Transcriptomic variation of locally-infected skin of Epinephelus coioides reveals the mucosal immune mechanism against Cryptocaryon irritans

Hu, Yazhou; Li, An‐Xing; Xu, Yang; Jiang, Biao; Lu, Guilan; Luo, Xiao‐Chun

doi:10.1016/j.fsi.2017.05.042

Cited by 65 publications

(43 citation statements)

References 62 publications

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“…With the development of next-generation high-throughput sequencing technique, RNA-seq has also been applied in the studies of the fish- C. irritans interaction. Two recent reports have examined the transcriptome of C. irritans infected large yellow croaker ( Larimichthys crocea ) in IR tissues through RNA-seq [ 6 , 22 ], and a transcriptomic variation analysis on the C. irritans locally-infected skin of orange-spotted grouper ( Epinephelus coioides ) has been reported [ 23 ]. These data provide a frame of reference to enhance our understanding of the mechanisms of immunity of fish to C. irritans infection at the molecular level, by combining a variety of bioinformatic analyses, such as evolutionary genealogy of genes: non-supervised orthologous groups (eggNOG), gene ontology (GO), and Kyoto encyclopedia of genes and genomes (KEGG).…”

Section: Introductionmentioning

confidence: 99%

“…In response to C. irritans infection, skin, gills, head kidney, spleen and liver are believed to be the most important immune responsive tissues [ 17 ]. Skin showed a local immune response against C. irritans infection [ 23 ]. Liver from C. irritans -immunized L. crocea was the first tissue examined with respect to a comparative gene transcription analysis [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

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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“…Transcriptome analysis of fish skin has been carried out to study the mucosal immunity using a model fish parasite Cryptocaryon irritans (Hu et al . ). This study emphasizes the significance of the skin's local immune response in fish defence against ectoparasite infection.…”

Section: Current Status Of Transcriptomics In Aquaculturementioning

confidence: 97%

Transcriptomics in aquaculture: current status and applications

Chandhini

Kumar

2018

Reviews in Aquaculture

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Transcriptomics is the analysis of total RNA transcript in a cell, which gives a broad idea of cellular processes that are active and dormant. Recent advancement in next-generation sequencing technologies like high-throughput mRNA sequencing (RNA-seq) facilitates in deciphering the functional complexity of the whole transcriptome of an organism. In the recent past, transcriptome profiling has been widely used in aquaculture for effective identification and expression analysis of candidate genes involved in growth, reproduction, development, immunity, disease, stress and toxicology. On the paucity of a comprehensive genome sequence, transcriptomics enables the detection of molecular markers such as simple sequence repeats and single-nucleotide polymorphism associated with the trait of interest. This review summarizes the process of transcriptome analysis and the current state of transcriptomics in aquaculture related to diseases and immunity, reproduction and development, growth and nutrition, toxicology and stress. Further, this review highlights the application of transcriptomics, including generation of genetic resources, differential gene expression, analysis of molecular pathways and development of molecular markers.

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“…A total of 337, 407 GO terms were assigned to 37,103 unigenes (39.15% of the total assembled sequences). The numbers of mapped GO terms for biological process, molecular function and cellular component were (172,651, 51.17%), (47,757,14.15%) and (116,999, 34.68%), respectively. Within the biological process category, contigs involved in cellular process (27,381,15.86%) and single-organism process (22,494,13.03%) were highly represented.…”

Section: Gene Ontology (Go) and Kyoto Encyclopedia Of Genes And Genommentioning

confidence: 99%

“…Although skin is an important component of the mucosal immune system, a few studies on the skin transcription profile have been characterized in fish [10][11][12]. Evidence is accumulating that skin is a peripheral immune organ in teleosts [2,13,14]. However, there is a lack of genomic information such as the skin transcriptome of crucian carp.…”

Section: Introductionmentioning

confidence: 99%

Skin transcriptome analysis of the genes involved in mucous immunity and discovery of SSRs and SNPs in Crucian carp Carassius auratus

wang¹,

Hu²,

Lv³

et al. 2019

Preprint

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Fish skin is first line of defence against attachment and penetration of pathogens. Crucian carp (Carassius auratus) is one of the major freshwater species and important food fish in China, yet its molecular mechanism of skin immune response remains unclear. In this study, a de novo transcriptome assembly of crucian carp skin was performed by using Illumina Hiseq 2000 platform. A total of 49,154,776 unigenes were assembled, among which 60,824 (25.16%) unigenes were annotated against the NCBI database. Gene ontology and KEGG mapping assigned the terms to 37,103 (39.15%), 9,337 (23.23%) unigenes, repectively. The best represented KEGG categories were immune system (8,871, 20.50%) and signal transduction (7,805, 18.04%), and several mucin proteins (MUC1, MUC2, MUC5B, MUC5AC, MUC18, etc.) as the main membrane-bound and secreted components of the mucosal layer, implying the differentiation of immune responses in the crucian carp skin. Moreover, the results revealed that potential 28,928 SSRs and 249,964 SNPs were detected in crucian carp. This is the first report on transcriptome analysis in the skin of C. auratus, which contribute to understanding the molecular mechanisms of mucous immunogenectics response and epidermal mucus secretion of the skin in fish.

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Transcriptomic variation of locally-infected skin of Epinephelus coioides reveals the mucosal immune mechanism against Cryptocaryon irritans

Cited by 65 publications

References 62 publications

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

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

Transcriptomics in aquaculture: current status and applications

Skin transcriptome analysis of the genes involved in mucous immunity and discovery of SSRs and SNPs in Crucian carp Carassius auratus

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