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

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Nakamura, Yoji ^a   Sasaki, Naobumi ^b   Kobayashi, Masahiro ^c   Ojima, Nobuhiko ^a   Yasuike, Motoshige ^a   Shigenobu, Yuya ^a   Satomi, Masataka ^a   Fukuma, Yoshiya ^d   Shiwaku, Koji ^d   Tsujimoto, Atsumi ^e   Kobayashi, Takanori ^f   Nakayama, Ichiro ^g   Ito, Fuminari ^h   Nakajima, Kazuhiro ⁱ   Sano, Motohiko ^a   Wada, Tokio ^f   Kuhara, Satoru ^j   Inouye, Kiyoshi ^f   Gojobori, Takashi ^b   Ikeo, Kazuho ^b  

^a FISHERIES RESEARCH AGENCY   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c FISHERIES RESEARCH AGENCY   (Japan)

^d Hitachi Solutions   (Japan)

^e Japan Software Management Co Ltd   (Japan)

^f JAPAN FISHERIES RESEARCH AND EDUCATION AGENCY   (Japan)

^g NATIONAL VETERINARY ASSAY LABORATORY   (Japan)

^h FISHERIES RESEARCH AGENCY   (Japan)

ⁱ FISHERIES RESEARCH AGENCY   (Japan)

^j KYUSHU UNIVERSITY   (Japan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

AQUACULTURE; ARTICLE; COLOR; CONTROLLED STUDY; CYANIDIOSCHYZON MEROLAE; GENE SEQUENCE; GENETIC MODEL; GENOME SIZE; INTRON; MARINE SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYCOBILISOME; PROTOPLAST; PYROPIA YEZOENSIS; RED ALGA; SEQUENCE HOMOLOGY; SYMBIONT;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; GENES, PLANT; GENOME SIZE; GENOME, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; PHOTOSYNTHESIS; PHYLOGENY; REPETITIVE SEQUENCES, NUCLEIC ACID; RHODOPHYTA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SYMBIOSIS; TELOMERE;

EID: 84874821421     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0057122     Document Type: Article

References (52)

