues indicated that 9 of 21 glut genes were expressed in liver of spotted sea bass. During short-term starvation, the mRNA expression levels of 3 glut genes (glut2, glut5, and glut10) were significantly up-regulated in liver (P < 0.05), indicating their potential roles in sugar transport and consumption. These findings in our study will facilitate the further evolutionary characterization of glut genes in fish species and provide a theoretical basis for their functional study.

Chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus

Background

The spotted sea bass (Lateolabrax maculatus) is a valuable commercial fish that is widely cultured in China. While analyses using molecular markers and population genetics have been conducted, genomic resources are lacking.

Findings

Here, we report a chromosome-scale assembly of the spotted sea bass genome by high-depth genome sequencing, assembly, and annotation. The genome scale was 0.67 Gb with contig and scaffold N50 length of 31 Kb and 1,040 Kb, respectively. Hi-C scaffolding of the genome resulted in 24 pseudochromosomes containing 77.68% of the total assembled sequences. A total of 132.38 Mb repeat sequences were detected, accounting for 20.73% of the assembled genome. A total of 22, 015 protein-coding genes were predicted, of which 96.52% were homologous to proteins in various databases. In addition, we constructed a phylogenetic tree using 1,586 single-copy gene families and identified 125 unique gene families in the spotted sea bass genome.

Conclusions

We assembled a spotted sea bass genome that will be a valuable genomic resource to understanding the biology of the spotted sea bass and will also lead to the development of molecular breeding techniques to generate spotted sea bass with better economic traits.

Evaluation of potential reference genes for quantitative RT-PCR analysis in spotted sea bass (Lateolabrax maculatus) under normal and salinity stress conditions

The aim of this study was to select the most suitable reference genes for quantitative real-time polymerase chain reaction (qRT-PCR) of spotted sea bass (Lateolabrax maculatus), an important commercial marine fish in Pacific Asia, under normal physiological and salinity stress conditions. A total of 9 candidate reference genes (HPRT, GAPDH, EF1A, TUBA, RPL7, RNAPol II, B2M, ACTB and 18S rRNA) were analyzed by qRT-PCR in 10 tissues (intestine, muscle, stomach, brain, heart, liver, gill, kidney, pectoral fins and spleen) of L. maculatus. Four algorithms, geNorm, NormFinder, BestKeeper, and comparative ΔCt method, were used to evaluate the expression stability of the candidate reference genes. The results showed the 18S rRNA was most stable in different tissues under normal conditions. During salinity stress, RPL7 was the most stable gene according to overall ranking and the best combination of reference genes was RPL7 and RNAPol II. In contrast, GAPDH was the least stable gene which was not suitable as reference genes. The study showed that different algorithms might generate inconsistent results. Therefore, the combination of several reference genes should be selected to accurately calibrate system errors. The present study was the first to select reference genes of L. maculatus by qRT-PCR and provides a useful basis for selecting the appropriate reference gene in L. maculatus. The present study also has important implications for gene expression and functional genomics research in this species or other teleost species.