Generation and Analysis of 10,443 ESTs from Cephalothorax of Fenneropenaeus Chinensis

Chinese shrimp, Fenneropenaeus chinensis (F. chinensis), is one of the main local mariculture species in China. To accelerate gene discovery, facilitate genetic mapping and develop marker-assisted selection, a total of 10,446 expressed sequence tags (ESTs) were created from the 5´ ends of randomly selected clones from a cephalothorax cDNA library of an adult female F. chinensis. The ESTs were clustered into 1399 contigs and 1720 singletons; represent about 3120 unique genes discovered. Among the discovered unique genes, 1373 EST clusters are known genes and 1747 EST clusters may represent novel genes, which do not match any known genes from other species. Known ESTs in the dataset were classified in to different molecular-function categories according to the KEGG-GO and the enzyme was the biggest category, which consist of 29.5% of known ESTs. The putative novel genes were characterized by motif search, and the functions of about 50% (786) of these genes were preliminarily determined. Among them, type I antifreeze protein was considered as the most redundant one. Besides the discovery of new genes through EST analysis, 324 (about 3%) perfect simple sequence repeats (SSRs) were found. This EST approach provides a foundation for the discovery of functional genes and furthermore gives great support for future microarray studies on gene expression.