Comparative transcriptomic analysis provides insights into antibacterial mechanisms of Branchiostoma belcheri under Vibrio parahaemolyticus infection

Zhang, Qi-Lin; Zhu, Qianhua; Liang, Mingzhu; Wang, Rui; Guo, Jun; Deng, Xian-Yu; Chen, Jun-Yuan; Wang, Yujun; Lü, Lin

doi:10.1016/j.fsi.2018.03.007

Cited by 20 publications

(13 citation statements)

References 57 publications

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“…Only a few DECs were found in common to both treatments (the intersections in Fig. 5 ), and neither TLR homologs nor orthologs of the Hydra ’s HyLRR-2 and HyTRR-1 genes [ 42 ] were identified in the Ep’s responses to LPS or Vp (Supplementary Table 8 versus Supplementary Tables 4 and 5 , respectively). Based on these comparisons (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Here, neither homologs of canonical vertebrate TLR or IL-1R, nor orthologs of the Hydra ’s HyTRR and HyLRR genes [ 42 ] were identified in the Ep transcriptomic responses. TLR and IL-1R-like homologs have been identified in several other anthozoans [ 49 ], however many of those genes lack the ectodomain LRR and only possess TMD- and TIR-domains [ 10 ].…”

Section: Discussionmentioning

confidence: 99%

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Gene expression kinetics of Exaiptasia pallida innate immune response to Vibrio parahaemolyticus infection

et al. 2020

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Background Recent sequencing projects on early-diverging metazoans such as cnidarians, have unveiled a rich innate immunity gene repertoire; however, little is known about immunity gene regulation in the host’s early response against marine bacterial pathogens over time. Here, we used RNA-seq on the sea anemone Exaiptasia pallida (Ep) strain CC7 as a model to depict the innate immune response during the onset of infection with the marine pathogenic bacteria Vibrio parahaemolyticus (Vp) clinical strain O3:K6, and lipopolysaccharides (LPS) exposure. Pairwise and time series analyses identified the genes responsive to infection as well as the kinetics of innate immune genes over time. Comparisons between the responses to live Vp and purified LPS was then performed. Results Gene expression and functional analyses detected hundreds to thousands of genes responsive to the Vp infection after 1, 3, 6 and 12 h, including a few shared with the response to LPS. Our results bring to light the first indications that non-canonical cytoplasmic pattern recognition receptors (PRRs) such as NOD-like and RIG-I-like receptor homologs take part in the immune response of Ep. Over-expression of several members of the lectin-complement pathways in parallel with novel transmembrane and Ig containing ficolins (CniFLs) suggest an active defense against the pathogen. Although lacking typical Toll-like receptors (TLRs), Ep activates a TLR-like pathway including the up-regulation of MyD88, TRAF6, NF-κB and AP-1 genes, which are not induced under LPS treatment and therefore suggest an alternative ligand-to-PRR trigger. Two cytokine-dependent pathways involving Tumor necrosis factor receptors (TNFRs) and several other potential downstream signaling genes likely lead to inflammation and/or apoptosis. Finally, both the extrinsic and intrinsic apoptotic pathways were strongly supported by over-expression of effector and executioner genes. Conclusions To our knowledge, this pioneering study is first to follow the kinetics of the innate immune response in a cnidarian during the onset of infection with a bacterial pathogen. Overall, our findings reveal the involvement of both novel immune gene candidates such as NLRs, RLRs and CniFLs, and previously identified TLR-like and apoptotic pathways in anthozoan innate immunity with a large amount of transcript-level evidence.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Gene expression kinetics of Exaiptasia pallida innate immune response to Vibrio parahaemolyticus infection

et al. 2020

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“…Fifteen DEGs were selected randomly for the qRT-PCR validation, normalized against the house-keeping gene GAPDH 21 . Each biological replicate was measured in triplicate technically and relative gene expression levels were calculated using the 2 −ΔΔCT method 22,23 . Pearson’s correlation coefficient ( r ) between RNA-Seq and qRT-PCR results were calculated using IBM SPSS 22 software.…”

