scholarly journals Comparative transcriptome profiling of immune response against Vibrio harveyi infection in Chinese tongue sole

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Hao Xu ◽  
Xiwen Xu ◽  
Xihong Li ◽  
Lei Wang ◽  
Jiayu Cheng ◽  
...  
Keyword(s):  
Immune Response ◽  
Molecular Mechanisms ◽  
Vibrio Harveyi ◽  
Bacterial Pathogen ◽  
Transcriptome Profiling ◽  
Transcript Level ◽  
Cynoglossus Semilaevis ◽  
Illumina Hiseq ◽  
Tongue Sole ◽  
And Control

Abstract Vibrio harveyi is a major bacterial pathogen that causes fatal vibriosis in Chinese tongue sole (Cynoglossus semilaevis), resulting in massive mortality in the farming industry. However, the molecular mechanisms of C. semilaevis response to V. harveyi infection are poorly understood. Here, we performed transcriptomic analysis of C. semilaevis, comparing resistant and susceptible families in response to V. harveyi challenge (CsRC and CsSC) and control conditions (CsRU and CsSU). RNA libraries were constructed using 12 RNA samples isolated from three biological replicates of the four groups. We performed transcriptome sequencing on an Illumina HiSeq platform, and generating a total of 1,095 million paired-end reads, with the number of clean reads per library ranging from 75.27 M to 99.97 M. Through pairwise comparisons among the four groups, we identified 713 genes exhibiting significant differences at the transcript level. Furthermore, the expression levels were validated by real-time qPCR. Our results provide a valuable resource and new insights into the immune response to V. harveyi infection.

scholarly journals Understanding physiological and molecular mechanisms of Populus deltoides ‘DanHongYang’ tolerance to waterlogging by comparative transcriptome analysis

2020 ◽  
Vol 48 (3) ◽  
pp. 1613-1636
Author(s):  
Gang LI ◽  
Qiusheng FU ◽  
Zhongbin LIU ◽  
Jiabao YE ◽  
Weiwei ZHANG ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Populus Deltoides ◽  
Transcriptome Profiling ◽  
Endogenous Hormones ◽  
Waterlogging Tolerance ◽  
Adventitious Root Development ◽  
Leaves And Roots ◽  
Waterlogging Treatment ◽  
And Control ◽  
Comparative Transcriptomic Analysis

Populus deltoides ‘DanHongYang’ (DHY) was identified as a waterlogging-resistant cultivar in our previous study. Here, the phenotype, physiological features and transcriptome profiling of P. deltoides ‘DHY’ between the treatments of waterlogging and control were compared. Waterlogging treatment led to distinctly formation of adventitious roots from P. deltoides ‘DHY’ stems. The activities of ascorbate peroxidase and glutathione reductase significantly increased in the leaves of P. deltoides ‘DHY’ by waterlogging treatment. Comparative transcriptomic analysis showed that 2,447 and 9,465 differentially expressed genes (DEGs) were screened between the leaves and roots of P. deltoides ‘DHY’ under waterlogging and control, respectively. The KEGG analysis showed the most significantly up-regulated DEGs in the leaves and roots were enriched to the pathways of glycolyis and proline synthesis. Some genes involved in stress response, endogenous hormones, antioxidant system and adventitious root development in the waterlogged were identified to contribute to the waterlogging tolerance of P. deltoides ‘DHY’. In addition, some candidate transcription factors such as RAP, NAC, WRKY, and bHLH were also found to be associated with the waterlogging tolerance of P. deltoides ‘DHY’. These findings provided the insights into the physiological and molecular mechanisms underlying the tolerance of P. deltoides ‘DHY’ to waterlogging stresses.

scholarly journals Brain and Pituitary Transcriptome Analyses Reveal the Differential Regulation of Reproduction-Related LncRNAs and mRNAs in Cynoglossus semilaevis

2021 ◽  
Vol 12 ◽  
Author(s):  
Yani Dong ◽  
Likang Lyu ◽  
Haishen Wen ◽  
Bao Shi
Keyword(s):  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Interaction ◽  
Cynoglossus Semilaevis ◽  
Rna Seq ◽  
Tongue Sole ◽  
Gene Interaction Networks ◽  
Half Smooth Tongue Sole ◽  
The Brain

