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Genome information

Genome information

1. Genome information

new Symbiodinium sp. NIES-4076 Whole-genome
Whole-genome (BGNK00000000)
Shoguchi, E., Beedessee, G., Tada, I., Hisata, K., Kawashima, T., Takeuchi, T., Arakaki, N., Fujie, M., Koyanagi, R., Roy, M. C., Kawachi, M., Hidaka, M., Satoh, N., Shinzato, C. 2018 Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes. BMC Genomics, 19, 458 (article ID).
new Symbiodinium sp. NIES-4077 Whole-genome
Whole-genome (BGPT00000000)
Shoguchi, E., Beedessee, G., Tada, I., Hisata, K., Kawashima, T., Takeuchi, T., Arakaki, N., Fujie, M., Koyanagi, R., Roy, M. C., Kawachi, M., Hidaka, M., Satoh, N., Shinzato, C. 2018 Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes. BMC Genomics, 19, 458 (article ID).
Yamagishiella unicocca NIES-3985 Whole-genome
Whole-genome (BDSJ00000000)
Hamaji, T., Kawai-Toyooka, H., Uchimura, H., Suzuki, M., Noguchi, H., Minakuchi, Y., Toyoda, A., Fujiyama, A., Miyagishima, S., Umen, J. G., Nozaki, H. 2018 Anisogamy evolved with a reduced sexdetermining region in volvocine green algae. Communications Biology, 17
Yamagishiella unicocca NIES-3983 Whole-genome
Whole-genome (BDSK00000000)

Hamaji, T., Kawai-Toyooka, H., Uchimura, H., Suzuki, M., Noguchi, H., Minakuchi, Y., Toyoda, A., Fujiyama, A., Miyagishima, S., Umen, J. G., Nozaki, H. 2018 Anisogamy evolved with a reduced sexdetermining region in volvocine green algae. Communications Biology, 17
Tetrabaena socialis NIES-571 Whole-genome
Chlamydomonas eustigma NIES-2499 Whole-genome
Anabaena variabilis NIES-23 Whole-genome
Anabaenopsis circularis NIES-21 Whole-genome
Aulosira laxa NIES-50 Whole-genome
Calothrix brevissima NIES-22 Whole-genome
Calothrix parasitica NIES-267 Whole-genome
Calothrix sp. NIES-2098 Whole-genome
Calothrix sp. NIES-2100 Whole-genome
Calothrix sp. NIES-4101 Whole-genome
Calothrix sp. NIES-4105 Whole-genome
Chondrocystis sp. NIES-4102 Whole-genome
Dolichospermum compactum NIES-806 Whole-genome
Fischerella sp. NIES-4106 Whole-genome
Fremyella diplosiphon NIES-3275 Whole-genome
Leptolyngbya boryana NIES-2135 Whole-genome
Nodularia sp. NIES-3585 Whole-genome
Nostoc carneum NIES-2107 Whole-genome
Nostoc linckia NIES-25 Whole-genome
Nostoc sp. NIES-4103 Whole-genome
Nostoc sp. NIES-2111 Whole-genome
Raphidiopsis curvata NIES-932 Whole-genomev
Sphaerospermopsis kisseleviana NIES-73 Whole-genome
Yamagishiella unicocca NIES-3982 Whole-genome
Whole-genome (BDSL00000000)
Hamaji, T., Kawai-Toyooka, H., Uchimura, H., Suzuki, M., Noguchi, H., Minakuchi, Y., Toyoda, A., Fujiyama, A., Miyagishima, S., Umen, J. G., Nozaki, H. 2018 Anisogamy evolved with a reduced sexdetermining region in volvocine green algae. Communications Biology, 17

Mitochondrial DNA (KY442293)
Hamaji, T., Kawai-Toyooka, H., Toyoda, A., Minakuchi, Y., Suzuki, M., Fujiyama, A., Nozaki, H., Smith, D. R. 2017 Multiple independent changes in mitochondrial genome conformation in chlamydomonadalean algae. Genome Biol. Evol., 9, 993-999.
Yamagishiella unicocca NIES-3984 Whole-genome
Whole-genome (BDSI00000000)
Hamaji, T., Kawai-Toyooka, H., Uchimura, H., Suzuki, M., Noguchi, H., Minakuchi, Y., Toyoda, A., Fujiyama, A., Miyagishima, S., Umen, J. G., Nozaki, H. 2018 Anisogamy evolved with a reduced sexdetermining region in volvocine green algae. Communications Biology, 17

