Strain Data

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Strain number		NIES-2285
Phylum		Streptophyta
Class		Klebsormidiophyceae
Scientific name		Klebsormidium nitens (Kützing) Lokhorst
Synonym		Ulothrix nitens Kützing; Hormidium nitens (Kützing) Rabenhorst 1863; Chlorhormidium flaccidum var. nitens (Kützing) Farooqui 1969; Chlorhormidium nitens (Meneghini) Komaromy 1976
Former name		Formerly identified as Klebsormidium flaccidum (Kützing) Silva, Mattox & Blackwell[2016 Jun]; Hormidium barlowi
Common name
Locality (Date of collection)		Barlow, Madison, Wisconsin, USA
Latitude / Longitude		43.073308 /
Habitat (Isolation source)		Freshwater
History		< IAM (2007) < BIU (UTEX; 1965);
Isolator (Date of isolation)		Pringsheim, E. G.
Identified by		Handa, Shinji (Reidentify)
State of strain		Subculture / Cryopreservation; Unialgal; Clonal; Axenic[2023 Jun]
Culture condition (Preculture condition)		Medium: C (agar) Temperature: 20 C Light intensity: 5-11 µmol photons/m²/sec, L/D cycle: 10L:14D Duration: 6 M
Gene information		Whole-genome ( BANV00000000 ) , Mitochondria genome ( DF238763 ) , Plastid genome ( DF238762 )
Cell size (min - max)		5 - 10 μm
Organization
Characteristics		Genome decoded strain (Hori et al. 2014)
Other strain no.		Other collection strain no. : IAM C-117; UTEX 321; SAG 335-1a; CCAP 335/1a
Remarks		Axenic
Movie

Related strain information (Large number of orders and same genus or species)
Strain number	Scientific name	Common name	Habitat (Isolation source)	Characteristics
NIES-2408	Klebsormidium flaccidum		Terrestrial (Soil)	Cryophilic ; Resting spore-forming
NIES-329	Klebsormidium sp.		Freshwater (Lake water)
NIES-2286	Klebsormidium nitens

Related strain information (Used in same reference)
Strain number	Scientific name	Common name	Habitat (Isolation source)	Characteristics
NIES-1604	Chara braunii	Stonewort	Freshwater	Monoecious
NIES-296	Mesostigma viride		Freshwater (Lake water)	Genome decoded strain (Lemieux, C. et al. 2000, Turmel, M. et al. 2002b, Liang et al. 2020)
NIES-144	Haematococcus lacustris	Green alga	Freshwater (Lake water)	Astaxanthin production ; Genome decoded strain (Morimoto et al. 2017) ; Homothallic ; Isogamous
NIES-2860	Vacuoliviride crystalliferum		Freshwater (Paste)	Benthic ; Authentic strain (Nakayama et al. 2015)
NIES-68	Closterium peracerosum-strigosum-littorale complex	Desmid	Freshwater (Pool soil)	Heterothallic: Mating type (−) ; Mating group I B ; Genome decoded strain (Sekimoto et al. 2023)

