A draft genome of the brown alga, Cladosiphon okamuranus, S-strain: a platform for future studies of 'mozuku' biology

Abstract

The brown alga, Cladosiphon okamuranus (Okinawa mozuku), is economically one of the most important edible seaweeds, and is cultivated for market primarily in Okinawa, Japan. C. okamuranus constitutes a significant source of fucoidan, which has various physiological and biological activities. To facilitate studies of seaweed biology, we decoded the draft genome of C. okamuranus S-strain. The genome size of C. okamuranus was estimated as ∼140 Mbp, smaller than genomes of two other brown algae, Ectocarpus siliculosus and Saccharina japonica Sequencing with ∼100× coverage yielded an assembly of 541 scaffolds with N50 = 416 kbp. Together with transcriptomic data, we estimated that the C. okamuranus genome contains 13,640 protein-coding genes, approximately 94% of which have been confirmed with corresponding mRNAs. Comparisons with the E. siliculosus genome identified a set of C. okamuranus genes that encode enzymes involved in biosynthetic pathways for sulfated fucans and alginate biosynthesis. In addition, we identified C. okamuranus genes for enzymes involved in phlorotannin biosynthesis. The present decoding of the Cladosiphon okamuranus genome provides a platform for future studies of mozuku biology.

Keywords: Cladosiphon okamuranus; brown alga; genes for enzymes of polysaccharide synthesis; genome decoding.

Figure 1

A diagram showing the life cycle of the brown alga, Cladosiphon okamuranus. The alga has n and 2n generations. Cladosiphon okamuranus is cultivated and sporophytes are harvested for market. Genomic DNA was extracted from 2n germlings, while RNA was extracted from 2n germlings and 2n sporophytes.

Figure 2

Heat maps compared with gene expression levels of germlings and sporophytes of Cladsiphon okamuranus based on FPKM values. Gene IDs for the genome browser are indicated by sXXX_XXXXX. (A) Expression levels of transcription factors shown in Table 2. (B) Expression levels of receptor kinase genes shown in Supplementary Fig. S2. (C) Expression levels of C. okamuranus genes potentially contributing to biosynthetic pathways of sulfated fucans, alginates, and phlorotannin shown in Figs. 3- -5 and Supplementary Table S3.

Figure 3

Identification of all genes in the predicted biosynthetic pathway of sulfated fucans in the draft genome of Cladosiphon okamuranus. (A) A schematic representation of the biosynthetic pathway of sulphated fucans in brown algae, based on the description of Michel et al. Genes encoding each of the enzymes in the genomes of Cladosiphon okamuranus (C.ok) and Ectocarpus siliculosus (E.si), and the number of identified genes is shown in broken squares. (B) The location of candidate genes for l-fucosinase (FK) and GDP-fucose pyrophosphorylase (GFPP) in the C. okamuranus genome, suggesting the presence of an enzymatic gene cluster having shared synteny with E. siliculosus (http://bioinformatics.psb.ugent.be/orcae/overview/Ectsi). Two enzymatic genes that contain sulphotransferase and hydrolase domains are clustered with a gene (magenta) for a bifunctional enzyme with FK and GHMP-kinase domains. Genes coloured grey encode conserved proteins with RNA-binding domains.

Figure 4

Predicted genes related to the alginate biosynthetic pathway in brown algae and conservation of a key enzyme, GDP-mannose 6-dehydrogenase (GMD). (A) A schematic representation of the alginate biosynthetic pathway in brown algae. As in Fig. 3, identified gene numbers in broken squares are followed by species identifiers, C.ok and E.si. (B) A molecular phylogenetic analysis of GMD revealing the conservation of a key enzyme for the alginate biosynthesis pathway between Cladosiphon okamuranus and Ectocarpus siliculosus. The maximum-likelihood (ML) tree was constructed with a WAG + G model. Numbers at nodes indicate more than 70% bootstrap support. Brown stars indicate Cladosiphon GMD proteins that were presumably transferred horizontally from bacteria. UDP glucose 6-dehydrogenase (UGD) is potentially involved in fucoidan biosynthesis, rather than alginate biosynthesis.

Figure 5

A molecular phylogenetic tree of two proteins similar to type III PKS in the Cladosiphon okamuranus genome. The ML tree was constructed with a WAG + G + I model. Proteins are indicated by brown stars. Other protein sequences refer to Meslet-Cladiere et al..