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. 2016 Apr 15;17(4):566.
doi: 10.3390/ijms17040566.

Profilings of MicroRNAs in the Liver of Common Carp (Cyprinus carpio) Infected with Flavobacterium columnare

Lijuan Zhao  1   2   3   4 , Hong Lu  5   6   7 , Qinglei Meng  8   9   10 , Jinfu Wang  11   12   13 , Weimin Wang  14 , Ling Yang  15   16   17 , Li Lin  18   19
Affiliations

Profilings of MicroRNAs in the Liver of Common Carp (Cyprinus carpio) Infected with Flavobacterium columnare

Lijuan Zhao et al. Int J Mol Sci. .

Abstract

MicroRNAs (miRNAs) play important roles in regulation of many biological processes in eukaryotes, including pathogen infection and host interactions. Flavobacterium columnare (FC) infection can cause great economic loss of common carp (Cyprinus carpio) which is one of the most important cultured fish in the world. However, miRNAs in response to FC infection in common carp has not been characterized. To identify specific miRNAs involved in common carp infected with FC, we performed microRNA sequencing using livers of common carp infected with and without FC. A total of 698 miRNAs were identified, including 142 which were identified and deposited in the miRbase database (Available online: http://www.mirbase.org/) and 556 had only predicted miRNAs. Among the deposited miRNAs, eight miRNAs were first identified in common carp. Thirty of the 698 miRNAs were differentially expressed miRNAs (DIE-miRNAs) between the FC infected and control samples. From the DIE-miRNAs, seven were selected randomly and their expression profiles were confirmed to be consistent with the microRNA sequencing results using RT-PCR and qRT-PCR. In addition, a total of 27,363 target genes of the 30 DIE-miRNAs were predicted. The target genes were enriched in five Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including focal adhesion, extracellular matrix (ECM)-receptor interaction, erythroblastic leukemia viral oncogene homolog (ErbB) signaling pathway, regulation of actin cytoskeleton, and adherent junction. The miRNA expression profile of the liver of common carp infected with FC will pave the way for the development of effective strategies to fight against FC infection.

Keywords: Flavobacterium columnare; common carp; deep sequencing; liver; miRNA.

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Figures

Figure 1
Figure 1
Length distribution of miRNA mapped rates in livers of common carp infected with Flavobacterium columnare (FC) and control. The miRNA mapped rates from the two samples with length between 18 and 30 nt were analyzed. The 100% was the clean read count of small RNAs of a certain length.
Figure 2
Figure 2
Validation of seven novel miRNAs by RT-PCR and qRT-PCR. M: marker; lane 1–7: the RT-PCR products of the seven novel miRNAs. (A) RT-PCR results; (B) qRT-PCR results.
Figure 2
Figure 2
Validation of seven novel miRNAs by RT-PCR and qRT-PCR. M: marker; lane 1–7: the RT-PCR products of the seven novel miRNAs. (A) RT-PCR results; (B) qRT-PCR results.
Figure 3
Figure 3
Comparison of miRNAs from different tissues of common carp. The number of over-lapping is shown in the parentheses. Tissue specific miRNA is shown in the parentheses and marked with “+”. L, S, M, and P represents liver, spleen, skeletal muscle and pooled tissues, respectively.
Figure 4
Figure 4
Functional enrichment of differentially expressed miRNA target genes.
Figure 5
Figure 5
KEGG pathway enrichment of differentially expressed miRNA target genes. KOBAS software (Availible online: http://kobas.cbi.pku.edu.cn/help.do) was used to test the statistical enrichment of differential expression genes in KEGG pathways.
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