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Transcriptome profiling reveals higher vertebrate orthologous of intra-cytoplasmic pattern recognition receptors in grey bamboo shark.

Krishnaswamy Gopalan T, Gururaj P, Gupta R, Gopal DR, Rajesh P, Chidambaram B, Kalyanasundaram A, Angamuthu R - PLoS ONE (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Biotechnology and Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, India.

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.

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Differential gene expression analysis.A- DESeq scatter plot depicting the differentially expressed transcripts across spleen and kidney tissues; B- list of the different transcripts across spleen and kidney; Gene ontology of the differentially expressed transcripts in spleen (C) and Kidney (D). Note the increased representation of the transcripts to immune system in spleen.
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pone-0100018-g004: Differential gene expression analysis.A- DESeq scatter plot depicting the differentially expressed transcripts across spleen and kidney tissues; B- list of the different transcripts across spleen and kidney; Gene ontology of the differentially expressed transcripts in spleen (C) and Kidney (D). Note the increased representation of the transcripts to immune system in spleen.

Mentions: There were 1,881 transcripts that were expressed at higher levels (p-value < = 0.01) across spleen or kidney. The DESeq scatter plot is shown in Figure 4A. The red dots show the differential levels of the transcripts across these two tissues. Of these identified transcripts, there were 695 transcripts expressed at higher levels in spleen (Table S12), and 1,186 transcripts expressed higher in kidney (Table S13). The transcripts that are expressed at higher levels in both these tissues with their BLASTX annotation is shown in Figure 4B. Several transcripts expressed at higher levels could be identified between the two tissues. The ILK-8, Troponin C, NK2 homeobox 5 are expressed at higher levels in spleen, whereas, Na/Pi co-transporter, solute carrier family genes, homeodomain gene Emx2, Alanine-glyoxylate aminotransferase 2, HNF1 hemeobox B are expressed at higher levels in the kidney tissue. Gene ontology revealed transcripts relating to immune system (TNFSF13B, SCYA107, CCL19, ILK-8, CXCR5, MIP3, CD154) are highly expressed in spleen (Figure 4C), whereas a number of highly expressed transcripts in kidney belonged to solute carrier family (slc13a3, slc5a2, slc5a11, slc5a12, slc13a4) (Figure 4D). In order to get more insight into the different levels of these transcripts we used MEGAN4 annotation pipeline and generated the tag cloud plot Figure S3. The highly expressed transcripts in spleen are enriched with immune and signalling pathways including cell adhesion molecules, cytokine-cytokine receptor interaction, T-cell receptor signalling pathway and chemokine signaling pathway.


Transcriptome profiling reveals higher vertebrate orthologous of intra-cytoplasmic pattern recognition receptors in grey bamboo shark.

Krishnaswamy Gopalan T, Gururaj P, Gupta R, Gopal DR, Rajesh P, Chidambaram B, Kalyanasundaram A, Angamuthu R - PLoS ONE (2014)

Differential gene expression analysis.A- DESeq scatter plot depicting the differentially expressed transcripts across spleen and kidney tissues; B- list of the different transcripts across spleen and kidney; Gene ontology of the differentially expressed transcripts in spleen (C) and Kidney (D). Note the increased representation of the transcripts to immune system in spleen.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4067322&req=5

pone-0100018-g004: Differential gene expression analysis.A- DESeq scatter plot depicting the differentially expressed transcripts across spleen and kidney tissues; B- list of the different transcripts across spleen and kidney; Gene ontology of the differentially expressed transcripts in spleen (C) and Kidney (D). Note the increased representation of the transcripts to immune system in spleen.
Mentions: There were 1,881 transcripts that were expressed at higher levels (p-value < = 0.01) across spleen or kidney. The DESeq scatter plot is shown in Figure 4A. The red dots show the differential levels of the transcripts across these two tissues. Of these identified transcripts, there were 695 transcripts expressed at higher levels in spleen (Table S12), and 1,186 transcripts expressed higher in kidney (Table S13). The transcripts that are expressed at higher levels in both these tissues with their BLASTX annotation is shown in Figure 4B. Several transcripts expressed at higher levels could be identified between the two tissues. The ILK-8, Troponin C, NK2 homeobox 5 are expressed at higher levels in spleen, whereas, Na/Pi co-transporter, solute carrier family genes, homeodomain gene Emx2, Alanine-glyoxylate aminotransferase 2, HNF1 hemeobox B are expressed at higher levels in the kidney tissue. Gene ontology revealed transcripts relating to immune system (TNFSF13B, SCYA107, CCL19, ILK-8, CXCR5, MIP3, CD154) are highly expressed in spleen (Figure 4C), whereas a number of highly expressed transcripts in kidney belonged to solute carrier family (slc13a3, slc5a2, slc5a11, slc5a12, slc13a4) (Figure 4D). In order to get more insight into the different levels of these transcripts we used MEGAN4 annotation pipeline and generated the tag cloud plot Figure S3. The highly expressed transcripts in spleen are enriched with immune and signalling pathways including cell adhesion molecules, cytokine-cytokine receptor interaction, T-cell receptor signalling pathway and chemokine signaling pathway.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Biotechnology and Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, India.

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.

Show MeSH
Related in: MedlinePlus