Characteristic and functional analysis of Toll-like receptors (TLRs) in the lophotrocozoan, Crassostrea gigas, reveals ancient origin of TLR-mediated innate immunity

Zhang, Y.; He, Xiaobo; Yu, Feifei; Zhou, Yu

doi:10.1016/j.fsi.2013.03.165

Cited by 16 publications

(23 citation statements)

References 33 publications

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“…The latter reads covered almost all the viral genome, in amounts adequate for a deep expression analysis of the OsHV‐1 genes (except for ORFs 34, 35 and 46). The average coverage resulted to be 718×, with a peak of 197 202 reads counted for ORF104; moreover, the GC content distribution of the oyster and viral reads did not overlap, in accordance with the different base composition of the two genomes (http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12706/suppinfo) (Davison et al ., ; Zhang et al ., ).…”

Section: Resultsmentioning

confidence: 97%

Dual analysis of host and pathogen transcriptomes in ostreid herpesvirus 1‐positive Crassostrea gigas

Rosani

Varotto

Domeneghetti

et al. 2014

Environmental Microbiology

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Ostreid herpesvirus type 1 (OsHV-1) has become a problematic infective agent for the Pacific oyster Crassostrea gigas. In particular, the OsHV-1 μVar subtype has been associated with severe mortality episodes in oyster spat and juvenile oysters in France and other regions of the world. Factors enhancing the infectivity of the virus and its interactions with susceptible and resistant bivalve hosts are still to be understood, and only few studies have explored the expression of oyster or viral genes during productive infections. In this work, we have performed a dual RNA sequencing analysis on an oyster sample with a high viral load. High sequence coverage allowed us to thoroughly explore the OsHV-1 transcriptome and identify the activated molecular pathways in C. gigas. The identification of several highly induced and defence-related oyster transcripts supports the crucial role played by the innate immune system against the virus and opportunistic microbes possibly contributing to subsequent spat mortality.

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Section: Resultsmentioning

confidence: 97%

Dual analysis of host and pathogen transcriptomes in ostreid herpesvirus 1‐positive Crassostrea gigas

Rosani

Varotto

Domeneghetti

et al. 2014

Environmental Microbiology

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“…Echinoderms and hemichordates comprise the Ambulacraria, the sister group to Chordata. (6,21). In contrast, virus-targeted TCAM1-dependent TLR signaling is known only from studies in select vertebrate taxa (e.g., mouse, human, and zebrafish) (9).…”

Section: Significancementioning

confidence: 99%

Toll-like receptor pathway evolution in deuterostomes

Tassia

Whelan

Halanych

2017

Proc. Natl. Acad. Sci. U.S.A.

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Animals have evolved an array of pattern-recognition receptor families essential for recognizing conserved molecular motifs characteristic of pathogenic microbes. One such family is the Toll-like receptors (TLRs). On pathogen binding, TLRs initiate specialized cytokine signaling catered to the class of invading pathogen. This signaling is pivotal for activating adaptive immunity in vertebrates, suggesting a close evolutionary relationship between innate and adaptive immune systems. Despite significant advances toward understanding TLR-facilitated immunity in vertebrates, knowledge of TLR pathway evolution in other deuterostomes is limited. By analyzing genomes and transcriptomes across 37 deuterostome taxa, we shed light on the evolution and diversity of TLR pathway signaling elements. Here, we show that the deuterostome ancestor possessed a molecular toolkit homologous to that which drives canonical MYD88-dependent TLR signaling in contemporary mammalian lineages. We also provide evidence that TLR3-facilitated antiviral signaling predates the origin of its TCAM1 dependence recognized in the vertebrates. SARM1, a negative regulator of TCAM1-dependent pathways in vertebrates, was also found to be present across all major deuterostome lineages despite the apparent absence of TCAM1 in invertebrate deuterostomes. Whether the presence of SARM1 is the result of its role in immunity regulation, neuron physiology, or a function of both is unclear. Additionally, Bayesian phylogenetic analyses corroborate several lineage-specific TLR gene expansions in urchins and cephalochordates. Importantly, our results underscore the need to sample across taxonomic groups to understand evolutionary patterns of the innate immunity foundation on which complex immunological novelties arose.

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“…Bivalve mollusks comprise approximately 14,000 existing species that are widely distributed worldwide. Many of these species are economically important aquaculture shellfish; therefore, extensive studies on the genes related to immunity [18][19][20], growth [21][22][23] and reproduction [24,25] have been conducted in this group of animals. Gene expression quantification via RT-qPCR has been extensively conducted, but mostly using a single reference gene, such as ACT and CYTC [26][27][28].…”

Section: Introductionmentioning

confidence: 99%

Systematic identification and validation of the reference genes from 60 RNA-Seq libraries in the scallop Mizuhopecten yessoensis

Zhang

et al. 2019

BMC Genomics

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Background: Reverse transcription quantitative PCR (RT-qPCR) is widely used for gene expression analysis in various organisms. Its accuracy largely relies on the stability of reference genes, making reference gene selection a vital step in RT-qPCR experiments. However, previous studies in mollusks only focused on the reference genes widely used in vertebrates. Results: In this study, we conducted the transcriptome-wide identification of reference genes in the bivalve mollusk Mizuhopecten yessoensis based on 60 transcriptomes covering early development, adult tissues and gonadal development. A total of 964, 1210 and 2097 candidate reference genes were identified, respectively, resulting in a core set of 568 genes. Functional enrichment analysis showed that these genes are significantly overrepresented in Gene Ontology (GO) terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to ribosomes, energy production, etc. Six genes (RS23, EF1A, NDUS4, SELR1, EIF3F, and OLA1) were selected from the candidate genes for RT-qPCR validation, together with 6 commonly used reference genes (ACT, CYTC, HEL, EF1B, GAPDH and RPL16). Stability analyses using geNorm, NormFinder and the comparative delta-Ct method revealed that the new candidate reference genes are more stable than the traditionally used genes, and ACT and CYTC are not recommended under either of the three circumstances. There was a significant correlation between the Ct of RT-qPCR and the log 2 (TPM) of RNA-Seq data (Ct = − 0.94 log 2 (TPM) + 29.67, R 2 = 0.73), making it easy to estimate the Ct values from transcriptome data prior to RT-qPCR experiments. Conclusion: Our study represents the first transcriptome-wide identification of reference genes for early development, adult tissues, and gonadal development in the Yesso scallop and will benefit gene expression studies in other bivalve mollusks.

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Characteristic and functional analysis of Toll-like receptors (TLRs) in the lophotrocozoan, Crassostrea gigas, reveals ancient origin of TLR-mediated innate immunity

Cited by 16 publications

References 33 publications

Dual analysis of host and pathogen transcriptomes in ostreid herpesvirus 1‐positive Crassostrea gigas

Dual analysis of host and pathogen transcriptomes in ostreid herpesvirus 1‐positive Crassostrea gigas

Toll-like receptor pathway evolution in deuterostomes

Systematic identification and validation of the reference genes from 60 RNA-Seq libraries in the scallop Mizuhopecten yessoensis

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