Comparative transcriptome analysis of tube feet of different colors in the sea urchin Strongylocentrotus intermedius

The Strongylocentrotus intermedius is an important commercially cultivated marine animal in China. In recent years, some individuals with diaphanous tube feet, rather than the normal red tube feet, have been observed among animals under cultivation; the basis of this phenotypic change is uncertain. In order to better understand the differences between two color tube feet of S. intermedius at the molecular level, we constructed four cDNA libraries from tube feet and coelomocytes of S. intermedius individuals with red or diaphanous tube feet. A total of 216,729,214 clean reads were assembled into 87,510 transcripts with an average size of 1677 bp. A BlastX search showed that 72,690 transcripts had significant matches in at least one target database. Expression profile analysis was performed on the four libraries and many differentially expressed genes were identified. Using gene enrichment analysis, several biological processes related to immune responses as well as immune-related candidate genes were identified. A total of 1694 genes were immune-related, and the genes expression of red tube feet were higher than that of diaphanous tube feet. In addition, 50,427 simple sequence repeats were obtained from the S. intermedius transcriptomes, while 32,650 and 42,264 single nucleotide polymorphisms were found in S. intermedius with diaphanous tube feet and red tube feet, respectively. These results provide valuable information for the future studies involving marker-assisted breeding and the studies of population genetics and genomics on S. intermedius.