Seaweeds are essential for marine ecosystems and have immense economic value. Here we present a comprehensive analysis of the draft genome ofSaccharina japonica, one of the most economically important seaweeds. The 537-Mb assembled genomic sequence covered 98.5% of the estimated genome, and 18,733 protein-coding genes are predicted and annotated. Gene families related to cell wall synthesis, halogen concentration, development and defence systems were expanded. Functional diversification of the mannuronan C-5-epimerase and haloperoxidase gene families provides insight into the evolutionary adaptation of polysaccharide biosynthesis and iodine antioxidation. Additional sequencing of seven cultivars and nine wild individuals reveal that the genetic diversity within wild populations is greater than among cultivars. All of the cultivars are descendants of a wildS. japonicaaccession showing limited admixture withS. longissima. This study represents an important advance toward improving yields and economic traits inSaccharinaand provides an invaluable resource for plant genome studies.

Ulva prolifera green tides in the Yellow Sea of China in the past 3 yr are among the largest macroalgal blooms ever recorded. Satellite images, as well as wind and current patterns, provide a clear picture of the formation of these green tides; however, their place of origin remains unclear. Terrestrial investigation along the coastline of the Jiangsu Province and two shipboard surveys in the Yellow Sea in 2009 showed that filamentous Ulvaceae algae were prevalent in various environments in Jiangsu Province including floating rafts for Porphyra cultivation, land‐based bivalve culturing ponds, estuaries, embankments, intertidal stones, wharfs, and hard muddy coasts. Vegetative fragments in sediment samples were found in both shipboard surveys during the bloom and postbloom periods, and all of the samples were U. prolifera. Phylogenetic analysis of 5S spacer sequences showed that the green tide in the Yellow Sea was not of terrestrial origin. However, settled vegetative fragments of U. prolifera were an important seed source for the successive and more serious green tide blooms.

Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, and are under considerable threat from climate change. In this study, analysis of multiple genomes has provided insights across the entire evolutionary history of this lineage, from initial emergence, through later diversification of the brown algal orders, down to microevolutionary events at the genus level. Emergence of the brown algal lineage was associated with a marked gain of new orthologous gene families, enhanced protein domain rearrangement, increased horizontal gene transfer events, and the acquisition of novel signaling molecules and key metabolic pathways, the latter notably related to biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. We show that brown algal genome diversification is tightly linked to phenotypic divergence, including changes in life cycle strategy and zoid flagellar structure. The study also showed that integration of large viral genomes has had a significant impact on brown algal genome content throughout the emergence of the lineage.

MiRNAs are a class of non-coding, small RNAs that are approximately 22 nucleotides long and play important roles in the translational level regulation of gene expression by either directly binding or cleaving target mRNAs. The red alga, Porphyra yezoensis is one of the most important marine economic crops worldwide. To date, only a few miRNAs have been identified in green unicellar alga and there is no report about Porphyra miRNAs. To identify miRNAs in Porphyra yezoensis, a small RNA library was constructed. Solexa technology was used to perform high throughput sequencing of the library and subsequent bioinformatics analysis to identify novel miRNAs. Specifically, 180,557,942 reads produced 13,324 unique miRNAs representing 224 conserved miRNA families that have been identified in other plants species. In addition, seven novel putative miRNAs were predicted from a limited number of ESTs. The potential targets of these putative miRNAs were also predicted based on sequence homology search. This study provides a first large scale cloning and characterization of Porphyra miRNAs and their potential targets. These miRNAs belong to 224 conserved miRNA families and 7 miRNAs are novel in Porphyra. These miRNAs add to the growing database of new miRNA and lay the foundation for further understanding of miRNA function in the regulation of Porphyra yezoensis development.