Long noncoding RNAs (lncRNAs) have been identified to be involved in half-smooth tongue sole (Cynoglossus semilaevis) reproduction. However, studies of their roles in reproduction have focused mainly on the ovary, and their expression patterns and potential roles in the brain and pituitary are unclear. Thus, to explore the mRNAs and lncRNAs that are closely associated with reproduction in the brain and pituitary, we collected tongue sole brain and pituitary tissues at three stages for RNA sequencing (RNA-seq), the 5,135 and 5,630 differentially expressed (DE) mRNAs and 378 and 532 DE lncRNAs were identified in the brain and pituitary, respectively. The RNA-seq results were verified by RT-qPCR. Moreover, enrichment analyses were performed to analyze the functions of DE mRNAs and lncRNAs. Interestingly, their involvement in pathways related to metabolism, signal transduction and endocrine signaling was revealed. LncRNA-target gene interaction networks were constructed based on antisense, cis and trans regulatory mechanisms. Moreover, we constructed competing endogenous RNA (ceRNA) networks. In summary, this study provides mRNA and lncRNA expression profiles in the brain and pituitary to understand the molecular mechanisms regulating tongue sole reproduction.

Genetic analysis of disease resistance to Vibrio harveyi by challenge test in Chinese tongue sole (Cynoglossus semilaevis)

Aquaculture ◽  
2019 ◽  
Vol 503 ◽  
pp. 430-435 ◽  
Author(s):  
Yangzhen Li ◽  
Lei Wang ◽  
Yingming Yang ◽  
Xue Li ◽  
Huan Dai ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Genetic Analysis ◽  
Vibrio Harveyi ◽  
Challenge Test ◽  
Cynoglossus Semilaevis ◽  
Tongue Sole

Cloning, characterization and functional analysis of dctn5 in immune response of Chinese tongue sole (Cynoglossus semilaevis)

2018 ◽  
Vol 77 ◽  
pp. 392-401 ◽  
Author(s):  
Min Wei ◽  
Wen-teng Xu ◽  
Kun-ming Li ◽  
Ya-dong Chen ◽  
Lei Wang ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Immune Response ◽  
Cynoglossus Semilaevis ◽  
Tongue Sole

scholarly journals Research Note. Transcriptomic study of the rat pinworm Syphacia muris

2015 ◽  
Vol 52 (4) ◽  
pp. 370-374 ◽  
Author(s):  
M. Okamoto ◽  
K. Taira ◽  
R. Ito ◽  
F. Asai
Keyword(s):  
Immune Response ◽  
Gene Ontology ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Profiling ◽  
Innate Immune ◽  
Gene Ontology Analysis ◽  
Laboratory Rats ◽  
Syphacia Muris ◽  
Generation Sequencing

Summary Syphacia muris is a ubiquitous nematode parasite and common contaminant of laboratory rats. A lthough S. muris infection is considered symptomless, it has some effects on the host’s immunity and therefore can interfere with experimental settings and interrupt final results. However, the molecular mechanisms involved in the alteration within the host’s immunity remain unclear because of the absence of information about mRNA expressed in this parasite. In this study we performed the transcriptome profiling of S. muris by next-generation sequencing. After de novo assembly and annotation, 14,821 contigs were found to have a sequence homology with any nematode sequence. Gene ontology analysis showed that the majority of the expressed genes are involved in cellular process, binding, and catalytic activity. Although the rate of expressed genes involved in the immune system was low, we found candidate genes that might be involved in the alteration within the host’s immunity by regulating the host’s innate immune response.

scholarly journals Effects of the amplitude and frequency of salinity fluctuations on antioxidant responses in juvenile tongue sole, Cynoglossus semilaevis

2016 ◽  
Vol 14 (2) ◽  
pp. e0503 ◽  
Author(s):  
Sachin O. Khairnar ◽  
Xiangli Tian ◽  
Shuanglin Dong ◽  
Ziheng Fang ◽  
Bhavesh V. Solanki ◽  
...  
Keyword(s):  
High Salinity ◽  
Cynoglossus Semilaevis ◽  
The Body ◽  
Sod Activity ◽  
Antioxidant Responses ◽  
Tongue Sole ◽  
Moderate Salinity ◽  
Cortisol Levels ◽  
And Control ◽  
Body Damage

