Molecular Biology Reports

, Volume 40, Issue 12, pp 6965–6975 | Cite as

Transcriptome generation and analysis from spleen of Indian catfish, Clarias batrachus (Linnaeus, 1758) through normalized cDNA library

  • Akanksha Singh
  • A. S. Barman
  • Neeraj Sood
  • Vindhya Mohindra


Catfishes are commercially important fish for both the fisheries and aquaculture industry. Clarias batrachus, an Indian catfish species is economically important owing to its high demand. A normalized cDNA library was constructed from spleen of the Indian catfish to identify genes associated with immune function. One thousand nine hundred thirty seven ESTs were submitted to the GenBank with an average read length of approximately 700 bp. Clustering analysis of ESTs yielded 1,698 unique sequences, including 184 contigs and 1,514 singletons. Significant homology to known genes was found by homology searches against data in GenBank in 576 (34 %) ESTs, including similarity to functionally annotated unigenes for 158 ESTs. Additionally, 433 ESTs revealed similarity to unigenes and ESTs in the dbEST but the remaining 658 EST sequences (39 %) did not match any sequence in GenBank. Of a total of 1,698 ESTs generated, 65 ESTs were found to be associated with immune functions. Gene Ontology and KEGG pathway analyses of C. batrachus ESTs collectively revealed a preponderance of immune relevant pathways apart from the presence of pathways involved in protein processing, localization, folding and protein degradation. This study constitutes first EST analysis of lymphoid organ in aquaculturally important Indian catfish species and could pave the way for further research of immune-related genes and functional genomics in this catfish.


Indian catfish Clarias batrachus Expressed sequence tags cDNA library Normalisation Functional annotation 



Expressed sequence tags


Open reading frame


Gene ontology


Kyoto encyclopedia of genes and genomes


KEGG automatic annotation server


Food and Agriculture Organization



This work was carried out under the project funded by Department of Biotechnology (DBT), Government of India and financial support provided by DBT is thankfully acknowledged.


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Akanksha Singh
    • 1
  • A. S. Barman
    • 1
  • Neeraj Sood
    • 1
  • Vindhya Mohindra
    • 1
  1. 1.National Bureau of Fish Genetic Resources (ICAR)LucknowIndia

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