Mitochondrial DNA (KY442294)
Hamaji, T., Kawai-Toyooka, H., Toyoda, A., Minakuchi, Y., Suzuki, M., Fujiyama, A., Nozaki, H., Smith, D. R. 2017 Multiple independent changes in mitochondrial genome conformation in chlamydomonadalean algae. Genome Biol. Evol., 9, 993-999.
Leptolyngbya sp. NIES-30 Whole-genome
Whole-genome (MRCG00000000)

Zhu, T., Hou, S., Lu, X., Hess, W. R. 2017 Draft genome sequences of nine cyanobacterial strains from diverse habitats. GenomeA, 5, e01676-16 (article ID).
Oscillatoria rosea NIES-208 Whole-genome
Whole-genome (MRBY00000000)

Zhu, T., Hou, S., Lu, X., Hess, W. R. 2017 Draft genome sequences of nine cyanobacterial strains from diverse habitats. GenomeA, 5, e01676-16 (article ID).
Fischerella major NIES-592 Whole-genome
Whole-genome (MRCA00000000)

Zhu, T., Hou, S., Lu, X., Hess, W. R. 2017 Draft genome sequences of nine cyanobacterial strains from diverse habitats. GenomeA, 5, e01676-16 (article ID).
Hydrococcus rivularis NIES-593 Whole-genome
Whole-genome (MRCB00000000)

Zhu, T., Hou, S., Lu, X., Hess, W. R. 2017 Draft genome sequences of nine cyanobacterial strains from diverse habitats. GenomeA, 5, e01676-16 (article ID).
Chroogloeocystis siderophila NIES-1031 Whole-genome
Whole-genome (MRCC00000000)

Zhu, T., Hou, S., Lu, X., Hess, W. R. 2017 Draft genome sequences of nine cyanobacterial strains from diverse habitats. GenomeA, 5, e01676-16 (article ID).
Calothrix sp. NIES-2101 Whole-genome
Whole-genome (MRCD00000000)

Zhu, T., Hou, S., Lu, X., Hess, W. R. 2017 Draft genome sequences of nine cyanobacterial strains from diverse habitats. GenomeA, 5, e01676-16 (article ID).
Phormidium ambiguum NIES-2119 Whole-genome
Whole-genome (MRCE00000000)

Zhu, T., Hou, S., Lu, X., Hess, W. R. 2017 Draft genome sequences of nine cyanobacterial strains from diverse habitats. GenomeA, 5, e01676-16 (article ID).
Scytonema sp. NIES-2130 Whole-genome
Whole-genome (MRCF00000000)

Zhu, T., Hou, S., Lu, X., Hess, W. R. 2017 Draft genome sequences of nine cyanobacterial strains from diverse habitats. GenomeA, 5, e01676-16 (article ID).
Synechococcus sp. NIES-970 Whole-genome
Chlamydomonas applanata NIES-2202 Whole-genome
Whole-genome (BDCZ00000000)

Hirashima, T., Tajima, N., Sato, N. 2016 Draft genome sequences of four species of Chlamydomonas containing phosphatidylcholine. GenomeA, 4, e01070-16 (article ID).
Chlamydomonas asymmetrica NIES-2207 Whole-genome
Whole-genome (BDDA00000000)

Hirashima, T., Tajima, N., Sato, N. 2016 Draft genome sequences of four species of Chlamydomonas containing phosphatidylcholine. GenomeA, 4, e01070-16 (article ID).
Chlamydomonas debaryana NIES-2212 Whole-genome
Whole-genome (BDDB00000000)

Hirashima, T., Tajima, N., Sato, N. 2016 Draft genome sequences of four species of Chlamydomonas containing phosphatidylcholine. GenomeA, 4, e01070-16 (article ID).
Chlamydomonas sphaeroides NIES-2242 Whole-genome
Whole-genome (BDDC00000000)

