Expression Profile of the Channel Catfish Spleen: Analysis of Genes Involved in Immune Functions

Abstract

Both qualitative and quantitative patterns of tissue-specific gene expression can be determined using gene profiling. Expressed sequence tag (EST) analysis is an efficient approach not only for gene discovery and examining gene expression, but also for development of molecular resources useful for functional genomics. As part of an ongoing transcriptome analysis of channel catfish (Ictalurus punctatus), EST analysis was conducted for gene annotations and profiling using a complementary DNA library developed from messenger RNA of the spleen. A total of 1204 spleen cDNA clones were analyzed. Of the 1204 clones, 665 clones (55.2%) were identified as orthologs of known genes from other organisms by BLAST searches and 539 clones (44.8%) as unknown gene clones. In total 147 novel genes were identified, and annotations were made to 118 of them. In addition, 389 novel EST clusters were identified. Expression profile was analyzed in relation to metabolic functional groups. A total of 28 known genes were involved in immune functions, of which 10 were identified for the first time in channel catfish. Microsatellite-containing clones were also identified that may be potentially useful for genome mapping. This work contributed to the Catfish Gene Index, and toward a Unigene set useful for functional genomics research concerning spleen gene functions in relation to disease defenses.

NK-lysin of channel catfish: Gene triplication, sequence variation, and expression analysis

“…Jx14 was made from the catfish autonomous (immortal) macrophage cell line 42TA (Miller et al, 1994b). The spleen cDNA library was previously reported (Kocabas et al, 2002).…”

EST-based identification of genes expressed in the hypothalamus of male orange-spotted grouper (Epinephelus coioides)

“…Currently, a lot of fish ESTs have been released from model fish and food fish species, but over 50% of the teleost ESTs were generated from model fish, such as zebrafish (Gong, 1999), medaka , and fugu (Jaillon et al, 2004). Only a few of specific tissues have become the object of EST projects from some aquaculture species, such as winter flounder (Douglas et al, 1999), Japanese flounder (Inoue et al, 1997), salmon (Davey et al, 2001;Martin et al, 2002), channel catfish (Karsi et al, 1998Ju et al, 2000;Kim et al, 2000;Kocabas et al, 2002), red sea bream (Chen et al, 2004), tilapia (Shiue et al, 2004), common carp (Kono et al, 2004), and gilthead sea bream (Sarropoulou et al, 2005). The lack of EST resources in commercial fish species prohibits use of modern functional genomic approaches for the study of growth, development, reproduction, stress biology and molecular breeding (Chen et al, 2004).…”

Characterization of a NK-lysin antimicrobial peptide gene from channel catfish

“…Three clones of channel catfish NK-lysin cDNA were initially identified from analysis of expressed sequence tags (ESTs) [28]. Sequence alignment revealed that all three cDNAs were transcripts from a single gene.…”