title: Transcriptome profiling reveals higher vertebrate orthologous of intra-cytoplasmic pattern recognition receptors in grey bamboo shark.
abstract: From an immunologist perspective, sharks are an important group of jawed cartilaginous fishes and survey of the public database revealed a great gap in availability of large-scale sequence data for the group of Chondrichthyans the elasmobranchs. In an attempt to bridge this deficit we generated the transcriptome from the spleen and kidney tissues (a total of 1,606,172 transcripts) of the shark, Chiloscyllium griseum using the Illumina HiSeq2000 platform. With a cut off of > = 300 bp and an expression value of >1RPKM we used 43,385 transcripts for BLASTX analysis which revealed 17,548 transcripts matching to the NCBI nr database with an E-value of < = 10(-5) and similarity score of 40%. The longest transcript was 16,974 bases with matched to HECT domain containing E3 ubiqutin protein ligase. MEGAN4 annotation pipeline revealed immune and signalling pathways including cell adhesion molecules, cytokine-cytokine receptor interaction, T-cell receptor signalling pathway and chemokine signaling pathway to be highly expressed in spleen, while different metabolism pathways such as amino acid metabolism, carbohydrate metabolism, lipid metabolism and xenobiotic biodegradation were highly expressed in kidney. Few of the candidate genes were selected to analyze their expression levels in various tissues by real-time PCR and also localization of a receptor by in-situ PCR to validate the prediction. We also predicted the domains structures of some of the identified pattern recognition receptors, their phylogenetic relationship with lower and higher vertebrates and the complete downstream signaling mediators of classical dsRNA signaling pathway. The generated transcriptome will be a valuable resource to further genetic and genomic research in elasmobranchs.
authors: Department of Animal Biotechnology and Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, India.
authors: Tirumurugaan
authors: T
authors: Krishnaswamy Gopalan
authors: Department of Animal Biotechnology, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, India.
authors: Pradheepa
authors: P
authors: Gururaj
authors: SciGenom Labs Pvt. Ltd., Kakkanad, Cochin, Kerala, India.
authors: Ravi
authors: R
authors: Gupta
authors: Department of Animal Biotechnology and Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, India.
authors: Dhinakar Raj
authors: DR
authors: Gopal
authors: SciGenom Labs Pvt. Ltd., Kakkanad, Cochin, Kerala, India.
authors: Preeti
authors: P
authors: Rajesh
authors: Department of Veterinary Pathology, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, India.
authors: Balachandran
authors: B
authors: Chidambaram
authors: Department of Animal Biotechnology, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, India.
authors: Aravindan
authors: A
authors: Kalyanasundaram
authors: Department of Animal Biotechnology, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, India.
authors: Raja
authors: R
authors: Angamuthu
mesh_terms: D000818:Animals; D029941:Fish Proteins / Q000096:biosynthesis* / Q000235:genetics; D020869:Gene Expression Profiling; D051192:Receptors, Pattern Recognition / Q000096:biosynthesis* / Q000235:genetics; D012754:Sharks / Q000235:genetics / Q000378:metabolism*; D059467:Transcriptome / Q000502:physiology*
chemical_list: D029941:Fish Proteins; D051192:Receptors, Pattern Recognition