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.

Diversity and evolution of cytochromes P450 in stramenopiles

“…Briefly, genome sequences of E. siliculosus V2016 v e r s i o n w e r e d o w n l o a d e d f r o m t h e w e b s i t e http://bioinformatics.psb.ugent.be/orcae/overview/Ectsi (Cormier et al 2016). Sequences of C. okamuranus were downloaded from http://marinegenomics.oist.jp/algae/ (Nishitsuji et al 2016). S e q u e n c e s o f S .…”

Convergent recruitment of life cycle regulators to direct sporophyte development in two eukaryotic supergroups

“…GenomeView was used together with publically available genome and RNA-seq sequence data (Nishitsuji et al, 2016;Ye et al, 2015) to improve the gene models for some of the brown algal TALE HD TFs (indicated in Table supplement 6 by adding the suffix "mod" for modified to the protein identifier).…”

Loss of a chloroplast encoded function could influence species range in kelp

“…Only a handful of brown algal nuclear genomes have so far been deciphered, namely Ectocarpus siliculosus (Cock et al, 2010), Saccharina japonica (Ye et al, 2015), and Cladosiphon okamuranus (Nishitsuji, Arimoto, & Iwai, 2016), S. japonica being the sole member of kelp species. Thus, it is currently not possible to comparatively examine complete nuclear genomes of kelp species for evolutionary changes and adaptations.…”