Strain Data

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Strain number		NIES-2565
Phylum		Heterokontophyta
Class		Bolidophyceae
Scientific name		Triparma laevis B.C.Booth f. inornata S.Konno, R.Ohira, C.Komuro, N.Harada, & R.W.Jordan
Synonym
Former name
Common name
Locality (Date of collection)		Pacific Ocean (Oyashio region) (Depth -80m) Japan (2008-07-20)
Latitude / Longitude		42.0 / 145.25
Habitat (Isolation source)		Marine (Seawater)
History		< Ichinomiya, Mutsuo
Isolator (Date of isolation)		Ichinomiya, Mutsuo (2008-07-27)
Identified by		Ichinomiya, Mutsuo
State of strain		Subculture; Unialgal; Axenic[2021 Jun]
Culture condition (Preculture condition)		Medium: ESM Temperature: 5 C Light intensity: 45-55 µmol photons/m²/sec, L/D cycle: 10L:14D Duration: 1 M
Gene information		Whole-genome ( BLQM00000000 ) , 16S rRNA ( LN735526 ) , 18S rRNA ( AB546639 ) , ITS-1-5.8S-ITS2 ( KR998385 ) , rbcL ( AB546640 ) , nadH1 ( KR998404 )
Cell size (min - max)
Organization
Characteristics		Genome decoded strain (Kuwata et al. 2020;（ Ban et al. 2023) ; Siliceous, Non-flagellated stage[2018 May]
Other strain no.		Other strain no. : TOY-0807
Remarks		Axenic; Fragile species to transportation stresses; Fragile species to temperature changes; Read and agree "How to order 4.1"
Movie

