Comparison of RNA expression profiles on generations of Porphyra yezoensis (Rhodophyta), based on suppression subtractive hybridization (SSH)

BACKGROUND: Porphyra yezoensis Ueda is one of the most important edible seaweed, with a dimorphic life cycle which consists of gametophyte as macroscopical blade and sporophyte as microscopic filamentous. Conspicuous differences exist in the two generations, such as morphology, cell structure, biochemistry, physiology, and so on. The developmental process of Porphyra yezoensis has been studied thoroughly, but the mechanism is still ambiguous and few studies on genetic expression have been carried out. In this study, the suppression subtractive hybridization (SSH) method conducted to generate large-scale expressed sequence tags (EST) is designed to identify gene candidates related to the morphological and physiological differences between the gametophytic and sporophytic generations of Porphyra yezoensis Ueda. FINDINGS: Each 300 clones of sporophyte and gametophyte cells were dipped onto the membrane for hybridization. The result of dot-blot suggested there were 222 positive clones in gametophyte library and 236 positive clones in sporophyte library. 383 positive clones of strongest signals had been sequenced, and 191 EST sequences of gametophyte and 192 of sporophyte were obtained. A total of 196 genes were obtained, within which 104 genes were identified from the gametophyte and 92 from the sporophyte. Thirty-nine genes of the gametophyte and 62 genes of the sporophyte showed sequence similarity to those genes with known or putative functions which were classified according to their putative biological roles and molecular functions. The GO annotation showed about 58% of the cellular component of sporophyte and gametophyte cells were mainly located in cytoplasm and nucleus. The special genes were located in Golgi apparatus, and high expression in plastid, ribosome and endoplasmic reticulum. The main biological functions of gametophyte cells contributed to DNA repair/replication, carbohydrate metabolism, transport and transcription, especially in response to heat and oxidative stress. The sporophyte cell expresses more genes in transcription, transport, carbohydrate metabolism, particularly in signal transduction, DNA and protein modification, protein and nucleotide metabolism. Four genes are expressed on both gametophyte and sporophyte cells and eighteen genes have not been annotated. CONCLUSION: According to the information of GO annotation, the gametophyte tends to growth and self- protection while the sporophyte tends to be more active in development. Interpretation of the differentially expressed genes revealed new insights into the molecular processes of the generation alternation of Porphyra yezoensis. Further investigation are needed due to insufficiency of functional genes research and indeterminancy of the functions of many sequences.