Transcriptic analysis of Huanghai No. 1 strain of Chinese shrimp Fenneropenaeus chinensis using 454 pyrosequencing

Abstract

The Huanghai No. 1 strain of Chinese shrimp Fenneropenaeus chinensis is an ecologically and economically important variety that is cultivated mainly in northern China. This strain has been subjected to multiple selective events in recent years. Conventional methods are insufficient to reveal the genetic background of Huanghai No. 1, especially with regard to a genome-wide transcription profile, and publicly available genomic resources for Huanghai No. 1 are limited. We obtained 907,945 original reads with an average length of 467.5 bp from muscle and haemocyte samples from Huanghai No. 1 using 454 pyrosequencing. After preprocessing, 867,245 high-quality reads were screened. Of the 64,830 assembled sequences, 34,633 of the unigenes had significant matches in the databases (similarity >30 %), including 14,138 isotigs and 20,495 singletons. A gene ontology analysis assigned 8,257 unigenes to 44 subcategories, with the majority of unigenes assigned to cellular component (28.2 %), biological process (20.5 %) and molecular function (5.0 %) categories. Pathway mapping based on information in the Kyoto Encyclopedia of Genes and Genomes database showed that 15,461 transcripts were associated with 223 pathways. A total of 14,981 putative SSRs, 72,370 SNPs, and candidate genes involved in growth, reproduction, and the immune response were identified. Our findings represent the most comprehensive transcriptomic resources currently available for Huanghai No. 1, and provide an important foundation for further genomic studies of F. chinensis.