To understand the tolerance of tongue sole, Cynoglossus semilaevis, to varying salinities, the effects of the amplitude (2, 4, 6 and 8 g/L) and frequency (2, 4 and 8 days) of salinity fluctuations on the activities of antioxidant responses, including acidic phosphatase (ACP), alkaline phosphatase (AKP), catalase (CAT) and superoxide dismutase (SOD) from antioxidant system in liver, muscle, gills and kidney, were investigated in this study. The results showed that the antioxidant responses of tongue sole were highly tissue-specific during the varying salinity fluctuations. In all tissues, ACP and AKP activity was found to be highest at moderate salinity fluctuations compared to the control, low and high salinity treatments (p<0.05). SOD and CAT activities had significant effect due to salinity fluctuations in all tissues (p<0.05), except in hepatic and renal tissues. Variations in branchial SOD activity proved that salinity fluctuations had greater impact on tongue sole at moderate and high fluctuating salinities compared to the control and low fluctuating salinities, whereas the branchial CAT activities showed contrasting trend. Further, cortisol levels were significantly affected in lower and higher salinity fluctuations. However, plasma cortisol levels remained low in moderate salinity fluctuations and control (p<0.05). Taken together, the results indicated that salinity fluctuations could effectively stimulate and enhance the antioxidant enzyme activity in the liver, kidney, gills and muscle of the juvenile tongue sole, thus effectively eliminating the excessive reactive oxygen species and minimizing the body damage in tongue sole or could be for any other euryhaline teleosts.

scholarly journals Development of a 38K Single Nucleotide Polymorphism Array and Application in Henomic Selection for Resistance Against Vibrio harveyi in Chinese Tongue sole, Cynoglossus Semilaevis

2020 ◽  
Author(s):  
Sheng Lu ◽  
Qian Zhou ◽  
Yadong Chen ◽  
Yang Liu ◽  
Yangzhen Li ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Vibrio Harveyi ◽  
Reference Group ◽  
Single Nucleotide Polymorphism Array ◽  
Snp Array ◽  
Cynoglossus Semilaevis ◽  
Breeding Value ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Tongue Sole

Abstract Background: In recent years, the disease outbreak caused by Vibrio harveyi upset the booming development of the Chinese tongue sole (Cynoglossus semilaevis) farming industry. Genomic selection (GS) is a powerful method to improve the traits of interest, which has been proved in livestock and some fishes. Besides, the single nucleotide polymorphism (SNP) array is an efficient genotyping platform that can be used for genetic studies. To improve V. harveyi resistance in C. semilaevis, we firstly constructed a reference group of 1,572 individuals and investigated accuracies of four genomic methods (genomic best linear unbiased prediction (GBLUP), weighted GBLUP, BayesB, and BayesC) at predicting the genomic estimated breeding value (GEBV) using five-fold cross-validation and SNPs varying from 0.5 k to 500 k. Then, an SNP array was developed using the Affymetrix Axiom technology, and its accuracy in genotyping was evaluated by comparing SNPs generated by the array and by the re-sequencing technology. Finally, we selected 44 candidates as the parents of 23 families of C. semilaevis to evaluate the feasibility of the SNP array for GS.Results: all genomic methods outperformed the pedigree-based BLUP (ABLUP) when at least 50 k SNPs used for prediction, of which GBLUP resulted in better estimation than ABLUP when more than 1 k SNPs used. A 38 k SNP array, “Solechip No.1”, was developed with an average of 10.5 kb inter-spacing between two adjacent SNPs. The SNPs generated by the array and by the re-sequencing reached an average consistency of 94.8 %, of which 79.3 % of loci had a more than 90 % of the consistency. The survival rates of these 23 offspring families had a correlation of 0.706 with the family GEBVs (mid-parental GEBVs), and the average survival rate of the top five families in GEBVs (79.1 %) is higher than the bottom five families (58.1 %).Conclusion: GS is an efficient method to improve the V. harveyi resistance in C. semilaevis, and the SNP array “Solechip No.1” is a convenient and reliable tool for the Chinses tongue sole selective breeding practice.

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