De novo assembly and characterization of the spleen transcriptome of common carp (Cyprinus carpio) using Illumina paired-end sequencing

Li, Guoxi; Zhao, Yaping; Liu, Zhonghu; Gao, Chengde; Yan, Fengbin; Liu, Bianzhi; Feng, Jianxin

doi:10.1016/j.fsi.2015.03.014

Cited by 57 publications

(42 citation statements)

References 43 publications

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“…High-throughput transcriptome sequencing is a large-scale, efficient, and economical method for functional gene identification, and has been proved to be valuable in finding of candidate genes from fish disease studies [27][28][29]. However, transcriptome data of KWM are still unavailable, especially immune mechanisms to the current bottleneck problem of Ich infection remain unknown.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Transcriptional Changes in the Liver of Kanglang White Minnow (Anabarilius grahami) in Response to the Infection of Parasite Ichthyophthirius multifiliis

Qiu

Yin

Ruan

et al. 2020

Animals

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The notorious parasite Ichthyophthirius multifiliis (Ich) has been recorded worldwide in fish species and causes white spot disease, posing major threats and resulting in severe losses to international fish production. Extensively effective strategies for treating Ich are not available yet, and genetic mechanisms of hosts in response to the parasite are still largely unknown. In this study, we selected Kanglang white minnow (KWM, Anabarilius grahami) to examine its liver transcriptional changes after Ich infection, as white spot disease is one bottleneck problem in exploring this economically important species. We divided the experimental fishes into three groups (control, early-infected, and late-infected) to examine differentially expressed genes (DEGs). A total of 831 DEGs were identified and classified into 128 significantly enriched GO (Gene Ontology) terms and 71 significantly enriched KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. Most of these terms or pathways were functionally enriched in immunity, inflammatory response, and apoptosis, such as nucleotide-binding oligomerization domain-like (NOD-like) receptor signaling, tumor necrosis factor (TNF) signaling, interleukin-17 (IL-17) signaling, and apoptosis pathways. We also identified 178 putative antimicrobial peptides (AMPs) and AMP precursors based on our previously reported genome assembly of KWM, and revealed that the expressional patterns varied according to different types. In summary, our work reported the first comprehensive transcriptional changes in KWM in response to the exogenous infection of Ich, which would lay a solid foundation for in-depth studies on disease defense or resistant strains selection in this valuable fish.

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Section: Introductionmentioning

confidence: 99%

Comprehensive Transcriptional Changes in the Liver of Kanglang White Minnow (Anabarilius grahami) in Response to the Infection of Parasite Ichthyophthirius multifiliis

Qiu

Yin

Ruan

et al. 2020

Animals

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“…RNA-sequencing (RNA-Seq) using next-generation sequencing is one of the most useful methods to survey the character of a transcriptome because it offers a great deal of data on gene expression. Recently, transcriptome profiling using next-generation sequencing technologies have provided new insights into immune responses against various pathogenic infections in many aquaculture animals, such as the zebrafish (Danio rerio) (Zhang et al, 2013), common carp (Cyprinus carpio) (Li et al, 2015), large yellow croaker (Pseudosciaena crocea) (Mu et al, 2014), turbot (Scophthalmus maximus) (Pereiro et al, 2012), and Japanese sea bass (Lateolabrax japonicus) (Xiang et al, 2010). These studies used a high-throughput sequencing approach to identify numerous novel genes and expression profiles relating to the immune response.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomics analysis reveals candidate genes and pathways for susceptibility or resistance to Singapore grouper iridovirus in orange-spotted grouper (Epinephelus coioides)

