De novo transcriptome assembly and analysis of differential gene expression following lipopolysaccharide challenge in Pelteobagrus fulvidraco

Liu, Qiu-Ning; Xin, Zhao-Zhe; Liu, Yu; Zhang, Dai-Zhen; Jiang, Senhao; Chai, Xin-Yue; Wang, Zheng-Fei; Zhang, Huabin; Xin-min, Bian; Zhou, Chun-Lin; Tang, Boping

doi:10.1016/j.fsi.2017.11.045

Cited by 17 publications

(4 citation statements)

References 43 publications

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“…Thus, transcriptome technology addresses key gene expression patterns of non-model organisms in specific environments and enables detection of unknown genes and discovery of new transcripts. In recent years, transcriptome technology has been widely used in transcriptome assembly and annotation of many non-model fish, such as Megalobrama amblycephala [ 18 ], Pelteobagrus fulvidraco [ 19 ] and Atlantic salmon [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

Gill Transcriptome Sequencing and De Novo Annotation of Acanthogobius ommaturus in Response to Salinity Stress

Sun

Lou

Zhang

et al. 2020

Genes

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Acanthogobius ommaturus is a euryhaline fish widely distributed in coastal, bay and estuarine areas, showing a strong tolerance to salinity. In order to understand the mechanism of adaptation to salinity stress, RNA-seq was used to compare the transcriptome responses of Acanthogobius ommaturus to the changes of salinity. Four salinity gradients, 0 psu, 15 psu (control), 30 psu and 45 psu were set to conduct the experiment. In total, 131,225 unigenes were obtained from the gill tissue of A. ommaturus using the Illumina HiSeq 2000 platform (San Diego, USA). Compared with the gene expression profile of the control group, 572 differentially expressed genes (DEGs) were screened, with 150 at 0 psu, 170 at 30 psu, and 252 at 45 psu. Additionally, among these DEGs, Gene Ontology (GO) analysis indicated that binding, metabolic processes and cellular processes were significantly enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis detected 3, 5 and 8 pathways related to signal transduction, metabolism, digestive and endocrine systems at 0 psu, 30 psu and 45 psu, respectively. Based on GO enrichment analysis and manual literature searches, the results of the present study indicated that A. ommaturus mainly responded to energy metabolism, ion transport and signal transduction to resist the damage caused by salinity stress. Eight DEGs were randomly selected for further validation by quantitative real-time PCR (qRT-PCR) and the results were consistent with the RNA-seq data.

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Section: Introductionmentioning

confidence: 99%

Gill Transcriptome Sequencing and De Novo Annotation of Acanthogobius ommaturus in Response to Salinity Stress

Sun

Lou

Zhang

et al. 2020

Genes

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“…Lipopolysaccharide (LPS) is considered to be a potential immunostimulant and it is the main component of the Gram-negative bacterial cell wall. The yellow catfish stimulated with LPS showed a significant upregulation in the nonspecific immune responses, such as CXCL2-like chemokine, goose-type lysozyme, and cathepsin K [ 148 ]. Plant-based immunostimulants are considered to be an effective prophylactic measure to prevent diseases by enhancing the nonspecific immune system of fish [ 149 ].…”

Section: Rna-seq Analysis Of Healthy Fishmentioning

confidence: 99%

Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review

Sudhagar

Kumar

El-Matbouli

2018

IJMS

132

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In recent years, with the advent of next-generation sequencing along with the development of various bioinformatics tools, RNA sequencing (RNA-Seq)-based transcriptome analysis has become much more affordable in the field of biological research. This technique has even opened up avenues to explore the transcriptome of non-model organisms for which a reference genome is not available. This has made fish health researchers march towards this technology to understand pathogenic processes and immune reactions in fish during the event of infection. Recent studies using this technology have altered and updated the previous understanding of many diseases in fish. RNA-Seq has been employed in the understanding of fish pathogens like bacteria, virus, parasites, and oomycetes. Also, it has been helpful in unraveling the immune mechanisms in fish. Additionally, RNA-Seq technology has made its way for future works, such as genetic linkage mapping, quantitative trait analysis, disease-resistant strain or broodstock selection, and the development of effective vaccines and therapies. Until now, there are no reviews that comprehensively summarize the studies which made use of RNA-Seq to explore the mechanisms of infection of pathogens and the defense strategies of fish hosts. This review aims to summarize the contemporary understanding and findings with regard to infectious pathogens and the immune system of fish that have been achieved through RNA-Seq technology.

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“…Although infectious disease outbreaks associated with pathogenic microorganisms have caused high mortality rates and led to catastrophic economic losses in farmed P. fulvidraco, little is known about the immune system of this species. We previously screened a cDNA library of P. fulvidraco upon immune challenge [37][38][39][40] and identified an ITLN homolog that showed high similarity with other fish ITLNs. The full-length cDNA was obtained via rapid amplification of cDNA ends (RACE)-PCR for the investigation of expression patterns in different tissues and of the immune responses.…”

Section: Introductionmentioning

confidence: 99%

Molecular Identification and Expression Analysis of an Intelectin Gene in the Yellow Catfish Pelteobagrus fulvidraco (Siluriformes: Bagridae)

Jiang,

Lei,

et al. 2023

Fishes

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Intelectins (ITLNs) are a family of calcium-dependent lectins with carbohydrate-binding capacity, are distributed across various vertebrates, and play an important role in the innate immune response against pathogen infection. The yellow catfish Pelteobagrus fulvidraco (Siluriformes: Bagridae) is an economically important fish in China. The aim of this study was to quantify the gene expression of ITLN in response to pathogen-associated molecular patterns (PAMPs) stimulation. Here, the ITLN gene of P. fulvidraco was characterized and named PfITLN. The full-length cDNA of PfITLN was 1132 bp, including a 5’-untranslated region (UTR) of 140 bp, a 3’-UTR of 110 bp, and an open reading frame (ORF) of 882 bp encoding a polypeptide of 293 amino acids, which contains a signal peptide and two fibrinogen-related domains (FReDs). PfITLN had a molecular weight of 32.39 kDa with a theoretical pI of 5.03. The deduced PfITLN amino acid sequence had 81%, 64%, and 55% homology with Ictalurus furcatus, Danio rerio, and Homo sapiens, respectively. Moreover, the predicted tertiary protein structure of PfITLN was highly similar to that of other animals, and phylogenetic analysis showed that the PfITLN protein was close to those of other Teleostei. Real-time quantitative reverse transcription-PCR (qRT-PCR) analysis showed PfITLN expression in all examined tissues, with the highest abundance seen in the liver, followed by the head kidney, spleen, trunk kidney, and muscle. After PAMP infection with lipopolysaccharide (LPS) and polyriboinosinic polyribocytidylic acid (poly I:C), the expression levels of PfITLN were significantly upregulated at different time points. These results suggested that PfITLN might be involved in innate immunity.

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De novo transcriptome assembly and analysis of differential gene expression following lipopolysaccharide challenge in Pelteobagrus fulvidraco

Cited by 17 publications

References 43 publications

Gill Transcriptome Sequencing and De Novo Annotation of Acanthogobius ommaturus in Response to Salinity Stress

Gill Transcriptome Sequencing and De Novo Annotation of Acanthogobius ommaturus in Response to Salinity Stress

Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review

Molecular Identification and Expression Analysis of an Intelectin Gene in the Yellow Catfish Pelteobagrus fulvidraco (Siluriformes: Bagridae)

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