RNA-Seq Transcriptome Analysis of the Liver and Brain of the Black Carp (Mylopharyngodon piceus) During Fasting.

The black carp (Mylopharyngodon piceus) is an important carnivorous freshwater-cultured species. To understand the molecular basis underlying the response of black carp to fasting, we used RNA-Seq to analyze the liver and brain transcriptome of fasting fish. Annotation to the NCBI database identified 66,609 unigenes, of which 22,841 were classified into the Gene Ontology database and 15,925 were identified in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.

Characterization of the intestinal digesta and mucosal microbiome of the grass carp (Ctenopharyngodon idella).

The intestinal microbiome plays a pivotal role in the nutritional digestion and metabolism of the grass carp (Ctenopharyngodon idella). Here, we characterized the digesta and mucosal microbiome of the anterior, middle, and posterior intestine of the grass carp, using 16S rRNA next-generation sequencing. Based on 16S rRNA amplicon data, Proteobacteria, Firmicutes and Bacteroides were the dominant phyla in the intestine of grass carp.

Complete mitochondrial genome of gray black carp ().

The black carp (), native to eastern Asian, is a large, commercially valuable fish, and has been widely introduced to other countries. In this study, the mitochondrial gene sequence of gray black carp ( MT084757) in Foshan, Guangdong Province was first determined using the Sanger sequencing method. The mitochondrial DNA genome was 16,616 bp in length, including 13 protein-coding genes (PCGs), two rRNA genes, 22 transfer RNA genes, and a non-coding control region (D-loop).

Identification, characterization, and immunological analysis of complement component 4 from grass carp (Ctenopharyngodon idella).

Complement component 4 (C4) has critical immunological functions in vertebrates. In the current study, a C4 homolog (gcC4) was identified in grass carp (Ctenopharyngodon idella). The full-length 5458 bp gcC4 cDNA contained a 5148 bp open reading frame (ORF) encoding a protein of 1715 amino acids with a signal peptide and eight conservative domains.

16S rRNA sequencing analysis of the correlation between the intestinal microbiota and body-mass of grass carp (Ctenopharyngodon idella).

There appears to be a close correlation between intestinal microbiotas and obesity. Still, our understanding of the relationship between the intestinal microbiota and body-mass in grass carp (Ctenopharyngodon idella) remains limited. Herein, we explored this association in the anterior, middle, and posterior intestine of cohabitating grass carp by using next-generation sequencing of the 16S rRNA gene.

Mannan-binding lectin-associated serine protease-1 (MASP-1) mediates immune responses against Aeromonas hydrophila in vitro and in vivo in grass carp.

The mannan-binding lectin-associated serine protease-1 (MASP-1) gene is a crucial component of the lectin pathway in the complement and coagulation cascade. Although MASP-1 has been found in the immune system of teleosts, its immune functions in response to bacterial infection are unclear. In this study, we identified a MASP-1 homolog (gcMASP-1) in the grass carp (Ctenopharyngodon idella).

MicroRNA-induced negative regulation of TLR-5 in grass carp, Ctenopharyngodon idella.

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play crucial roles in numerous biological processes. However, the role of miRNAs in antibacterial defence in fish has not been fully determined. Here, we identified that nine miRNAs are differentially expressed in kidney between susceptible and resistant grass carp strains.

Identification, characterization and immunological analysis of Ras related C3 botulinum toxin substrate 1 (Rac1) from grass carp Ctenopharyngodon idella.

Rac1, a Rho GTPase, serves critical immunological functions in mammals. Here, a Rac1 homolog (gcRac1) was identified in grass carp (Ctenopharyngodon idella). The full-length 2023-base pair gcRac1 cDNA contained a 579-bp open reading frame encoding a 192-residue protein, including a conserved RHO domain and nuclear localization signal.

Determination of reference microRNAs for relative quantification in grass carp (Ctenopharyngodon idella).

Relative quantification is the strategy of choice for processing real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) data in microRNA (miRNA) expression studies. Normalization of relative quantification data is performed by comparison to reference genes. In teleost species, such as grass carp (Ctenopharyngodon idella), the determination of reference miRNAs and the optimal numbers of these that should be used has not been widely studied.

Characterization of MMP-9 gene from grass carp (Ctenopharyngodon idella): an Aeromonas hydrophila-inducible factor in grass carp immune system.

Matrix metalloproteinase-9 (MMP-9) belongs to a family of zinc-dependent endopeptidases and is associated with vital inflammatory processes. Here, we isolated and characterized MMP-9 cDNA from grass carp (Ctenopharyngodon idella) (designated as CiMMP-9). The cDNA was 2880 bp long and encoded a putative protein of 675 amino acids, with a predicted molecular mass of 75.

[Genetic variation analysis of wild populations of grass carp (Ctenopharyngodon idella) using microsatellite markers].

Twelve microsatellites were used to analyze the genetic diversity and genetic structure of eight wild populations of grass carp, among which six populations from Yangtze River (Hanjiang, Wujian, Jiujiang, Shishou, Mudong, and Wanzhou), one population from Pearl River and Heilongjiang River for each, Zhaoqing, and Nenjiang, respectively. Twelve markers showed highly polymorphic and all the eight populations contained high genetic variations. The variations of six populations of Yangtze River and Zhaoqing population of Pearl River were higher than Nenjiang population of Heilongjiang River.

Matrix metalloproteinase 2 of grass carp Ctenopharyngodon idella (CiMMP2) is involved in the immune response against bacterial infection.

The gene encoding matrix metalloproteinase 2 (MMP2) was cloned from grass carp (Ctenopharyngodon idella), and its expression levels during Aeromonas hydrophila infection and embryonic development stages were evaluated. The complete open reading frame of CiMMP2 was 1974 bp in length, encoding a 658-amino acid polypeptide. The deduced MMP2 protein contained four conserved domain structures, including an N-terminal signal sequence, a propeptide domain, three repeats of fibronectin-type II domain inserted in the catalytic domain and a C-terminal hemopexin-like domain.

Molecular cloning, characterization and expression patterns of HSP60 in the grass carp (Ctenopharyngodon idella).

HSP60 is a highly immunogenic molecule, which is able to activate a large number of T cell types and is implicated in a variety of autoimmune diseases. The grass carp (Ctenopharyngodon idella), a freshwater fish species of the family Cyprinidae, accounts for the third biggest value (USD 4.8 billion) at single species level of major cultured fish species in the world.

Cloning and characterization of TIMP-2b gene in grass carp.

Tissue inhibitors of metalloproteinases (TIMPs) are the primary inhibitors of matrix metalloproteinases (MMPs) in tissues. In this study, a TIMP-2 gene was isolated from grass carp Ctenopharyngodon idella (CiTIMP-2b) and characterized. This cDNA sequence encoded a signal peptide, N- and C-terminal domains.

Molecular cloning, characterization and expression analysis of the complement component C6 gene in grass carp.

The complement system, as a representative of innate immunity, plays a key role in the host defense against infections. C6 is the member of complement components creating the membrane attack complex (MAC). In this study, we cloned and characterized the grass carp complement component C6 (gcC6) gene.