Comparative transcriptome analysis between floating and attached Ulva prolifera in studying green tides in the Yellow Sea

Ulva prolifera is the main alga resulting in "green tides", which have occurred continually every summer in the Yellow Sea (YS) since 2007. The "green tide" disaster has caused negative impacts on both the economy and environment. The mainstream view is that the floating U. prolifera in the YS derives from attached U. prolifera of Pyropia aquaculture rafts on the Subei Shoal. In this study, we used the Illumina sequencing platform to compare the transcriptional profiles of floating U. prolifera and attached U. prolifera samples collected at the same time. A total of 278.1 million clean reads with 57.7 % GC content and 37,181 unigenes were generated from six libraries. A total of 21,475 genes were differentially expressed between the floating and attached U. prolifera samples. The expression profiles of 33 genes, which are related to the main metabolism in U. prolifera, were detected in the two samples of U. prolifera through FPKM and qRT-PCR analyses. The results showed that the expression levels of 26 of the 33 genes we studied in floating U. prolifera were higher than the levels in attached U. prolifera. This indicates that the main metabolic activities are more vigorous in floating U. prolifera than in attached U. prolifera. This finding furthers our understanding of metabolic mechanisms in U. prolifera with regard to the adaption to the marine environment and reveals the material basis of vigorous metabolic activity, which is related to U. prolifera blooms.