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Abstract
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Article Information:
Ubiquitous Expression of Genes in tissues of Goat (Capra hircus) Using RNA-seq
Upasna Sharma, Priyanka Banerjee, Jyoti Joshi and Ramesh Kumar vijh
Corresponding Author: Ramesh Kumar Vijh
Submitted: June 19, 2012
Accepted: July 09, 2012
Published: August 20, 2012 |
Abstract:
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Since very little information is available on goat transcriptome (only few sequenced genes and ESTs are
available in the database), our main aim was to analyze the goat transcriptome for identification of ubiquitous genes
through RNA-Seq approach, expression of genes across tissues and analyse the functional pathways which these
highly expressed genes follow. RNA-Seq analysis was carried out on 10 tissues of Osmanabadi goats. The data was
2x76 base pair paired end reads generated using Illumina Genome Analyser GAIIx. More than 40 million reads per
tissue were generated. The data was mapped using CLC Genomics Workbench on Ensembl cattle (Btau_4.0) genes
version 62 downloaded from BioMart. The mapping statistics was discerned for each of the mapped gene for all the
10 tissues. There was a great deal of homology between the genes of cattle and goats and this was expected as both
are ruminants and phylogenetically close to one another. The expression profile for genes of each of the 10 tissues
was calculated in terms of RPKM values. The differential expression of genes among the different tissues was
carried out using 3 algorithms. The genes common among the 3 algorithms were associated with GO IDs and the
functional annotation was carried out by estimating the GO term occurrences using CateGOrizer web server. The
study revealed that more than 75% genes are ubiquitously expressed (expressed in all tissues) with very limited
number of tissue specific genes based on expression values (expressed in only one tissue). These genes are mostly
related with the specific functions performed by various tissues.
Key words: Capra hircus , differential gene expression, gene ontology, RNA-Seq, transcriptome, ,
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Cite this Reference:
Upasna Sharma, Priyanka Banerjee, Jyoti Joshi and Ramesh Kumar vijh, . Ubiquitous Expression of Genes in tissues of Goat (Capra hircus) Using RNA-seq. International Journal of Animal and Veterinary Advances, (4): 292-302.
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ISSN (Online): 2041-2908
ISSN (Print): 2041-2894 |
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