Hirashima, T., Tajima, N., Sato, N. 2016 Draft genome sequences of four species of Chlamydomonas containing phosphatidylcholine. GenomeA, 4, e01070-16 (article ID).
Microcystis aeruginosa NIES-98 Whole-genome
Cyanobium sp. NIES-981 Whole-genome
Whole-genome (LT578417)

Yamaguchi, H., Shimura, Y., Suzuki, S., Yamagishi, T., Tatarazako, N., Kawachi, M. 2016 Complete genome sequence of Cyanobium sp. NIES-981, a marine strain potentially useful for ecotoxicological bioassays. GenomeA, 4, e00736-16 (article ID).
Stanieria sp. NIES-3757 Whole-genome
Microcystis aeruginosa NIES-88 Whole-genome
Whole-genome (JXYX00000000)

Parajuli, A., Kwak, D. H., Dalponte, L., Leikoski, N., Galica, T., Umeobika, U., Trembleau, L., Bent, A., Sivonen, K., Wahlsten, M. 2016 A unique tryptophan c-prenyltransferase from the kawaguchipeptin biosynthetic pathway. Angew. Chem.-Int. Edit., 7, 3596-3599.
Fischerella sp. NIES-3754 Whole-genome
Whole-genome (AP017305)

Hirose, Y. et al. 2016. Complete genome sequence of cyanobacterium Fischerella sp. strain NIES-3754, providing thermoresistant optogenetic tools. J. Biotechnol., 220, 45-46.
Leptolyngbya sp. NIES-3755 Whole-genome
Whole-genome (AP017308)

Hirose, Y. et al. 2016. Complete genome sequence of cyanobacterium Fischerella sp. strain NIES-3754, providing thermoresistant optogenetic tools. J. Biotechnol., 220, 45-46.
Parachlorella kessleri NIES-2152 Whole-genome
Whole-genome (BBXU00000000)

Ota, S., Oshima, K., Yamazaki, T., Kim, S., Yu, Z., Yoshihara, M., Takeda, K., Takeshita, T., Hirata, A., Bišová, K., Zachleder, V., Hattori, M., Kawano, S. 2016 Highly efficient lipid production in the green alga Parachlorella kessleri: draft genome and transcriptome endorsed by whole-cell 3D ultrastructure. Biotechnol. Biofuels, 9, 13 (article ID).
Nostoc sp. NIES-3756 Whole-genome
Whole-genome (AP017295)

Hirose, Y., Fujisawa, T., Ohtsubo, Y., Katayama, M., Misawa, N., Wakazuki, S., Shimura, Y., Nakamura, Y., Kawachi, M., Yoshikawa, H., Eki, T., Kanesaki, Y. 2016 Complete genome sequence of cyanobacterium Nostoc sp. NIES-3756, a potentially useful strain for phytochrome-based bioengineering. J. Biotechnol., 218, 51-52.
Hafniomonas laevis NIES-257 Organella Genome
Plastid DNA (KT625415)

Lemieux, C., Vincent, A. T., Labarre, A., Otis, C., Turmel M. 2015 Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae). BMC Evol. Biol., 15, 264 (article ID).
Carteria cerasiformis NIES-425 Organella Genome
Plastid DNA (KT625415)

Lemieux, C., Vincent, A. T., Labarre, A., Otis, C., Turmel M. 2015 Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae). BMC Evol. Biol., 15, 264 (article ID).
Leptolyngbya sp. NIES-2104 Whole-genome
Whole-genome (BBWW00000000)

Shimura, Y., Hirose, Y., Misawa, N., Osana, Y., Katoh, H., Yamaguchi, H., Kawachi, M. 2015 Comparison of the terrestrial cyanobacterium Leptolyngbya sp. NIES-2104 and the freshwater Leptolyngbya boryana PCC 6306 genomes. DNA Res., 22, 403-412.
Diphylleia rotans NIES-3764 Organella Genome
Mitochondrial DNA (AP015014)

Kamikawa, R., Shiratori, T., Ishida, K-I., Miyashita, H., Roger, A. J. 2016 Group II intron-mediated trans-splicing in the green-rich mitochondrial genome of an enigmatic eukaryote, Diphylleia rotans. Genome Biol. Evol., 8, 458-466.
Microcystis aeruginosa NIES-2481 Whole-genome
Whole-genome (CP012375)

