Analysis of expressed sequence tags from body wall, intestine and respiratory tree of sea cucumber (Apostichopus japonicus)

Sea cucumber (Apostichopus japonicus) is one of the most important aquaculture species in China. To profile gene expression in different tissues and to identify immune-related genes, we constructed three independent cDNA libraries that were derived from intestine (Int), body wall (BW) and respiratory tree (RT) of healthy individuals. From these libraries, a total of 5728 high-quality expressed sequence tags (ESTs) of longer than 100 bp were generated. Clustering and assembly of the ESTs identified 495 contigs and 2118 singletons, representing 2613 unigenes. Basic Local Alignment Search Tool (BLAST) analysis showed that 902 unigenes (34.52%) had significant homology (E value ≤10− 5) to genes with known or putative functions in GenBank. These unigenes were grouped into 18 functional categories. When compared among these three libraries, RT library showed fewer categories (9) while the other two libraries displayed more (17 and 16 for Int and BW libraries respectively). Considering the components among the three cDNA libraries, 655, 259 and 484 tissue-specific unigenes were observed in Int, BW and RT libraries respectively; however, only 95 unigenes were common to all three libraries. The most abundant contigs in the three libraries were identified as genes related to cell and organism defense (551 ESTs), metabolism (415 ESTs), translation/ribosomal structure and biogenesis (342 ESTs), gene/protein expression (178 ESTs), structure and motility (75 ESTs), energy production and conversion (51 ESTs), and cytoskeleton (39 ESTs). The list of 636 ESTs that matched with immune-related genes were categorized as pattern recognition receptors and signaling, complement components, transferrin superfamily members, cytokines and growth factors, and effector genes. The present manuscript presents a fair amount of data regarding the spatial expression pattern of many genes (BW vs. Int vs. RT of A. japonicus).