Transcriptome Profiling Reveals Higher Vertebrate Orthologous of Intra-Cytoplasmic Pattern Recognition Receptors in Grey Bamboo Shark

Gopalan, Tirumurugaan Krishnaswamy; Gururaj, Pradheepa; Raj, Gopal Dhinakar; Rajesh, Preeti; Chidambaram, Balachandran; Kalyanasundaram, Aravindan; Amri, R.

doi:10.1371/journal.pone.0100018

Cited by 19 publications

(14 citation statements)

References 38 publications

(44 reference statements)

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“…However, relatively few studies have focused on the TLRs of cartilaginous fish and, accordingly, there is a need to fill the gaps in the current knowledge about this group. TLR2, TLR3, TLR6, and TLR9 have been identified in the gray bamboo shark Chiloscyllium griseum based on a survey of transcriptome data ( 148 , 149 ). TLR2 of C. griseum is closely related to homologs in Sus scrofa and Gallus gallus , whereas TLR3 is closely related to homologs in Rattus norvegicus and Canis lupus familiaris .…”

Section: Tlrs In Non-mammalian Vertebratesmentioning

confidence: 99%

Toll-Like Receptors, Associated Biological Roles, and Signaling Networks in Non-Mammals

et al. 2018

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The innate immune system is the first line of defense against pathogens, which is initiated by the recognition of pathogen-associated molecular patterns (PAMPs) and endogenous damage-associated molecular patterns (DAMPs) by pattern recognition receptors (PRRs). Among all the PRRs identified, the toll-like receptors (TLRs) are the most ancient class, with the most extensive spectrum of pathogen recognition. Since the first discovery of Toll in Drosophila melanogaster, numerous TLRs have been identified across a wide range of invertebrate and vertebrate species. It seems that TLRs, the signaling pathways that they initiate, or related adaptor proteins are essentially conserved in a wide variety of organisms, from Porifera to mammals. Molecular structure analysis indicates that most TLR homologs share similar domain patterns and that some vital participants of TLR signaling co-evolved with TLRs themselves. However, functional specification and emergence of new signaling pathways, as well as adaptors, did occur during evolution. In addition, ambiguities and gaps in knowledge still exist regarding the TLR network, especially in lower organisms. Hence, a systematic review from the comparative angle regarding this tremendous signaling system and the scenario of evolutionary pattern across Animalia is needed. In the current review, we present overview and possible evolutionary patterns of TLRs in non-mammals, hoping that this will provide clues for further investigations in this field.

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Section: Tlrs In Non-mammalian Vertebratesmentioning

confidence: 99%

Toll-Like Receptors, Associated Biological Roles, and Signaling Networks in Non-Mammals

et al. 2018

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“…The high number of the spiny dogfish predicted proteins align to the different databases searched provide a more complete annotation than obtained by previous studies involving other shark transcriptomes [ 43 – 45 ]. Although the activities of all the enzymes involved in urea synthesis in spiny dogfish have been biochemically studied since the 1960s [ 1 ], sequence information of the genes that code for those proteins is still incomplete in this shark species.…”

Section: Discussionmentioning

confidence: 99%

“…Apart from rectal gland tissue [ 39 ], transcript information on other individual tissues is lacking for spiny dogfish. Genomic and transcriptomic resources for this animal group and particularly for sharks remain scarce even though there have been previous studies generating sequence data for cartilaginous fishes [ 39 , 41 – 45 ]. To overcome these limitations, we performed extensive transcriptome sequencing of this shark using next generation sequencing (NGS) technology.…”

