Differentially expressed immune-related genes in hemocytes of the pearl oyster Pinctada fucata against allograft identified by transcriptome analysis

Wei, Jinjia; Liu, Bao-Suo; Fan, Sigang; Li, Haimei; Chen, Mingqiang; Zhang, Bo; Su, Jiaqi; Meng, Zhen; Yu, Dahui

doi:10.1016/j.fsi.2017.01.025

Cited by 36 publications

(16 citation statements)

References 49 publications

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“…splendidus, with fold changes of 1.29 and 15.11, respectively. Several molluscan TLRs were found up-regulated after immune challenge [ 44 , 53 , 54 , 55 , 56 ], confirming their function in the immune response. In addition, one inhibitor of NF-κB kinase ( So -IKK-h) sharing 27.29% sequence identity with Cyclina sinensis IKK (ASE55486.1) and one Rel/NF-κB ( So -Rel/NF-κB-h) sharing 78.57% sequence identity with Euprymna scolopes Rel/NF-κB (AAY27981.1) and possessing the Rel identity domain (RHD) were newly identified in the hct transcriptome.…”

Section: Results—discussionmentioning

confidence: 90%

In-Depth In Silico Search for Cuttlefish (Sepia officinalis) Antimicrobial Peptides Following Bacterial Challenge of Haemocytes

et al. 2020

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Cuttlefish (Sepia officinalis) haemocytes are potential sources of antimicrobial peptides (AMPs). To study the immune response to Vibrio splendidus and identify new AMPs, an original approach was developed based on a differential transcriptomic study and an in-depth in silico analysis using multiple tools. Two de novo transcriptomes were retrieved from cuttlefish haemocytes following challenge by V. splendidus or not. A first analysis of the annotated transcripts revealed the presence of Toll/NF-κB pathway members, including newly identified factors such as So-TLR-h, So-IKK-h and So-Rel/NF-κB-h. Out of the eight Toll/NF-κB pathway members, seven were found up-regulated following V. splendidus challenge. Besides, immune factors involved in the immune response were also identified and up-regulated. However, no AMP was identified based on annotation or conserved pattern searches. We therefore performed an in-depth in silico analysis of unannotated transcripts based on differential expression and sequence characteristics, using several tools available like PepTraq, a homemade software program. Finally, five AMP candidates were synthesized. Among them, NF19, AV19 and GK28 displayed antibacterial activity against Gram-negative bacteria. Each peptide had a different spectrum of activity, notably against Vibrio species. GK28—the most active peptide—was not haemolytic, whereas NF19 and AV19 were haemolytic at concentrations between 50 and 100 µM, 5 to 10 times higher than their minimum inhibitory concentration.

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Section: Results—discussionmentioning

confidence: 90%

In-Depth In Silico Search for Cuttlefish (Sepia officinalis) Antimicrobial Peptides Following Bacterial Challenge of Haemocytes

et al. 2020

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“…Moreover, the surgical implantation practiced in pearl grafting can induce the immune reaction in host oyster to some extent in response to receiving a transplant and the oyster survival [32, 33]. Therefore, it is very important to explore the key genes involved in the immunological changes that occur upon graft transplantation.…”

Section: Introductionmentioning

confidence: 99%

Gene expression profiles at different stages for formation of pearl sac and pearl in the pearl oyster Pinctada fucata