Reference
Fawley, M. W. 1991 Disjunct distribution of the xanthophyll loroxanthin in the green algae (Chlorophyta). J. Phycol., 27, 544-548. Keywords: carotenoids; Chlorophyta; high-performance liquid chromatography; loroxanthin; xanthophylls Strain(s): 2285 DOI: 10.1111/j.0022-3646.1991.00544.x Hori, K. Maruyama, F., Fujisawa, T., Togashi, T., Yamamoto, N., Seo, M., Sato, S., Yamada, T., Mori, H., Tajima, N., Moriyama, T., Ikeuchi, M., Watanabe, M., Wada, H., Kobayashi, K., Saito, M., Masuda, T., Sasaki-Sekimoto, Y., Mashiguchi, K., Awai, K., Shimojima, M., Masuda, S., Iwai, M., Nobusawa, T., Narise, T., Kondo, S., Saito, H., Sato, R., Murakawa, M., Ihara, Y., Oshima-Yamada, Y., Ohtaka, K., Satoh, M., Sonobe, K., Ishii, M., Ohtani, R., Kanamori-Sato, M., Honoki, R., Miyazaki, D., Mochizuki, H., Umetsu, J., Higashi, K., Shibata, D., Kamiya, Y., Sato, N., Nakamura, Y., Tabata, S., Ida, S., Kurokawa, K., Ohta, H. 2014 Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation. Nat. Commun., 5, 3978 (article ID). Strain(s): 2285 PubMed: 24865297 DOI: 10.1038/ncomms4978 Koeduka, T., Ishizaki, K., Mwenda, C. M., Hori, K., Sasaki-Sekimoto, Y., Ohta, H., Kohchi, T., Matsui, K. 2015 Biochemical characterization of allene oxide synthases from the liverwort Marchantia polymorpha and green microalgae Klebsormidium flaccidum provides insight into the evolutionary divergence of the plant CYP74 family. Planta, 242, 1175-1186. Keywords: Allene oxide synthase; Plant evolution; CYP74; Hydroperoxide lyase; C8 volatiles Strain(s): 2285 PubMed: 26105654 DOI: 10.1007/s00425-015-2355-8 Kobayashi, Y., Takusagawa, M., Harada, N., Fukao, Y., Yamaoka, S., Kohchi, T., Hori, K., Ohta, H., Shikanai, T., Nishimura, Y. 2016 Eukaryotic components remodeled chloroplast nucleoid organization during the green plant evolution. Genome Biol. Evol., 8, 1-16. Keywords: chloroplast; nucleoid; evolution; endosymbiosis Strain(s): 2285 PubMed: 26608058 DOI: 10.1093/gbe/evv233 Ohtaka,K., Hori, K., Kanno, Y., Seo, M., Ohta, H. 2017 Primitive Auxin Response without TIR1 and Aux/IAA in the Charophyte Alga Klebsormidium nitens. Plant Physiol., 174, 1621-1632. Strain(s): 2285 PubMed: 28533212 DOI: 10.1104/pp.17.00274 de Mendoza, A., Bonnet, A., Vargas-Landin, D. B., Ji, N., Li, H., Yang, F., Li, L., Hori, K., Pflueger, J., Buckberry, S., Ohta, H., Rosic, N., Lesage, P., Lin, S., Lister, R. 2018 Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons. Nat. Commun., 9, 1341 (article ID). Keywords: DNA methylation; Epigenomics; Molecular evolution; Transposition Strain(s): 2285 PubMed: 29632298 DOI: 10.1038/s41467-018-03724-9 Yokono, M., Takabayashi, A., Kishimoto, J., Fujita, T., Iwai, M., Murakami, A., Akimoto, S., Tanaka, A. 2019 The PSI-PSII megacomplex in green plants. Plant Cell Physiol., 60, 1098–1108. Keywords: Energy transfer; Nonphotochemical quenching; Photosystem Strain(s): 144, 296, 303, 2285, 2541 PubMed: 30753722 DOI: 10.1093/pcp/pcz026 Mojzeš, P., Gao, L., Ismagulova, T., Pilátová, J., Moudříková, Š., Gorelova, O., Solovchenko, A., Nedbal, L., Salih, A. 2020 Guanine, a high-capacity and rapid-turnover nitrogen reserve in microalgal cells. Proc. Natl. Acad. Sci. U. S. A., 117, 32722-32730. Strain(s): 2285, 2587, 2860 PubMed: 33293415 DOI: 10.1073/pnas.2005460117 Rosas-Santiago, P., Zechinelli Pérez, K., Gómez Méndez, M. F., Vera López Portillo, F., Ruiz Salas, J. L., Cordoba Martínez, E., Acosta Maspon, A., Pantoja, O. 2021 A differential subcellular localization of two copper transporters from the COPT family suggests distinct roles in copper homeostasis in Physcomitrium patens. Plant Physiol. Biochem., 167, 459-469. Keywords: Copper transport; Copper uptake; COPT; Physcomitrium patens Strain(s): 2285 PubMed: 34418592 DOI: 10.1016/j.plaphy.2021.08.023 Takano, H., Tsunefuka, T., Takio, S., Ishikawa, H., Takechi, K. 2018 Visualization of plastid peptidoglycan in the charophyte alga Klebsormidium nitens using a metabolic labeling method. Cytologia, 83, 375-380. Keywords: charophyte; Evolution; Klebsormidium nitens; Plastid peptidoglycan; Streptophyte Strain(s): 2285 DOI: 10.1508/cytologia.83.375 Pilátová, J., Pánek, T., Oborník, M., Čepička, I., Mojzeš, P. 2022 Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes. ISME J., 16, 2290-2294. Strain(s): 67, 303, 995, 1604, 2146, 2285, 2860 PubMed: 35672454 DOI: 10.1038/s41396-022-01264-1 Chatelain, P., Blanchard, C., Astier, J., Klinguer,A., Wendehenne, D., Jeandroz, S., Rosnoblet, C. 2022 Reliable reference genes and abiotic stress marker genes in Klebsormidium nitens. Sci Rep, 12, 18988 (article ID). Strain(s): 2285 PubMed: 36348043 DOI: 10.1038/s41598-022-23783-9 Ferrari, C., Proost, S., Janowski, M., Becker, J., Nikoloski, Z., Bhattacharya, D., Price, D., Tohge, T., Bar-Even, A., Fernie, A., Stitt, M., Mutwil, M. 2019 Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida. Nat. Commun., 10, 737 (article ID). Strain(s): 2285 PubMed: 30760717 DOI: 10.1038/s41467-019-08703-2 Tansley, C., Houghton, J., Rose, A. M. E., Witek, B., Payet, R. D., Wu, T., Miller, J. B. 2023 CIPK-B is essential for salt stress signalling in Marchantia polymorpha. New Phytol., 237, 2210-2223. Keywords: calcineurin B-like protein; calcium signalling; CBL-interacting protein kinase; evolution; liverwort; Marchantia polymorpha; salt stres Strain(s): 2285 PubMed: 36660914 DOI: 10.1111/nph.18633 Kondo, S., Hori, K., Sasaki-Sekimoto, Y., Kobayashi, A., Kato, T., Yuno-Ohta, N., Nobusawa, T., Ohtaka, K., Shimojima, M., Ohta, H. 2016 Primitive extracellularlipid components on the surface of the charophytic alga Klebsormidium flaccidum and their possible biosynthetic pathways as deduced from the genome sequence. Front. Plant Sci., 7, 952 (article ID). Keywords: Klebsormidium flaccidum; Chlamydomonas reinhardtii; Arabidopsis thaliana; extracellular lipids; polyester backbone; wax; cuticle Strain(s): 2285 PubMed: 27446179 DOI: 10.3389/fpls.2016.00952 Nazipova, A., Makshakova, O., Kozlova, L. 2023 The in silico characterization of monocotyledonous α-L-Arabinofuranosidases on the example of maize. Life-Basel, 13, 266 (article ID). Keywords: α-L-arabinofuranosidase; arabinoxylan; maize; homology modeling; molecular docking Strain(s): 2285 PubMed: 36836625 DOI: 10.3390/life13020266 Tounosu, N., Sesoko, K., Hori, K., Shimojima, M., Ohta, H. 2023 Cis‑regulatory elements and transcription factors related to auxin signaling in the streptophyte algae Klebsormidium nitens. Sci Rep, 13, 9635 (article ID). Strain(s): 2285 PubMed: 37322074 DOI: 10.1038/s41598-023-36500-x Knosp, S., Kriegshauser, L., Tatsumi, K., Malherbe, L., Erhardt, M., Wiedemann, G., Bakan, B., Kohchi, T., Reski, R., Renault, H. 2024 An ancient role for CYP73 monooxygenases in phenylpropanoid biosynthesis and embryophyte development. Embo J., 43, 4092-4109. Keywords: Plant Evolution; Bryophytes; Cytochromes P450; Biopolymers; Cinnamic Acid 4-Hydroxylase Strain(s): 2285 PubMed: 39090438 DOI: 10.1038/s44318-024-00181-7 Dong, Y. T., Krishnamoorthi, S., Tan, G. Z. H., Poh, Z. Y., Urano, D. 2024 Co-option of plant gene regulatory network in nutrient responses during terrestrialization. Nat. Plants, 10, 1955–1968. Strain(s): 67, 68, 2285 PubMed: 39592744 DOI: 10.1038/s41477-024-01851-4

