A chromosome-level genome assembly of Hong Kong catfish (Clarias fuscus) uncovers a sex-determining region.

BACKGROUND: Hong Kong catfish (Clarias fuscus) is an ecologically and economically important species that is widely distributed in freshwater regions of southern China. Hong Kong catfish has significant sexual growth dimorphism. The genome assembly of the Hong Kong catfish would facilitate study of the sex determination and evolution mechanism of the species. RESULTS: The first high-quality chromosome-level genome of the Hong Kong catfish was constructed. The total genome was 933.4 Mb, with 416 contigs and a contig N50 length of 8.52 Mb. Using high-throughput chromosome conformation capture (Hi-C) data, the genome assembly was divided into 28 chromosomes with a scaffold N50 length of 36.68 Mb. A total of 23,345 protein-coding genes were predicted in the genome, and 94.28% of the genes were functionally annotated in public databases. Phylogenetic analysis indicated that C. fuscus and Clarias magur diverged approximately 63.7 million years ago. The comparative genome results showed that a total of 60 unique, 353 expanded and 851 contracted gene families were identified in Hong Kong catfish. A sex-linked quantitative trait locus identified in a previous study was located in a sex-determining region of 30.26 Mb (0.02 to 30.28 Mb) on chromosome 13 (Chr13), the predicted Y chromosome. This QTL region contained 785 genes, of which 18 were identified as sex-related genes. CONCLUSIONS: This study is the first to report the chromosome-level genome assembly of Hong Kong catfish. The study provides an excellent genetic resource that will facilitate future studies of sex determination mechanisms and evolution in fish.

Regulation of the activity and expression of aryl hydrocarbon receptor by ethanol in mouse hepatic stellate cells.

BACKGROUND: During the course of alcohol-induced liver damage, hepatic stellate cells are transformed into proliferative, fibrogenic, and contractile myofibroblasts. Aryl hydrocarbon receptor (AhR) is a transcription factor that controls the expression of genes involved in the metabolism of xenobiotics, inflammation, cell proliferation, and death. METHODS: Immortal mouse hepatic stellate cells (MHSCs) were isolated from transgenic mice that expressed a thermolabile SV40 tumor antigen. Quantitative real-time reverse transcription polymerase chain reaction assays, Western blot analysis, promoter activity assays, and chromatin immunoprecipitation analyses were performed for studying the effect of ethanol (EtOH) on AhR expression and transcriptional activity. RESULTS: Treatment of MHSCs with 50 to 200 mM EtOH for 6 hours induced AhR nuclear translocation, enhanced the promoter activity of cytochrome P450 (CYP) 1A1, increased the amount of AhR bound to the promoter of CYP1A1 and 1B1, and up-regulated the mRNA expression of these AhR target genes in a dose-dependent manner. In contrast, EtOH exposure down-regulated AhR mRNA and protein expression. Similarly, benzo(a)pyrene (BaP) at 10 nM reduced AhR and increased CYP1A1 and 1B1 mRNAs. Pretreatment of MHSCs with 50 mM EtOH for 7 days diminished the capacity of MHSCs to express CYP1A1 and 1B1 induced by a 200 mM EtOH challenge, or by 10 nM BaP. However, the up-regulatory effect of EtOH on solute carrier family 16, member 6 (SLC16a6) was unaffected by EtOH pretreatment. Similar to EtOH, dimethyl sulfoxide (DMSO) at concentrations of 50 to 100 mM down-regulated AhR and up-regulated CYP1A1 mRNA expression in a dose-dependent manner. CONCLUSIONS: These data, for the first time, demonstrate that EtOH activates MHSC AhR and down-regulates its expression. Chronic EtOH pretreatment lowers the availability of AhR, and specifically diminishes the inducibility of CYP genes. The effect on AhR appears to not be an EtOH-specific response, as DMSO alone (and possibly other organic solvents) was also able to activate AhR.

[Effect of temperature on the fertility restoration of different two-line hybrid rice].

On the basis of the fertility observation of hybrids from Pei'ai 64S and Nongken 58S crossed with an indica variety Nanjing11 and japonica marker line FL235, respectively, The plant growth chambers were employed to expose the F2 plant individuals to such different day mean temperature as 24 degrees C, 27 degrees C and 30 degrees C during natural long hour daylight from July to August in Wuhan (30 degrees 27' N), with a view to analyzing the difference in the temperature sensitivity of fertility between the two kinds of different fertility-restoring genes for two years running. The results showed that, whether it was under long daylight and high temperature or under long daylight and middle temperature, the mean natural seed-set percent of F1 was higher than 68.75%, suggesting that Nanjing11 could completely restore the fertility of Pei'ai 64S. And however, under natural high temperature condition, N58S x FL235 F1 could set seed naturally with 21.93%-26.75%, the mean natural seed set percent of F1 was 46.36%-48.38% in natural middle temperature condition, ability of FL235 to restore the fertility of N58S was affected by high temperature. Further analysis proved that temperature could not alter the inheritance mode of F2 but affect the extent of fertility genes expression in Nanjing11. On the other hand, the expression of fertility-genes of FL235 was sensitive to high temperature, whose the putative critical temperature was 27 degrees C, and high temperature influenced not only the genetic interactions but also the segregation modes in F2 generations.