et al. 2019

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BackgroundThe most critical step in the pearl formation during aquaculture is issued to the proliferation and differentiation of outer epithelial cells of mantle graft into pearl sac. This pearl sac secretes various matrix proteins to produce pearls by a complex physiological process which has not been well-understood yet. Here, we aimed to unravel the genes involved in the development of pearl sac and pearl, and the sequential expression patterns of different shell matrix proteins secreted from the pearl sac during pearl formation by pearl oyster Pinctada fucata using high-throughput transcriptome profiling.ResultsPrincipal component analysis (PCA) showed clearly different gene expression profiles between earlier (before 1 week) and later stages (1 week to 3 months) of grafting. Immune-related genes were highly expressed between 0 h – 24 h (donor dependent) and 48 h – 1 w (host dependent), and in the course of wound healing process pearl sac was developed by two weeks of graft transplantation. Moreover, for the first time, we identified some stem cell marker genes including ABCG2, SOX2, MEF2A, HES1, MET, NRP1, ESR1, STAT6, PAX2, FZD1 and PROM1 that were expressed differentially during the formation of pearl sac. The expression profiling of 192 biomineralization-related genes demonstrated that most of the shell matrix proteins (SMPs) involved in prismatic layer formation were first up-regulated and then gradually down-regulated indicating their involvement in the development of pearl sac and the onset of pearl mineralization. Most of the nacreous layer forming SMPs were up-regulated at 2 weeks after the maturation of pearl sac. Nacrein, MSI7 and shematrin involved in both layer formation were highly expressed during 0 h – 24 h, down-regulated up to 1 week and then up-regulated again after accomplishment of pearl sac formation.ConclusionsUsing an RNA-seq approach we unraveled the expression pattern of the key genes involved in the development of pearl sac and pearl as a result of host immune response after grafting. These findings provide valuable information in understanding the molecular mechanism of pearl formation and immune response in P. fucata.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5579-3) contains supplementary material, which is available to authorized users.

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“…RNA sequencing (RNA-Seq) technology combined with the analysis of differentially expressed genes (DEGs) are reliable and precise ways to provide useful information for molecular mechanism of complex characters [ 17 ]. Moreover, RNA-Seq has attracted considerable interests and received great success concerning many economic traits in some other cultured species [ 18 , 19 , 20 ]. An increasing number of studies have addressed the transcriptomic profiles of tissues and organs to examine the variety of functional pathways underlying inter-individual difference in feed efficiency [ 21 , 22 , 23 , 24 , 25 ], which focused on target organs such as intestine [ 21 ] and liver [ 22 , 23 ], but no similar analysis has been done in neural organs.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic Profiles of Brain Provide Insights into Molecular Mechanism of Feed Conversion Efficiency in Crucian Carp (Carassius auratus)

Pang

Luo

et al. 2018

IJMS

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Feed efficiency is an economically crucial trait for cultured animals, however, progress has been scarcely made in the genetic analyses of feed conversion efficiency (FCE) in fish because of the difficulties in measurement of trait phenotypes. In the present investigation, we present the first application of RNA sequencing (RNA-Seq) combined with differentially expressed genes (DEGs) analysis for identification of functional determinants related to FCE at the gene level in an aquaculture fish, crucian carp (Carassius auratus). Brain tissues of six crucian carp with extreme FCE performances were subjected to transcriptome analysis. A total of 544,612 unigenes with a mean size of 644.38 bp were obtained from Low- and High-FCE groups, and 246 DEGs that may be involved in FCE traits were identified in these two groups. qPCR confirmed that genes previously identified as up- or down-regulated by RNA-Seq were effectively up- or down-regulated under the studied conditions. Thirteen key genes, whose functions are associated with metabolism (Dgkk, Mgst3 and Guk1b), signal transduction (Vdnccsa1b, Tgfα, Nr4a1 and Tacr2) and growth (Endog, Crebrtc2, Myh7, Myh1, Myh14 and Igfbp7) were identified according to GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations. Our novel findings provide useful pathway information and candidate genes for future studies of genetic mechanisms underlying FCE in crucian carp.

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Differentially expressed immune-related genes in hemocytes of the pearl oyster Pinctada fucata against allograft identified by transcriptome analysis

Cited by 36 publications

References 49 publications

In-Depth In Silico Search for Cuttlefish (Sepia officinalis) Antimicrobial Peptides Following Bacterial Challenge of Haemocytes

In-Depth In Silico Search for Cuttlefish (Sepia officinalis) Antimicrobial Peptides Following Bacterial Challenge of Haemocytes

Gene expression profiles at different stages for formation of pearl sac and pearl in the pearl oyster Pinctada fucata

Transcriptomic Profiles of Brain Provide Insights into Molecular Mechanism of Feed Conversion Efficiency in Crucian Carp (Carassius auratus)

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