title: 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.
authors.affiliation: National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan. yojnakam@affrc.go.jp
authors.forename: Yoji
authors.initials: Y
authors.lastname: Nakamura
authors.forename: Naobumi
authors.initials: N
authors.lastname: Sasaki
authors.forename: Masahiro
authors.initials: M
authors.lastname: Kobayashi
authors.forename: Nobuhiko
authors.initials: N
authors.lastname: Ojima
authors.forename: Motoshige
authors.initials: M
authors.lastname: Yasuike
authors.forename: Yuya
authors.initials: Y
authors.lastname: Shigenobu
authors.forename: Masataka
authors.initials: M
authors.lastname: Satomi
authors.forename: Yoshiya
authors.initials: Y
authors.lastname: Fukuma
authors.forename: Koji
authors.initials: K
authors.lastname: Shiwaku
authors.forename: Atsumi
authors.initials: A
authors.lastname: Tsujimoto
authors.forename: Takanori
authors.initials: T
authors.lastname: Kobayashi
authors.forename: Ichiro
authors.initials: I
authors.lastname: Nakayama
authors.forename: Fuminari
authors.initials: F
authors.lastname: Ito
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Nakajima
authors.forename: Motohiko
authors.initials: M
authors.lastname: Sano
authors.forename: Tokio
authors.initials: T
authors.lastname: Wada
authors.forename: Satoru
authors.initials: S
authors.lastname: Kuhara
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Inouye
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
authors.forename: Kazuho
authors.initials: K
authors.lastname: Ikeo
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D017343:Genes, Plant; D059646:Genome Size; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010788:Photosynthesis / Q000235:genetics; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid; D000461:Rhodophyta / Q000145:classification / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013559:Symbiosis; D016615:Telomere
references.citation: PLoS One. 2011 Jan 31;6(1):e16526
references.pmid: 21304975
references.citation: Nature. 2001 Apr 26;410(6832):1091-6
references.pmid: 11323671
references.citation: Bioinformatics. 2008 Mar 1;24(5):637-44
references.pmid: 18218656
references.citation: Nucleic Acids Res. 2008 Sep;36(16):e105
references.pmid: 18660515
references.citation: BMC Bioinformatics. 2005 Feb 15;6:31
references.pmid: 15713233
references.citation: Science. 2007 Oct 12;318(5848):245-50
references.pmid: 17932292
references.citation: Mol Biol Evol. 1987 Jul;4(4):406-25
references.pmid: 3447015
references.citation: BMC Res Notes. 2011 Oct 20;4:428
references.pmid: 22013916
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: DNA Res. 2000 Jun 30;7(3):223-7
references.pmid: 10907854
references.citation: Nat Methods. 2009 Apr;6(4):291-5
references.pmid: 19287394
references.citation: Plant Cell. 2010 Sep;22(9):2943-55
references.pmid: 20852019
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W585-7
references.pmid: 17517783
references.citation: Brief Bioinform. 2008 Jul;9(4):286-98
references.pmid: 18372315
references.citation: Int J Plant Genomics. 2008;2008:619832
references.pmid: 18483572
references.citation: Nature. 2004 Apr 8;428(6983):653-7
references.pmid: 15071595
references.citation: Protein Sci. 1999 May;8(5):978-84
references.pmid: 10338008
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W293-7
references.pmid: 16845012
references.citation: Bioinformatics. 2005 Jun;21 Suppl 1:i351-8
references.pmid: 15961478
references.citation: Mol Biol Evol. 2011 Oct;28(10):2921-33
references.pmid: 21551270
references.citation: Mol Biol Evol. 2004 May;21(5):809-18
references.pmid: 14963099
references.citation: Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):19908-13
references.pmid: 18077423
references.citation: Nucleic Acids Res. 1999 Jan 15;27(2):573-80
references.pmid: 9862982
references.citation: Mol Biol Evol. 2007 Jan;24(1):110-21
references.pmid: 17035354
references.citation: Biosci Biotechnol Biochem. 2009 Mar 23;73(3):740-3
references.pmid: 19270416
references.citation: BMC Biol. 2007 Jul 10;5:28
references.pmid: 17623057
references.citation: Genome Biol Evol. 2012;4(3):248-64
references.pmid: 22247428
references.citation: Genome Res. 2002 Apr;12(4):656-64
references.pmid: 11932250
references.citation: Genome Biol Evol. 2011;3:44-54
references.pmid: 21147880
references.citation: EMBO J. 1994 Mar 1;13(5):1039-47
references.pmid: 8131738
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: BMC Bioinformatics. 2006 Oct 25;7:474
references.pmid: 17064419
references.citation: Int J Syst Evol Microbiol. 2004 May;54(Pt 3):693-697
references.pmid: 15143010
references.citation: Nature. 2010 Jun 3;465(7298):617-21
references.pmid: 20520714
references.citation: Bioinformatics. 2006 Feb 1;22(3):361-2
references.pmid: 16332714
references.citation: Nature. 2005 Nov 3;438(7064):90-3
references.pmid: 16267554