Reference
Ban, H., Sato, S., Yoshikawa, S., Yamada, K., Nakamura, Y., Ichinomiya, M., Sato, N., Blanc-Mathieu, R., Endo, H., Kuwata, A., Ogata, H. 2023 Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs. Commun. Biol., 6, 697 (article ID). Strain(s): 2565, 3699, 3700, 3701 PubMed: 37420035 DOI: 10.1038/s42003-023-05002-x Kuwata, A., Saitoh, K., Nakamura, Y., Ishinomiya, M., Sato, N. 2020 Draft whole-genome sequence of Triparma laevis f. inornata (Parmales, Bolidophyceae), isolated from the Oyashio region, Western North Pacific Ocean. Microbiol. Resour. Ann.., 9, e00367-20 (article ID). Strain(s): 2565 PubMed: 32817146 DOI: 10.1128/MRA.00367-20 Yamada, K., Katsura, H., Noël, M.-H., Ichinomiya, M., Kuwata, A., Sato, S., Yoshikawa, S. 2019 Ontogenetic analysis of siliceous cell wall formation in Triparma laevis f. inornata (Parmales, Stramenopiles). J. Phycol., 55, 196-203. Keywords: annulus; diatom; pattern center; scale; sternum Strain(s): 2565 PubMed: 30320892 DOI: 10.1111/jpy.12800 Kuwata, A., Yamada, K., Ichinomiya, M., Yoshikawa, S., Tragin, M., Vaulot, D., Lopes dos Santos, A. 2018 Bolidophyceae, a sister picoplanktonic group of diatoms – a review. Front. Mar. Sci., 5, 370 (article ID). Keywords: bolidophyceae; parmales; diatoms; genetic diversity; mitosis; geographical distribution; seasonal dynamics and silicification Strain(s): 2565, 2682, 3369, 3370, 3371, 3699, 3700, 3701 DOI: 10.3389/fmars.2018.00370 Yamada, K., Nagasato, C., Motomura, T., Ichinomiya, M., Kuwata, A., Kamiya, M., Ohki, K., Yoshikawa, S. 2017 Mitotic spindle formation in Triparma laevis NIES-2565 (Parmales, Heterokontophyta). Protoplasma, 254, 461-471. Keywords: Central spindle; Centriole; Diatom; Extranuclear spindle; Mitosis; Nuclear envelope Strain(s): 2565 PubMed: 27048177 DOI: 10.1007/s00709-016-0967-x Ichinomiya, M., Lopes dos Santos, A., Gourvil, P., Yoshikawa, S., Kamiya, M., Ohki, K., Audic, S., De Vargas, C., Noël, M. H., Vaulot, D., Kuwata, A. 2016 Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms. ISME J., 10, 2419-2434. Strain(s): 2565, 2682, 3369, 3370, 3371, 3699, 3700, 3701 PubMed: 27003244 DOI: 10.1038/ismej.2016.38 Tajima, N., Saitoh, K., Sato, S., Maruyama, F., Ichinomiya, M.,Yoshikawa, S., Kurokawa, K., Ohta, H., Tabata, S., Kuwata, A., Sato, N. 2016 Sequencing and analysis of the complete organellar genomes of Parmales, a closely related group to Bacillariophyta (diatoms). Curr. Genet., 62, 887-896. Keywords: Genome sequencing; Heterokonta; Mitochondrial genome; Parmales; Plastid genome; Triparma laevis Strain(s): 2565 PubMed: 27091756 DOI: 10.1007/s00294-016-0598-y Yamada, K., Yoshikawa, S., Ohki, K., Ichinomiya, M., Kuwata, K., Motomura, T., Nagasato, C. 2016 Ultrastructural analysis of siliceous cell wall regeneration in the stramenopile Triparma laevis (Parmales, Bolidophyceae). Phycologia, 55, 602-609. Keywords: Cell wall regeneration; Chloroplast endoplasmic reticulum; Exocytosis; Silica biomineralization; Silica deposition vesicle Strain(s): 2565 DOI: 10.2216/16-32.1 Decelle, J., Romac, S., Stern, R. F., Bendif, E., Zingone, A., Audic, S., Guiry, M. D., Guillou, L., Tessier, D., Le Gall, F., Gourvil, P., Dos Santos, A. L., Probert, I., Vaulot, D., de Vargas, C., Christen, R. 2015 PhytoREF: a reference database of the plastidial 16S rRNAgene of photosynthetic eukaryotes with curated taxonomy. Mol. Ecol. Resour., 15, 1435-1445. Keywords: high-throughput sequencing; metabarcoding; photosynthesis; phytoplankton; plastidial 16S rRNA gene; protists Strain(s): 763, 764, 2565 PubMed: 25740460 DOI: 10.1111/1755-0998.12401 Yamada, K., Yoshikawa, S., Ichinomiya, M., Kuwata, A., Kamiya, M., Ohki, K. 2014 Effects of silicon-limitation on growth and morphology of Triparma laevis NIES-2565 (Parmales, Heterokontophyta). PLoS One, 9, e103289 (article ID). Strain(s): 2565 PubMed: 25054645 DOI: 10.1371/journal.pone.0103289 Ichinomiya, M., Nakamachi, M., Shimizu, Y., Kuwata, A. 2013 Growth characteristics and vertical distribution of Triparma laevis (Parmales) during summer in the Oyashio region, western North Pacific. Aquat. Microb. Ecol., 68, 107-116. Keywords: Triparma laevis; Parmales; Vertical distribution; Growth characteristics; Oyashio region Strain(s): 2565 DOI: 10.3354/ame01606 Ichinomiya, M., Yoshikawa, S., Kmiya, M., Ohki, K., Takaichi, S., Kuwata, A. 2011 Isolation and characterization of Parmales (Heterokonta/Heterokontophyta/Stramenopiles) from the Oyashio region, Western North Pacific. J. Phycol., 47, 144-151. Keywords: Bolidophyceae; diatoms; heterokonts; Parmales; PDMPO; phylogeny; stramenopiles; Triparma laevis Strain(s): 2565, 2682 PubMed: 27021720 DOI: 10.1111/j.1529-8817.2010.00926.x

Reference

Ban, H., Sato, S., Yoshikawa, S., Yamada, K., Nakamura, Y., Ichinomiya, M., Sato, N., Blanc-Mathieu, R., Endo, H., Kuwata, A., Ogata, H. 2023 Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs. Commun. Biol., 6, 697 (article ID).
Strain(s): 2565, 3699, 3700, 3701
PubMed: 37420035
DOI: 10.1038/s42003-023-05002-x

Kuwata, A., Saitoh, K., Nakamura, Y., Ishinomiya, M., Sato, N. 2020 Draft whole-genome sequence of Triparma laevis f. inornata (Parmales, Bolidophyceae), isolated from the Oyashio region, Western North Pacific Ocean. Microbiol. Resour. Ann.., 9, e00367-20 (article ID).
Strain(s): 2565
PubMed: 32817146
DOI: 10.1128/MRA.00367-20

Yamada, K., Katsura, H., Noël, M.-H., Ichinomiya, M., Kuwata, A., Sato, S., Yoshikawa, S. 2019 Ontogenetic analysis of siliceous cell wall formation in Triparma laevis f. inornata (Parmales, Stramenopiles). J. Phycol., 55, 196-203.
Keywords: annulus; diatom; pattern center; scale; sternum
Strain(s): 2565
PubMed: 30320892
DOI: 10.1111/jpy.12800

