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Transcriptome analysis and microsatellite discovery in the blunt snout bream (Megalobrama amblycephala) after challenge with Aeromonas hydrophila

Tran, Ngoc Tuan, Gao, Ze-Xia, Zhao, Hong-Hao, Yi, Shao-Kui, Chen, Bo-Xiang, Zhao, Yu-Hua, Lin, Li, Liu, Xue-Qin, Wang, Wei-Min
Fish & shellfish immunology 2015 v.45 no.1 pp. 72-82
Aeromonas hydrophila, Danio rerio, Megalobrama amblycephala, National Center for Biotechnology Information, aquaculture, bacteria, bacterial infections, cDNA libraries, complementary DNA, databases, defense mechanisms, farmed fish, freshwater, freshwater fish, gene expression, gene expression regulation, herbivores, immune response, immunogenetics, indigenous species, microsatellite repeats, pathogens, proteins, quantitative polymerase chain reaction, reverse transcriptase polymerase chain reaction, sequence homology, signal transduction, tissues, transcriptome, transcriptomics, unigenes, China
The blunt snout bream, Megalobrama amblycephala, is a herbivorous freshwater fish species native to China and a major aquaculture species in Chinese freshwater polyculture systems. In recent years, the bacterium Aeromonas hydrophila has been reported to be its pathogen causing great losses of farmed fish. To understand the immune response of the blunt snout bream to A. hydrophila infection, we used the Solexa/Illumina technology to analyze the transcriptomic profile after artificial bacterial infection. Two nonnormalized cDNA libraries were synthesized from tissues collected from control blunt snout bream or those injected with A. hydrophila. After assembly, 155,052 unigenes (average length 692.8 bp) were isolated. All unigenes were annotated using BLASTX relative to several public databases: the National Center for Biotechnology Information nonreduntant (Nr) database, SwissProt, Eukaryotic Orthologous Groups of proteins (KOG), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO). The sequence similarity (86%) of the assembled unigenes was to zebrafish based on the Nr database. A number of unigenes (n = 30,482) were assigned to three GO categories: biological processes (25,242 unigenes), molecular functions (26,096 unigenes), and cellular components (22,778 unigenes). 20,909 unigenes were classified into 25 KOG categories and 28,744 unigenes were assigned into 315 specific signaling pathways. In total, 238 significantly differentially expressed unigenes (mapped to 125 genes) were identified: 101 upregulated genes and 24 downregulated genes. Another 303 unigenes were mapped to unknown or novel genes. Among the known expressed genes identified, 53 were immune-related genes and were distributed in 71 signaling pathways. The expression patterns of selected up- and downregulated genes from the control and injected groups were determined with reverse transcription–quantitative PCR (RT–qPCR). Microsatellites (n = 10,877), including di-to pentanucleotide repeat motifs, were also identified in the blunt snout bream transcriptome profiles. This study extends our understanding of the immune defense mechanisms of the blunt snout bream against A. hydrophila and provides useful data for further studies of the immunogenetics of this species.