1. Mumford TF, Miura A (1988) Porphyra as food: cultivation and economics. In: Lembi CA, Waaland JR, editors. Algae and Human Affairs: Cambridge University Press. 87-117.
2. Colenso W (1880) On the vegetable food of the ancient New Zealanders before Cook's visit. Christchurch: Kiwi Publishers. 35 p.
3. Hoffmann A, Santelices B (1997) Marine Flora of Central Chile. Santiago de Chile: Univesidad Católica de Chile. 434 p.
4. Brodie J, Irvine LM (2003) Seaweeds of the British Isles: Vol. 1, Rodophyta, Part 3B, Bangiophycidae: The Natural History Museum (London). 167 p.
5. Williams MD, (1979) The harvesting of sluckus (Porphyra-Perforata) by the Straits Salish Indians of Vancouver Island, British-Columbia. Syesis 12: 63-69.
6. Turner NJ, (2003) The ethnobotany of edible seaweed (Porphyra abbottae and related species; Rhodophyta: Bangiales) and its use by First Nations on the Pacific Coast of Canada. Canadian Journal of Botany-Revue Canadienne De Botanique 81: 283-293.
7. Drew KM, (1949) Conchocelis-phase in the life-history of Porphyra-Umbilicalis (L) Kutz. Nature 164: 748-749.
8. Drew KM, (1954) Life-history of Porphyra. Nature 173: 1243-1244.
9. Croft M, Lawrence A, Raux-Deery E, Warren M, Smith A, (2005) Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature 438: 90-93.
10. Namba A, Shigenobu Y, Kobayashi M, Kobayashi T, Oohara I (2010) A new primer for 16S rDNA analysis of microbial communities associated with Porphyra yezoensis. Fisheries Science 76.
11. Matsuzaki M, Misumi O, Shin-I T, Maruyama S, Takahara M, et al. (2004) Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428: 653-657.
12. Nozaki H, Takano H, Misumi O, Terasawa K, Matsuzaki M, et al. (2007) A 100%-complete sequence reveals unusually simple genomic features in the hot-spring red alga Cyanidioschyzon merolae. BMC biology 5: 28.
13. Douglas S, Zauner S, Fraunholz M, Beaton M, Penny S, et al. (2001) The highly reduced genome of an enslaved algal nucleus. Nature 410: 1091-1096.
14. Lane CE, van den Heuvel K, Kozera C, Curtis BA, Parsons BJ, et al. (2007) Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function. Proc Natl Acad Sci U S A 104: 19908-19913.
15. Tanifuji G, Onodera N, Wheeler T, Dlutek M, Donaher N, et al. (2011) Complete nucleomorph genome sequence of the nonphotosynthetic alga Cryptomonas paramecium reveals a core nucleomorph gene set. Genome biology and evolution 3: 44-54.
16. Kapraun DF, Freshwater DW, (1987) Karyological studies of 5 species of Porphyra (Bangiales, Rhodophyta) from the North-Atlantic and Mediterranean. Phycologia 26: 82-87.
17. Kapraun DF, Hinson TK, Lemus AJ, (1991) Karyology and cytophotometric estimation of interspecific and intraspecific nuclear-DNA variation in 4 species of Porphyra (Rhodophyta). Phycologia 30: 458-466.
18. Matsuyama-Serisawa K, Yamamoto M, Fujishita M, Endo H, Serisawa Y, et al. (2007) DNA content of the cell nucleus in the macroalga Porphyra yezoensis (Rhodophyta). Fisheries Science 73.
19. Waaland JR, Stiller JW, Cheney DP, (2004) Macroalgal candidates for genomics. Journal of Phycology 40: 26-33.
20. Nikaido I, Asamizu E, Nakajima M, Nakamura Y, Saga N, et al. (2000) Generation of 10,154 expressed sequence tags from a leafy gametophyte of a marine red alga, Porphyra yezoensis. DNA Res 7: 223-227.
21. Asamizu E, Nakajima M, Kitade Y, Saga N, Nakamura Y, et al. (2003) Comparison of RNA expression profiles between the two generations of Porphyra yezoensis (Rhodophyta), based on expressed sequence tag frequency analysis. Journal of Phycology 39: 923-930.
22. Shen S, Zhang G, Li Y, Wang L, Xu P, et al. (2011) Comparison of RNA expression profiles on generations of Porphyra yezoensis (Rhodophyta), based on suppression subtractive hybridization (SSH). BMC Res Notes 4: 428.
23. Araki T, Hayakawa M, Tamaru Y, Yoshimatsu K, Morishita T, (1994) Isolation and regeneration of haploid protoplasts from Bangia-Atropurpurea (Rhodophyta) with marine bacterial enzymes. Journal of Phycology 30: 1040-1046.
24. Kurahashi M, Yokota A, (2004) Agarivorans albus gen. nov., sp. nov., a gamma-proteobacterium isolated from marine animals. Int J Syst Evol Microbiol 54: 693-697.
25. Benson G, (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27: 573-580.
26. Sobreira TJ, Durham AM, Gruber A, (2006) TRAP: automated classification, quantification and annotation of tandemly repeated sequences. Bioinformatics 22: 361-362.
27. Price AL, Jones NC, Pevzner PA, (2005) De novo identification of repeat families in large genomes. Bioinformatics 21Suppl 1: i351-358.
28. Flutre T, Duprat E, Feuillet C, Quesneville H, (2011) Considering transposable element diversification in de novo annotation approaches. PLoS One 6: e16526.
29. Kohany O, Gentles AJ, Hankus L, Jurka J, (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7: 474.
30. Slater GS, Birney E, (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6: 31.
31. Stanke M, Diekhans M, Baertsch R, Haussler D, (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24: 637-644.
32. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
33. Kent WJ, (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664.
34. Conesa A, Gotz S, (2008) Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 2008: 619832.
35. Ye J, Fang L, Zheng H, Zhang Y, Chen J, et al. (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34: W293-297.
36. Katoh K, Toh H, (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9: 286-298.
37. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
38. Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
39. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, et al. (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35: W585-587.
40. Emanuelsson O, Nielsen H, von Heijne G, (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci 8: 978-984.
41. Fulneckova J, Hasikova T, Fajkus J, Lukesova A, Elias M, et al. (2012) Dynamic evolution of telomeric sequences in the green algal order Chlamydomonadales. Genome Biol Evol 4: 248-264.
42. Blanc G, Duncan G, Agarkova I, Borodovsky M, Gurnon J, et al. (2010) The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex. Plant Cell 22: 2943-2955.
43. Merchant S, Prochnik S, Vallon O, Harris E, Karpowicz S, et al. (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science (New York, NY) 318: 245-250.
44. Cock JM, Sterck L, Rouze P, Scornet D, Allen AE, et al. (2010) The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature 465: 617-621.
45. Bhattacharya D, Medlin L, (1995) The phylogeny of plastids: a review based on comparisons of small-subunit ribosomal RNA coding regions. Journal of Phycology 31: 489-498.
46. Kawakami T, Sakaguchi K, Takechi K, Takano H, Takio S, (2009) Ammonium induced expression of the red algal chloroplast gene Ycf18, a putative homolog of the cyanobacterial NblA gene involved in nitrogen deficiency-induced phycobilisome degradation. Biosci Biotechnol Biochem 73: 740-743.
47. Dohm JC, Lottaz C, Borodina T, Himmelbauer H, (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 36: e105.
48. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, et al. (2009) Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods 6: 291-295.
49. Nakamura Y, Itoh T, Martin W, (2007) Rate and polarity of gene fusion and fission in Oryza sativa and Arabidopsis thaliana. Molecular biology and evolution 24: 110-121.
50. Yoon HS, Hackett JD, Ciniglia C, Pinto G, Bhattacharya D, (2004) A molecular timeline for the origin of photosynthetic eukaryotes. Mol Biol Evol 21: 809-818.
51. Helliwell KE, Wheeler GL, Leptos KC, Goldstein RE, Smith AG, (2011) Insights into the evolution of vitamin B12 auxotrophy from sequenced algal genomes. Mol Biol Evol 28: 2921-2933.
52. Collier JL, Grossman AR, (1994) A small polypeptide triggers complete degradation of light-harvesting phycobiliproteins in nutrient-deprived cyanobacteria. EMBO J 13: 1039-1047.