Yang

Wang

et al. 2019

Developmental & Comparative Immunology

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In this study, the transcriptional response of grouper to Singapore grouper iridovirus (SGIV) stimulation was characterized using RNA sequencing. Transcriptome sequencing of three test groups in the grouper was performed using the Illumina MiSeq platform. The three test groups were a control group, which was injected with PBS buffer; a high-susceptible (HS) group, which died shortly after the SGIV injection; and a high-resistance (HR) group, which survived the SGIV injection. In total, 38,253 unigenes were generated. When the HS group was compared with the control group, 885 unigenes were upregulated and 487 unigenes were downregulated. When the HR and control groups were compared, 1114 unigenes were upregulated and 420 were downregulated, and when the HR and HS groups were compared, 1010 unigenes were upregulated and 375 were downregulated. In the KEGG analysis, two immune-related pathways, the p53 and peroxisome proliferator-activated receptor pathways, were detected with highly significant enrichment. In addition, 7465 microsatellites and 22,1569 candidate single nucleotide polymorphisms were identified from our transcriptome data. The results suggested several pathways that are associated with traits of disease susceptibility or disease resistance, and provided extensive information about novel gene sequences, gene expression profiles, and genetic markers. This may contribute to vaccine research and a breeding program against SGIV infection in grouper.

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“…The next‐generation RNA‐Seq technology lays the key technical foundation for DEG analysis, identification of immune and developmental genes, and genome studies (Zakrzewska et al, ; Li et al, ). It is a powerful tool for fast and accurate transcriptome analysis in any species (Kolev et al, ).…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic responses to yam ( Dioscorea oppositifolia L .) extract dietary supplementation in rainbow trout ( Oncorhynchus mykiss ) liver

et al. 2019

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Infectious diseases in rainbow trout (Oncorhynchus mykiss) have been seen in rainbow trout farming industry. Yam (Dioscorea oppositifolia L.) has a functional impact upon anti‐disease and strengthens immunity. Understanding the molecular mechanisms which occur in rainbow trout in response to yam will be useful to decrease disease‐related morbidity and mortality. In the present study, we conducted transcriptome analysis of liver in rainbow trout fed diets including yam extract (0, 0.2% and 0.4%), to identify yam extract‐induced genes and pathways. Over 451 million clean reads were obtained from nine liver libraries. Two comparisons were separately implemented between yam extract groups and control group. Using |log2Fold‐change|>1 and p‐value < .05 as the threshold, a total of 2,693 differentially expressed unigenes (DEGs) were identified, including 1599 up‐regulated and 1,094 down‐regulated unigenes. The RNA‐Seq results were verified by RT‐qPCR. DEGs were classified into three categories by GO annotation and functional enrichment analysis: biological process (23 subclasses), cellular component (16 subclasses) and molecular function (16 subclasses). KEGG annotation and classifications of DEGs indicated endocrine system, immune system, lipid metabolism, carbohydrate metabolism and signal transduction pathways include a large number of DEGs. In addition, 526 overlap DEGs in two comparisons were annotated to 174 pathways in KEGG analysis, 7 top significantly enriched pathway terms include chemokine signalling pathway, platelet activation, progesterone‐mediated oocyte maturation, insulin signalling pathway, FoxO signalling pathway, cGMP‐PKG signalling pathway and sphingolipid signalling pathway. These findings provide valuable information for further analysis of the disease resistance mechanisms of rainbow trout fed yam.

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De novo assembly and characterization of the spleen transcriptome of common carp (Cyprinus carpio) using Illumina paired-end sequencing

Cited by 57 publications

References 43 publications

Comprehensive Transcriptional Changes in the Liver of Kanglang White Minnow (Anabarilius grahami) in Response to the Infection of Parasite Ichthyophthirius multifiliis

Comprehensive Transcriptional Changes in the Liver of Kanglang White Minnow (Anabarilius grahami) in Response to the Infection of Parasite Ichthyophthirius multifiliis

Transcriptomics analysis reveals candidate genes and pathways for susceptibility or resistance to Singapore grouper iridovirus in orange-spotted grouper (Epinephelus coioides)

Transcriptomic responses to yam ( Dioscorea oppositifolia L .) extract dietary supplementation in rainbow trout ( Oncorhynchus mykiss ) liver

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