Abstract Background As a unique sulfated polysaccharide, fucoidan is the major component of cell wall in brown seaweeds. Its biochemical properties are determined by the positions and quantity of sulfate groups. The sulfation process is catalyzed by sulfotransferases (STs), which transfer the sulfuryl groups to carbohydrate backbones and are crucial for fucoidan biosynthesis. Nevertheless, the structures and functions of STs in brown seaweeds are not completely understood.Results There are a total of 27 ST genes identified from our genome and transcriptome analysis of Saccharina japonica and they were located in the 12 scaffolds and seven contigs. The S. japonica ST genes have many introns and alternative splicing sites, and four tandem duplicated gene clusters were identified among this genes family. Generally, the ST genes could be classified into five groups (Group I~V) based on phylogenetic analysis, and the ST proteins, which were encoded by genes within the same group, contained similar conserved motifs. In group I sequences, we found two highly conserved regions (region I: TxPKSGTxW; region IV: RKGxxGDWKxxFT), and Lys 81 and Arg 287 are critical for catalysis and substrate binding. Members of the S. japonica ST gene family show various expression patterns in different tissues and developmental stages. Transcripttional profiles indicate that more than half of ST genes transcriptional levels in kelp basal blades are higher than in distal blades, and decrease with the kelp development stages, while only ST 5 , 9 , 12 , 18 and 25 are increased. The co-down-regulated pathways are related to oxidative phosphorylation, fatty acid biosynthesis and metabolic pathways, while the up-regulated pathways are involved with ribosome, nitrogen and sulfur metabolism.Conclusion Various characteristics of the STs allow the feasibilities of S. japonica to adapt to the costal environments, meet the needs of S. japonica growth and support their giant blades. This also reflects the complexity of fucoidan biosynthesis in different marine environments, tissues, and developmental stages.
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