De novo transcriptome profiling of Saccharina japonica sporophyte

Saccharina japonica is one of the most important economic seaweeds worldwide. The genome has not been sequenced and only a few ESTs are deposited in public databases, making genome–wide experimental biology study of this species unavailable. In order to characterize the functional genome, we sequenced the transcriptome of S. japonica sporophyte using high throughput Illumina sequencing technology. The obtained unigenes were annotated by aligning them with protein databases or predicted using the software ESTScan. In total, 26 million reads generated 2.4 G nucleotides, which were finally assembled into 95135 unigenes with a mean length of 389 bp. A total of 30095 unigenes were annotated by blast analysis with more than half (16987) were mapped to the E. siliculosus genome. 6183 non-annotated unigenes were predicted to be novel protein-coding genes in S. japonica by ESTScan. The functional gene tags revealed most aspects in the lives of S. japonica, including the carbohydrate metabolism, halogen metabolism, pathogen and stress defense, photosynthesis, and signal transduction mechanisms. Specifically, all the essential enzymes involved in C4 carbon fixation were identified, providing a direct and perfect evidence of C4 pathway existence in kelp. Thirty-two unigenes were characterized as light receptor genes, including phytochromes, cryptochromes, as well as aureochromes – the blue light receptor specific to phototrophic Stramenopiles. The large set of S. japonica functional gene sequences provided a genome-wide resource for further molecular biology studies and for reference gene models when its genome is eventually sequenced.