Abstract
In order to understand the molecular basis underlying the host immune response of koi carp (Cyprinus carpio), Illumina HiSeqTM 2000 is used to analyze the muscle and spleen transcriptome of koi carp infected with Aeromonas sobria (A. sobria). De novo assembly of paired-end reads yielded 69,480 unigenes, of which the total length, average length, N50, and GC content are 70,120,028 bp, 1037 bp, 1793 bp, and 45.77%, respectively. Annotation is performed by comparison against various databases, yielding 42,229 (non-redundant protein sequence (NR): 60.78%), 59,255 (non-redundant nucleotide (NT): 85.28%), 35,900 (Swiss-Prot: 51.67%), 11,772 (clusters of orthologous groups (COG): 16.94%), 33,057 (Kyoto Encyclopedia of Genes and Genomes (KEGG): 47.58%), 18,764 (Gene Ontology (GO): 27.01%), and 32,085 (Interpro: 46.18%) unigenes. Comparative analysis of the expression profiles between bacterial challenge fish and control fish identifies 7749 differentially expressed genes (DEGs) from the muscle and 7846 DEGs from the spleen. These DEGs are further categorized with KEGG. Enrichment analysis of the DEGs and unigenes reveals major immune-related functions, including up-regulation of genes related with Toll-like receptor signaling, complement and coagulation cascades, and antigen processing and presentation. The results from RNA-Seq data are also validated and confirmed the consistency of the expression levels of seven immune-related genes after 24 h post infection with qPCR. Microsatellites (11,534), including di-to hexa nucleotide repeat motifs, are also identified. Altogether, this work provides valuable insights into the underlying immune mechanisms elicited during bacterial infection in koi carp that may aid in the future development of disease control measures in protection against A. sobria.
Highlights
Aeromonas (Aeromonadaceae) species are ubiquitous and can cause infections in humans and in fish
The functional annotations of unigenes according to GO, COG, and KEGG databases provided ample numbers of candidate genes and valuable information about biological features of koi carp challenged with A. sobria in this study
This is the first study to provide information on host defense gene activities based on differential transcriptomic profiling in koi carp against A. sobria
Summary
Aeromonas (Aeromonadaceae) species are ubiquitous and can cause infections in humans and in fish. Aeromonas are isolated from various sources, such as fresh, estuarine, or surface waters, sewage, food products, healthy or diseased fish, or animal and human feces and are ubiquitous in aquatic ecosystems [1,2,3,4,5]. Aeromonas species are known as active spoilers of fish and meat [9,10]. They are opportunistic pathogens of fish and can cause outbreak during stress conditions, such as poor water quality, overcrowding, and rough handling [1,11,12]. Aeromonas septicemia causes fatal infectious disease in cold-blooded animals [13]; in humans [14,15,16], disease is often caused by the motile Aeromonas, Aeromonas hydrophila, Aeromonas sobria (A. sobria), and Aeromonas caviae
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