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Article

Immune-Related Functional Differential Gene Expression in Koi Carp (Cyprinus carpio) after Challenge with Aeromonas sobria

1
Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
2
International Degree Program of Ornamental Fish Science and Technology, International College, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Neipu, Pingtung 91201, Taiwan
3
Southern Taiwan Fish Disease Center, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Neipu, Pingtung 91201, Taiwan
4
Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung, No. 1, Shuefu Road, Neipu, Pingtung 91201, Taiwan
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2018, 19(7), 2107; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms19072107
Received: 21 May 2018 / Revised: 3 July 2018 / Accepted: 16 July 2018 / Published: 20 July 2018
(This article belongs to the Special Issue Host-Microbe Interaction 2018)
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. View Full-Text
Keywords: Illumina paired-end sequencing; immune response; koi carp (Cyprinus carpio); Aeromonas sobria; transcriptome Illumina paired-end sequencing; immune response; koi carp (Cyprinus carpio); Aeromonas sobria; transcriptome
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MDPI and ACS Style

Byadgi, O.; Chen, Y.-C.; Maekawa, S.; Wang, P.-C.; Chen, S.-C. Immune-Related Functional Differential Gene Expression in Koi Carp (Cyprinus carpio) after Challenge with Aeromonas sobria. Int. J. Mol. Sci. 2018, 19, 2107. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms19072107

AMA Style

Byadgi O, Chen Y-C, Maekawa S, Wang P-C, Chen S-C. Immune-Related Functional Differential Gene Expression in Koi Carp (Cyprinus carpio) after Challenge with Aeromonas sobria. International Journal of Molecular Sciences. 2018; 19(7):2107. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms19072107

Chicago/Turabian Style

Byadgi, Omkar, Yao-Chung Chen, Shun Maekawa, Pei-Chyi Wang, and Shih-Chu Chen. 2018. "Immune-Related Functional Differential Gene Expression in Koi Carp (Cyprinus carpio) after Challenge with Aeromonas sobria" International Journal of Molecular Sciences 19, no. 7: 2107. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms19072107

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