Abstract
Digital gene expression (DGE) analysis using next-generation sequencer is a high-throughput method for accurate quantification of the transcripts. In this study, we analyzed the transcriptome of apical nervous system in echinoderm sea urchin larvae by using Illumina Genome Analyzer to examine the homology of nervous system between echinoderms and chordates. We found that the genes for specifying early neurogenic ectoderm, such as Six3 and its downstream genes, are highly expressed in apical nervous system. In addition, orthologues for forebrain patterning genes are expressed at high level in apical nervous system while those for midbrain and hindbrain patterning genes are not. This result indicates that apical nervous system is comparable to the chordate forebrain. Our analysis also found previously unknown gene expressions, suggesting that DGE analysis is a useful tool to clarify a tissue-specific gene expression patterns.