The First Symbiont-Free Genome Sequence of Marine Red Alga, Susabi-nori (Pyropia yezoensis)

Abstract

Nori, a marine red alga, is one of the most profitable mariculture crops in the world. However, the biological properties of this macroalga are poorly understood at the molecular level. In this study, we determined the draft genome sequence of susabi-nori (Pyropia yezoensis) using next-generation sequencing platforms. For sequencing, thalli of P. yezoensis were washed to remove bacteria attached on the cell surface and enzymatically prepared as purified protoplasts. The assembled contig size of the P. yezoensis nuclear genome was approximately 43 megabases (Mb), which is an order of magnitude smaller than the previously estimated genome size. A total of 10,327 gene models were predicted and about 60% of the genes validated lack introns and the other genes have shorter introns compared to large-genome algae, which is consistent with the compact size of the P. yezoensis genome. A sequence homology search showed that 3,611 genes (35%) are functionally unknown and only 2,069 gene groups are in common with those of the unicellular red alga, Cyanidioschyzon merolae. As color trait determinants of red algae, light-harvesting genes involved in the phycobilisome were predicted from the P. yezoensis nuclear genome. In particular, we found a second homolog of phycobilisome-degradation gene, which is usually chloroplast-encoded, possibly providing a novel target for color fading of susabi-nori in aquaculture. These findings shed light on unexplained features of macroalgal genes and genomes, and suggest that the genome of P. yezoensis is a promising model genome of marine red algae.

Seaweed reproductive biology: environmental and genetic controls

“…A similar approach, applied to seaweeds and drawing on the extensive existing ecophysiological data, has the potential to significantly increase our knowledge of seaweed reproduction. At present, considerable progress is being made by establishing a number of model organisms for which whole genome data are already available or are in the process of being generated, including Ectocarpus , Pyropia (Nakamura et al 2013), Chondrus (Collén et al 2013), Saccharina (Ye et al 2015) and Ulva (see Wichard et al 2015). These genomic resources, in combination with genetic maps and the possibility of creating developmental mutants for forward genetics (e.g.…”

“…Whole genome data of the economically important species Pyropia yezoensis (Nakamura et al 2013) and Chondrus crispus (Collén et al 2013) have provided a first glimpse into the gene repertoire involved in reproduction. Additional insights have been provided by transcriptomic analyses in a number of species, including Pyropia (Uji et al 2013) and Gracilariopsis (Kamiya et al 2011), which have identified sets of genes upregulated in different phases of the life cycle.…”

The iron content and ferritin contribution in fresh, dried, and toasted nori, Pyropia yezoensis

“…Recently, genome project of nori, P. yezoensis, has just been completed. [42][43][44] Hence, nori can be one of the candidates for a model in exploring a mechanism for iron acquisition and storage in macroalgae in addition to its economical and nutritional significance.…”

The Glaucophyta: the blue-green plants in a nutshell

“…org/index) [81], and genomic information from several red algae has been recently published [82][83][84][85]. However, only the Cyanophora paradoxa nuclear genome (ca.…”