Analysis of the transcriptomic profilings of Mandarin fish (Siniperca chuatsi) infected with Flavobacterium columnare with an emphasis on immune responses

Zhou, Weidong; Zhang, Yulei; Wen, Yi; Ji, Wei; Zhou, Yang; Ji, Yachan; Liu, Xiaoling; Wang, Weimin; Asim, Muhammad; Liang, Xu‐Fang; Ai, Taoshan; Lin, Li

doi:10.1016/j.fsi.2014.12.006

Cited by 39 publications

(20 citation statements)

References 31 publications

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“…The GO and KEGG classification analysis of the annotated unigenes showed that of the GO annotated unigenes the “biological process” category was dominant, and in KEGG classification a dominant “metabolism” category was obtained. Similar results were also observed in other transcriptomic assays with fish liver, and these results conformed to the physiological roles of fish liver, which is a metabolism center of fish and plays vital roles in a wide range of biological processes 35 – 37 .…”

Section: Discussionsupporting

confidence: 87%

Moderate levels of dietary arachidonic acid reduced lipid accumulation and tended to inhibit cell cycle progression in the liver of Japanese seabass Lateolabrax japonicus

Wang

Zhang

et al. 2018

Sci Rep

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To investigate the physiological roles of dietary arachidonic acid (ARA) in fish, a feeding trial with Japanese seabass was conducted, followed by a hepatic transcriptome assay. Six experimental diets differing basically in ARA level (0.05%, 0.22%, 0.37%, 0.60%, 1.38% and 2.32% of dry matter) were used in the feeding trial. Liver samples from fish fed diets with 0.05% and 0.37% ARA were subjected to transcriptomic assay, generating a total of 139 differently expressed unigenes, which were primarily enriched in lipid metabolism and cell cycle-related signaling pathways. Then, qRT-PCR validation on lipid metabolism and cell cycle-related genes as well as corresponding enzyme-linked immunosorbent assay of selected proteins were conducted with liver samples from all six groups. Moderated ARA levels reduced lipogenesis and stimulated β-oxidation concurrently, but high ARA levels seemed to affect lipid metabolism in complicated ways. Both gene expression and protein concentration of cell cycle-related proteins were decreased by moderate levels of dietary ARA. The lipid content and fatty acid composition in fish confirmed the transcription and protein concentration results related to lipid metabolism. In conclusion, moderate levels of dietary ARA (0.37% and 0.60%) reduced lipid accumulation and tended to inhibit cell cycle progression in the liver of Japanese seabass.

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Section: Discussionsupporting

confidence: 87%

Moderate levels of dietary arachidonic acid reduced lipid accumulation and tended to inhibit cell cycle progression in the liver of Japanese seabass Lateolabrax japonicus

Wang

Zhang

et al. 2018

Sci Rep

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“…Common carp is an important commercial fish worldwide. Recently, the whole genome of common carp was sequenced [ 2 ]. There have been three reports about the miRNAs of common carp [ 9 , 10 , 11 ].…”

Section: Discussionmentioning

confidence: 99%

“…It can cause world-wide fish diseases with high mortality and heavy economical losses in aquaculture industry, including channel catfish ( Ictalurus punctatus ), grass carp ( Ctenopharygodon idella ), Mandarin fish ( Siniperca chuatsi ), and common carp ( Cyprinus carpio ), etc. [ 1 , 2 ]. Common carp is the number one fish of aquaculture in the world with the annual products amounting to approximately three million tonnes [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

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

Zhao

Lü

Meng

et al. 2016

IJMS

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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: ) 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.

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“…A custom Perl program was used to remove short sequences (< 50 bp). Trinity ( https://github.com/trinityrnaseq/ trinityrnaseq/wiki) was used to perform the de novo assembles, and the resulting high-quality sequences were assembled into contigs and transcripts [ 28 ]. To reduce data redundancy, TGICL was used to assemble and cluster transcripts with a minimum length of 200 bp.…”

Section: Methodsmentioning

confidence: 99%

Transcriptomic analysis reveals the key immune-related signalling pathways of Sebastiscus marmoratus in response to infection with the parasitic ciliate Cryptocaryon irritans

Yin

Dong

2017

Parasites Vectors

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BackgroundFalse kelpfish (Sebastiscus marmoratus) is one of the target species in artificial breeding in China, and is susceptible to infection by Cryptocaryon irritans, which is an obligate parasitic ciliate that lives in the epithelium of the fish gills, skin and fins. Here, we sought to understand the mechanisms of molecular immunity of S. marmoratus against C. irritans infection.MethodsWe carried out an extensive analysis of the transcriptome of S. marmoratus immune-related tissues. A paired-end library was constructed from the cDNA synthesized using a Genomic Sample Prep Kit. Five normalized cDNA libraries were constructed using RNA from the control group and the four groups of C. irritans-infected fish. The libraries were sequenced on an Illumina Mi-Seq platform, and functional annotation of the transcriptome was performed using bioinformatics software.ResultsThe data produced a total of 149,983,397 clean reads from five cDNA libraries constructed from S. marmoratus immune-related tissues. A total of 33,291 unigenes were assembled with an average length of 1768 bp. In eggNOG (Evolutionary Genealogy of Genes: non-supervised orthologous groups) categories, 333 unigenes (0.94%) were assigned to defense mechanisms. In the immune system process sub-categories of gene ontology (GO) enrichment analysis, with the passage of time post-infection, the number of differentially expressed genes (DEGs) was reduced from 24 h to 48 h but then increased from 72 h to 96 h. Specifically, the immune-related differentially expressed genes (IRDEGs), which belong to the KEGG (Kyoto encyclopedia of genes and genomes) pathways, such as the complement and coagulation cascades, chemokine signalling pathways and toll-like receptor signalling pathways were mainly observed at 24 h post-infection.ConclusionsInfection with C. irritans resulted in a large number of DEGs in the immune-related tissues of S. marmoratus. The rapid and significant response of the S. marmoratus immune signalling pathways following C. irritans infection may be associated with their involvement in the immune process.Electronic supplementary materialThe online version of this article (10.1186/s13071-017-2508-7) contains supplementary material, which is available to authorized users.

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Analysis of the transcriptomic profilings of Mandarin fish (Siniperca chuatsi) infected with Flavobacterium columnare with an emphasis on immune responses

Cited by 39 publications

References 31 publications

Moderate levels of dietary arachidonic acid reduced lipid accumulation and tended to inhibit cell cycle progression in the liver of Japanese seabass Lateolabrax japonicus

Moderate levels of dietary arachidonic acid reduced lipid accumulation and tended to inhibit cell cycle progression in the liver of Japanese seabass Lateolabrax japonicus

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

Transcriptomic analysis reveals the key immune-related signalling pathways of Sebastiscus marmoratus in response to infection with the parasitic ciliate Cryptocaryon irritans

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