Yamaguchi, H., Suzuki, S., Osana, Y., Kawachi, M. 2018 Complete genome sequence of Microcystis aeruginosa NIES-2481 and common genomic features of group G M. aeruginosa. J. Genomics, 6, 30-33.
Microcystis aeruginosa NIES-2549 Whole-genome
Whole-genome (CP011304)

Yamaguchi, H., Suzuki, S., Tanabe, Y., Osana, Y., Shimura, Y., Ishida, K-I., Kawachi, M. 2015 Complete genome sequence of Microcystis aeruginosa NIES-2549, a bloom-forming cyanobacterium from lake Kasumigaura, Japan. GenomeA, 3, e00551-15 (article ID).
Aphanizomenon flos-aquae NIES-81 Whole-genome
Whole-genome (AZYY00000000)

Cao, H. et al. 2014. Draft genome sequence of the toxic bloom-forming cyanobacterium Aphanizomenon ﬂos-aquae NIES-81. GenomeA, 2, e00044-14.
Arthrospira platensis NIES-39 Whole-genome
NITE DOGAN
Whole-genome (AP011615)

Fujisawa, T. et al. 2010. Genomic structure of an economically important cyanobacterium, Arthrospira(Spirulina) platensis NIES-39. DNA Res., 17:85-103.
Geminocystis sp. NIES-3708 Whole-genome
Whole-genome (AP014815 - AP014820)

Hirose, Y. et al. 2015. Complete genome sequence of cyanobacterium Geminocystis sp. strain NIES-3708, which performs type II complementary chromatic acclimation. GenomeA, 3, e00357-15.
Geminocystis sp. NIES-3709 Whole-genome
Whole-genome (AP014821 - AP014832)

Hirose, Y. et al. 2015. Complete genome sequence of cyanobacterium Geminocystis sp. strain NIES-3709, which harbors a phycoerythrin-rich phycobilisome. GenomeA, 3, e00385-15.
Leptolyngbya sp. NIES-2104 Whole-genome
Whole-genome (BBWW00000000)

Shimura, Y., Hirose, Y., Misawa, N., Osana, Y., Katoh, H., Yamaguchi, H., Kawachi, M. 2015 Comparison of the terrestrial cyanobacterium Leptolyngbyasp. NIES-2104 and the freshwater Leptolyngbya boryana PCC 6306 genomes. DNA Res.
Microcystis aeruginosa NIES-44 Whole-genome
Whole-genome (BBPA00000000)

Okano, K., Miyata, N., Ozaki, Y. 2015. Whole genome sequence of the non-microcystin-producing Microcystis aeruginosastrain NIES-44. GenomeA, 3, e00135-15.
Microcystis aeruginosa NIES-298 Draft genome
Whole-genome (PRJNA91065)

Rhee, JS. et al. 2012. Draft genome database construction from four strains (NIES-298, FCY-26, -27, and -28) of the Cyanobacterium Microcystis aeruginosa. J. Microbiol. Biotechnol., 22, 1208-1213.
Microcystis aeruginosa NIES-843 Whole-genome
A typical bloom-forming unicellular cyanobacterium with gas vacuoles, which accumulates in the surface of lakes and reservoirs. Some strains produce hepatotoxins known as microcystins. Whole genome sequences were determined by the collaborative research group of Kazusa DNA Research Institute, University of Tsukuba and National Institute for Environmental Studies (NIES) in 2007.
The genome of M. aeruginosa is a single, circular chromosome of ca. 6 Mbp, comprising 6,325 protein-encoding genes. The microcystin synthase gene cluster (mcyA-J) was also found. Transposons amount to ca. 12% of the entire genome, whereas the number of genes for histidine kinases and response regulators is small.
CyanoBase
Thermosynechococcus elongatus NIES-2133 Whole-genome
T. elongatus is unicellular, non-nitrogen-fixing cyanobacterium isolated from a hot spring in Beppu, Japan. This alga is thermophilic and maximum growth is obtained at 57°C.
Whole genome sequences were determined in 2002 as the strain BP-1. The genome of T. elongatus is a single circular chromosome of ca. 2.6 Mbp, comprising 2,475 protein-encoding genes.
CyanoBase
Coccomyxa subellipsoidea NIES-2166 Whole-genome
Coccomyxa subellipsoidea C-169 Genome sequencing project
Chlamydomonas reinhardtii NIES-2235 EST information
This green, unicellular flagellate is famous as an experimental material for genetics and photosynthesis. This strain was transferred to the NIES-Collection from the IAM Collection, in which it was known as C-9, which has been widely used and deposited as a descendant of the original pair derived from a single zygospore isolated in Massachusetts in 1945, through Professors Sager and then Tsubo to the IAM Collection. Kazusa DNA Research Institute and Kyoto University have conducted EST analyses of the strain.
Chlamydomonas reinhardtii EST index
ChlamyBase
Chrysochromulina sp. NIES-1333 Organella Genome
Mitochondria DNA (AB930144)