Section: Methodsmentioning

confidence: 99%

Transcriptomic profiling of cotton Gossypium hirsutum challenged with low-temperature gradients stress

XiaoYan

et al. 2019

Sci Data

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Gossypium hirsutum, a cotton species widely cultivated around the world, is a typical cold-sensitive crop. Low-temperature (LT) stress is one of the main environmental stressors that can affect growth and the quality of cotton fibers. LT is also a major challenge for cotton survival, growth maturity and geographical distribution. However, few genome-wide transcriptional response and profiling datasets are available to explore the LT-tolerant mechanism of cotton. This study treated G. hirsutum with four LT gradients (control at 25 °C and cold temperatures at 4 °C, 10 °C and 15 °C) for 24 hour to generate 12 RNA-Seq datasets (three biological replicates per treatment) with approximately 280 million clean reads per dataset. The quality of the datasets obtained in the current study was validated through a series of quality checks including verification of RNA sample quality and RNA-Seq read quality. Data analyses included novel gene discovery, global gene expression profiling and quantitative real-time PCR. This is the first study to report genome-wide transcriptomic datasets for cotton in response to LT exposure.

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“…qRT‐PCR was used to validate gene expression levels determined by RNA‐Seq. The RNA samples used for qRT‐PCR assays were the same as those used in the RNA‐Seq analyses (Li et al, ; Xu et al, ; Zhang et al, ). Gene‐specific primers (Table ) were designed based on the reference genomic sequences using the Primer Premier 5.0 software package.…”

Section: Methodsmentioning

confidence: 99%

Differential Gene expression related to morphological variation in the adductor muscle tissues of diploid and triploid fujian oysters, Crassostrea angulata

Zeng

Tan²,

Huang

et al. 2019

Aquac Res

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The Fujian oyster, Crassostrea angulata, accounts for approximately 50% of the total oyster production in China and is one of the most economically important marine products. In this study, we investigated differential gene expression profiles between diploid (n = 2) and triploid (n = 3) oysters that may indicate the specific adaptation associated with ploidy. A total of 14,626,126 and 15,492,551 reads were generated from diploid and triploid oyster muscle transcriptomes using Illumina RNA‐Seq respectively. Gene expression analysis revealed a total of 2,045 differentially expressed genes between 2n and 3n individuals, from which 814 genes were significantly up‐regulated in the 2n transcriptome while 1,231 were down‐regulated. In addition, 24 differentially expressed genes (DEGs) were uniquely expressed in 2n individuals while 28 DEGs were uniquely expressed in 3n individuals. Furthermore, our pathway analysis suggested that the DEGs up‐regulated in 2n oysters were enriched in the pathways related to normal growth, development and reproduction, whereas DEGs up‐regulated in 3n individuals may be involved in faster growth and metabolism. Finally, we validated the expression levels of 15 genes using quantitative real‐time PCR (qRT‐PCR), and 14 out of 15 genes showed consistent expression patterns with RNA‐Seq data. This study provides an important foundation for further investigations on distinct gene expression patterns and signalling pathways that differ between diploid and triploid oysters.

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Comparative transcriptomic analysis provides insights into antibacterial mechanisms of Branchiostoma belcheri under Vibrio parahaemolyticus infection

Cited by 20 publications

References 57 publications

Gene expression kinetics of Exaiptasia pallida innate immune response to Vibrio parahaemolyticus infection

Gene expression kinetics of Exaiptasia pallida innate immune response to Vibrio parahaemolyticus infection

Transcriptomic profiling of cotton Gossypium hirsutum challenged with low-temperature gradients stress

Differential Gene expression related to morphological variation in the adductor muscle tissues of diploid and triploid fujian oysters, Crassostrea angulata

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