Y. Nakamura, N. Sasaki, M. Kobayashi, N. Ojima, M. Yasuike, Y. Shigenobu, M. Satomi, Y. Fukuma, K. Shiwaku, A. Tsujimoto, T. Kobayashi, I. Nakayama, F. Itoh, K. Nakajima, M. Sano, T. Wada, S. Kuhara, K. Inouye, T. Gojobori, K. Ikeo
PLOS ONE, 8(3), e57122, 1-11, (2013)
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.