Kuwata, A., Yamada, K., Ichinomiya, M., Yoshikawa, S., Tragin, M., Vaulot, D., Lopes dos Santos, A. 2018 Bolidophyceae, a sister picoplanktonic group of diatoms – a review. Front. Mar. Sci., 5, 370 (article ID).
Keywords: bolidophyceae; parmales; diatoms; genetic diversity; mitosis; geographical distribution; seasonal dynamics and silicification
Strain(s): 2565, 2682, 3369, 3370, 3371, 3699, 3700, 3701
DOI: 10.3389/fmars.2018.00370

Yamada, K., Nagasato, C., Motomura, T., Ichinomiya, M., Kuwata, A., Kamiya, M., Ohki, K., Yoshikawa, S. 2017 Mitotic spindle formation in Triparma laevis NIES-2565 (Parmales, Heterokontophyta). Protoplasma, 254, 461-471.
Keywords: Central spindle; Centriole; Diatom; Extranuclear spindle; Mitosis; Nuclear envelope
Strain(s): 2565
PubMed: 27048177
DOI: 10.1007/s00709-016-0967-x

Ichinomiya, M., Lopes dos Santos, A., Gourvil, P., Yoshikawa, S., Kamiya, M., Ohki, K., Audic, S., De Vargas, C., Noël, M. H., Vaulot, D., Kuwata, A. 2016 Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms. ISME J., 10, 2419-2434.
Strain(s): 2565, 2682, 3369, 3370, 3371, 3699, 3700, 3701
PubMed: 27003244
DOI: 10.1038/ismej.2016.38

Tajima, N., Saitoh, K., Sato, S., Maruyama, F., Ichinomiya, M.,Yoshikawa, S., Kurokawa, K., Ohta, H., Tabata, S., Kuwata, A., Sato, N. 2016 Sequencing and analysis of the complete organellar genomes of Parmales, a closely related group to Bacillariophyta (diatoms). Curr. Genet., 62, 887-896.
Keywords: Genome sequencing; Heterokonta; Mitochondrial genome; Parmales; Plastid genome; Triparma laevis
Strain(s): 2565
PubMed: 27091756
DOI: 10.1007/s00294-016-0598-y

Yamada, K., Yoshikawa, S., Ohki, K., Ichinomiya, M., Kuwata, K., Motomura, T., Nagasato, C. 2016 Ultrastructural analysis of siliceous cell wall regeneration in the stramenopile Triparma laevis (Parmales, Bolidophyceae). Phycologia, 55, 602-609.
Keywords: Cell wall regeneration; Chloroplast endoplasmic reticulum; Exocytosis; Silica biomineralization; Silica deposition vesicle
Strain(s): 2565
DOI: 10.2216/16-32.1

Decelle, J., Romac, S., Stern, R. F., Bendif, E., Zingone, A., Audic, S., Guiry, M. D., Guillou, L., Tessier, D., Le Gall, F., Gourvil, P., Dos Santos, A. L., Probert, I., Vaulot, D., de Vargas, C., Christen, R. 2015 PhytoREF: a reference database of the plastidial 16S rRNAgene of photosynthetic eukaryotes with curated taxonomy. Mol. Ecol. Resour., 15, 1435-1445.
Keywords: high-throughput sequencing; metabarcoding; photosynthesis; phytoplankton; plastidial 16S rRNA gene; protists
Strain(s): 763, 764, 2565
PubMed: 25740460
DOI: 10.1111/1755-0998.12401

Yamada, K., Yoshikawa, S., Ichinomiya, M., Kuwata, A., Kamiya, M., Ohki, K. 2014 Effects of silicon-limitation on growth and morphology of Triparma laevis NIES-2565 (Parmales, Heterokontophyta). PLoS One, 9, e103289 (article ID).
Strain(s): 2565
PubMed: 25054645
DOI: 10.1371/journal.pone.0103289

Ichinomiya, M., Nakamachi, M., Shimizu, Y., Kuwata, A. 2013 Growth characteristics and vertical distribution of Triparma laevis (Parmales) during summer in the Oyashio region, western North Pacific. Aquat. Microb. Ecol., 68, 107-116.
Keywords: Triparma laevis; Parmales; Vertical distribution; Growth characteristics; Oyashio region
Strain(s): 2565
DOI: 10.3354/ame01606

Ichinomiya, M., Yoshikawa, S., Kmiya, M., Ohki, K., Takaichi, S., Kuwata, A. 2011 Isolation and characterization of Parmales (Heterokonta/Heterokontophyta/Stramenopiles) from the Oyashio region, Western North Pacific. J. Phycol., 47, 144-151.
Keywords: Bolidophyceae; diatoms; heterokonts; Parmales; PDMPO; phylogeny; stramenopiles; Triparma laevis
Strain(s): 2565, 2682
PubMed: 27021720
DOI: 10.1111/j.1529-8817.2010.00926.x

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