Analysis of immune-relevant genes expressed in red sea bream ( Chrysophrys major) spleen

• Published in: Aquaculture 2004-10, Vol.240 (1), p.115-130
• Main Authors: Chen, Song-Lin, Xu, Mei-Yu, Hu, Song-Nian, Li, Lin
• Format: Article
• Language: English
• Subjects: amino acid sequences; Animal aquaculture; Animal productions; Aquaculture; Biological and medical sciences; bream; Chrysophrys major; Cichlidae; complementary DNA; Danio rerio; Dicentrarchus labrax; DNA libraries; EST; Evolution; expressed sequence tags; Fish; Fugu; Fundamental and applied biological sciences. Psychology; Gene expression; gene expression regulation; General aspects; Ictalurus punctatus; Immune system; Immune-relevant genes; major histocompatibility complex; Marine; marine fish; MHC II; molecular sequence data; phylogeny; Platichthys; Pleuronectiformes; RAP2c; Red sea bream; Salmo salar; sequence alignment; sequence analysis; Sparidae; Spleen
• ISSN: 0044-8486; 1873-5622
• DOI: 10.1016/j.aquaculture.2004.07.008

Expressed sequence tag (EST) analysis is an efficient tool for gene discovery and for profiling gene expression. In order to isolate functional genes involved in immunity in fish, a cDNA library was constructed from red sea bream ( Chrysophrys major) spleen by unidirectional cloning. A total of 2010 ESTs from the library was sequenced and compared with sequences in the GenBank database. Of the 2010 ESTs, 320 ESTs (15.9%) were identified as orthologs of known gene from other organisms by BLAST searches, whereas 1690 ESTs (84.1%) appeared to be unknown and are likely to represent newly described genes. These identified clones were derived from at least 81 genes, which were categorized into eight categories: 9 in cell structure/motility (11.1%), 14 in metabolism (17.3%), 8 in cell defense/immunity (10%), 5 in cell division (6.2%), 7 in cell signal transduction/communication (8.6%), 30 in gene/protein expression (37%), 5 hemoglobin (6.2%) and 3 genes lacking enough information to be classified (3.7%). Several important cDNAs involved in immune functions, such as immunoglobulin light chain (IgL), MHC class IIα, MHC class IIβ and RAP2c, were identified in red sea bream and compared for their structure with those from other organisms. Alignment showed that the red sea bream IgL precursor was closer to that of spotted wolfish than to that of yellowtail, Europe sea bass, orange spotted grouper, Atlantic salmon, channel catfish, fugu and sterlet. Phylogenetic analysis indicated that the red sea bream MHC IIα and MHC IIβ were more related to those from striped sea bass than to those from cichlid, flounder, salmonids, zebrafish and carp. High identity (over 92%) in deduced amino acid sequence of RAP2c between red sea bream and mammals implied that RAP2c gene was highly conserved during evolution.