Nishimura, Y., Kamikawa, R., Hashimoto, T., Inagaki, Y. 2014. An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyte Chrysochromulina sp. NIES-1333. Mobile Genetic Elements, 4, e29384 (article ID).
Cyanidioschyzon merolae NIES-3377 Whole-genome
C. merolae is a tiny unicellular red alga isolated from high temperature (45-50°C) and acidic (pH=1.0-3.0) environment, with simple organization containing each one organelle such as nucleus, mitochondrion, chloroplast, microbody and Golgi apparatus. Whole genome analyses (including nuclear, mitochondrioal and chloroplast genomes) were completed until 2004 as the strain 10D by the research team of Prof. Kuroiwa.
The genome size of C. merolae is ca. 16 Mbp. The genome includes 20 chromosomes and comprises 4,775 protein-encoding proteins. The genome lacks introns in almost all genes and contains only three copies of ribosomal DNA units.

Cyanidioschyzon merolae Genome Project
Heterosigma akashiwo NIES-293 Organella Genome
Plastid DNA (EU168190, NC_010772)

Cattolico, R. A., Jacobs, M. A., Zhou, Y., Chang, J., Duplessis, M., Lybrand, T., McKay, J., Ong, H. C., Sims, E., Rocap, G. 2008. Chloroplast genome sequencing analysis of Heterosigma akashiwo CCAM452 (West Atlantic) and NIES293 (West Pacific) strains. BMC Genomics, 9, 211-230.
Klebsormidium flaccidum NIES-2285 Whole-genome
Klebsormidium flaccidum genome project
Whole-genome (BANV00000000)
Mitochondria DNA (DF238763)
Plastid DNA (DF238762)

Hori, K. et al. 2014. Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation. Nat. Commun.
Gonium pectorale NIES-2863 Organella Genome
Mitochondoria DNA (AP012493, NC_020437)
Plastid DNA (AP012494, NC_020438)

Hamaji, T. et al. 2013. Mitochondrial and Plastid Genomes of the Colonial Green Alga, Gonium pectorale Give Insights into the Origins of Organelle DNA Architecture within the Volvocales. PLoS ONE, 8: e57177.
Mesostigma viride NIES-296 Organella Genome
Mitochondoria DNA (DQ365900)
Plastid DNA (DQ291132)
Nephroselmis olivacea NIES-484 Organella Genome
Mitochondoria DNA (AF110138)
Plastid DNA (AF137379)
Oltmansiellopsis viridis NIES-360 Organella Genome
Mitochondoria DNA (DQ365900)
Plastid DNA (DQ291132)
Pleodorina starrii NIES-1363 Organella Genome
Mitochondria DNA ( NC_021108, JX977845)
Plastid DNA (NC_021109, JX977846)

Smith, D. R., Hamaji, T., Olson, B. J., Durand, P. M., Ferris, P., Michod, R. E., Featherston, J., Nozaki, H., Keeling, P. J. 2013. Organelle genome complexity scales positively with organism size in volvocine green algae. Mol. Biol. Evol., 30, 793-797.
Porphyridium purpureum NIES-2140 Organella Genome
Plastid DNA (AP012987, NC_023133)

Tajima, N. et al. 2014. Analysis of the complete plastid genome of the unicellular red alga Porphyridium purpureum. J. Plant Res., 127:389-397.
Symbiodinium minutum NIES-3808 Whole-genome
Whole-genome (BASF00000000)

Shoguchi, E. et al. 2013. Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure. Curr. Biol., 23, 1399–1408.