Section: Introductionmentioning

confidence: 99%

Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation

et al. 2017

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The spiny dogfish shark (Squalus acanthias) is one of the most commonly used cartilaginous fishes in biological research, especially in the fields of nitrogen metabolism, ion transporters and osmoregulation. Nonetheless, transcriptomic data for this organism is scarce. In the present study, a multi-tissue RNA-seq experiment and de novo transcriptome assembly was performed in four different spiny dogfish tissues (brain, liver, kidney and ovary), providing an annotated sequence resource. The characterization of the transcriptome greatly increases the scarce sequence information for shark species. Reads were assembled with the Trinity de novo assembler both within each tissue and across all tissues combined resulting in 362,690 transcripts in the combined assembly which represent 289,515 Trinity genes. BUSCO analysis determined a level of 87% completeness for the combined transcriptome. In total, 123,110 proteins were predicted of which 78,679 and 83,164 had significant hits against the SwissProt and Uniref90 protein databases, respectively. Additionally, 61,215 proteins aligned to known protein domains, 7,208 carried a signal peptide and 15,971 possessed at least one transmembrane region. Based on the annotation, 81,582 transcripts were assigned to gene ontology terms and 42,078 belong to known clusters of orthologous groups (eggNOG). To demonstrate the value of our molecular resource, we show that the improved transcriptome data enhances the current possibilities of osmoregulation research in spiny dogfish by utilizing the novel gene and protein annotations to investigate a set of genes involved in urea synthesis and urea, ammonia and water transport, all of them crucial in osmoregulation. We describe the presence of different gene copies and isoforms of key enzymes involved in this process, including arginases and transporters of urea and ammonia, for which sequence information is currently absent in the databases for this model species. The transcriptome assemblies and the derived annotations generated in this study will support the ongoing research for this particular animal model and provides a new molecular tool to assist biological research in cartilaginous fishes.

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“…TLR2, TLR3, TLR6, and TLR9 have been identified in the gray bamboo shark ( Chiloscyllium griseum ) genome whereas no TLR6 or TLR10 homolog has been identified in teleost fish. In addition, a novel TLR with sequence similarity to TLR4 and TLR13 in mammals, and TLR21 in teleost fish, has been identified in the whale shark ( Rhincodon typus ) (80, 83).…”

Section: Recognition Of Non-selfmentioning

confidence: 99%

A Comparison of the Innate and Adaptive Immune Systems in Cartilaginous Fish, Ray-Finned Fish, and Lobe-Finned Fish

2019

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The immune system is composed of two subsystems—the innate immune system and the adaptive immune system. The innate immune system is the first to respond to pathogens and does not retain memory of previous responses. Innate immune responses are evolutionarily older than adaptive responses and elements of innate immunity can be found in all multicellular organisms. If a pathogen persists, the adaptive immune system will engage the pathogen with specificity and memory. Several components of the adaptive system including immunoglobulins (Igs), T cell receptors (TCR), and major histocompatibility complex (MHC), are assumed to have arisen in the first jawed vertebrates—the Gnathostomata. This review will discuss and compare components of both the innate and adaptive immune systems in Gnathostomes, particularly in Chondrichthyes (cartilaginous fish) and in Osteichthyes [bony fish: the Actinopterygii (ray-finned fish) and the Sarcopterygii (lobe-finned fish)]. While many elements of both the innate and adaptive immune systems are conserved within these species and with higher level vertebrates, some elements have marked differences. Components of the innate immune system covered here include physical barriers, such as the skin and gastrointestinal tract, cellular components, such as pattern recognition receptors and immune cells including macrophages and neutrophils, and humoral components, such as the complement system. Components of the adaptive system covered include the fundamental cells and molecules of adaptive immunity: B lymphocytes (B cells), T lymphocytes (T cells), immunoglobulins (Igs), and major histocompatibility complex (MHC). Comparative studies in fish such as those discussed here are essential for developing a comprehensive understanding of the evolution of the immune system.

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Transcriptome Profiling Reveals Higher Vertebrate Orthologous of Intra-Cytoplasmic Pattern Recognition Receptors in Grey Bamboo Shark

Cited by 19 publications

References 38 publications

Toll-Like Receptors, Associated Biological Roles, and Signaling Networks in Non-Mammals

Toll-Like Receptors, Associated Biological Roles, and Signaling Networks in Non-Mammals

Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation

A Comparison of the Innate and Adaptive Immune Systems in Cartilaginous Fish, Ray-Finned Fish, and Lobe-Finned Fish

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