EST-based identification of immune-relevant genes from spleen of Indian catfish, Clarias batrachus (Linnaeus, 1758)

• Published in: Gene 2012-07, Vol.502 (1), p.53-59
• Main Authors: Singh, Akanksha, Sood, Neeraj, Chauhan, U.K., Mohindra, Vindhya
• Format: Article
• Language: English
• Subjects: Adaptive Immunity - genetics; alleles; Amino Acid Sequence; Animals; catfish; Catfishes - genetics; Catfishes - immunology; cDNA libraries; cDNA library; Clarias batrachus; clones; complementary DNA; Cytokines - genetics; Cytokines - metabolism; defense mechanisms; EST-SSR, SNP; Expressed Sequence Tags; Fish Proteins - chemistry; Fish Proteins - genetics; Fish Proteins - metabolism; Gene Expression Profiling; Gene Library; Genetic Markers; immune response; Immune-relevant genes; Immunity, Innate - genetics; marker-assisted selection; Microsatellite Repeats; Molecular Sequence Data; Muramidase - chemistry; Muramidase - genetics; Muramidase - metabolism; Polymorphism, Single Nucleotide; Sequence Homology, Amino Acid; spleen; Spleen - immunology; Spleen - metabolism; stress response; Teleostei; Thrombomodulin - chemistry; Thrombomodulin - genetics; Thrombomodulin - metabolism; Transcriptome
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2012.04.019

A normalized cDNA library from spleen of Indian catfish, Clarias batrachus, was constructed with a redundancy factor of 2.29. A total of 2045 clones from the library were single-pass sequenced, which generated 1937 high quality ESTs with an average read length of approximately 700bp. Based on sequence similarities, 65 ESTs were found to be associated with immune functions, which were mainly associated with response to stress, response to chemical stimulus, cellular response to stimulus, response to external stimulus, immune response and regulation of response to stimulus. The immune-relevant gene for CD141, thrombomodulin, has been identified in Teleosts for the first time. Six EST-SSRs and three SNPs were found associated with eight immune-relevant genes. These markers associated with important immune genes would be useful for the identification of trait associated alleles for marker-assisted selection. The identification of the putative immune-related genes provides a meaningful framework to understand the Indian catfish immune system and defense mechanisms. ► 1937 ESTs were generated, from a normalized Clarias batrachus spleen cDNA library. ► Based on similarities, 65 ESTs were found to be associated with immune functions. ► Immune-relevant gene CD141, thrombomodulin, was identified in teleost for first time. ► Six EST-SSRs and three SNPs were found associated with eight immune-relevant genes.