Reference

Fawley, M. W. 1991 Disjunct distribution of the xanthophyll loroxanthin in the green algae (Chlorophyta). J. Phycol., 27, 544-548.
Keywords: carotenoids; Chlorophyta; high-performance liquid chromatography; loroxanthin; xanthophylls
Strain(s): 2285
DOI: 10.1111/j.0022-3646.1991.00544.x

Hori, K. Maruyama, F., Fujisawa, T., Togashi, T., Yamamoto, N., Seo, M., Sato, S., Yamada, T., Mori, H., Tajima, N., Moriyama, T., Ikeuchi, M., Watanabe, M., Wada, H., Kobayashi, K., Saito, M., Masuda, T., Sasaki-Sekimoto, Y., Mashiguchi, K., Awai, K., Shimojima, M., Masuda, S., Iwai, M., Nobusawa, T., Narise, T., Kondo, S., Saito, H., Sato, R., Murakawa, M., Ihara, Y., Oshima-Yamada, Y., Ohtaka, K., Satoh, M., Sonobe, K., Ishii, M., Ohtani, R., Kanamori-Sato, M., Honoki, R., Miyazaki, D., Mochizuki, H., Umetsu, J., Higashi, K., Shibata, D., Kamiya, Y., Sato, N., Nakamura, Y., Tabata, S., Ida, S., Kurokawa, K., Ohta, H. 2014 Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation. Nat. Commun., 5, 3978 (article ID).
Strain(s): 2285
PubMed: 24865297
DOI: 10.1038/ncomms4978

Koeduka, T., Ishizaki, K., Mwenda, C. M., Hori, K., Sasaki-Sekimoto, Y., Ohta, H., Kohchi, T., Matsui, K. 2015 Biochemical characterization of allene oxide synthases from the liverwort Marchantia polymorpha and green microalgae Klebsormidium flaccidum provides insight into the evolutionary divergence of the plant CYP74 family. Planta, 242, 1175-1186.
Keywords: Allene oxide synthase; Plant evolution; CYP74; Hydroperoxide lyase; C8 volatiles
Strain(s): 2285
PubMed: 26105654
DOI: 10.1007/s00425-015-2355-8

Kobayashi, Y., Takusagawa, M., Harada, N., Fukao, Y., Yamaoka, S., Kohchi, T., Hori, K., Ohta, H., Shikanai, T., Nishimura, Y. 2016 Eukaryotic components remodeled chloroplast nucleoid organization during the green plant evolution. Genome Biol. Evol., 8, 1-16.
Keywords: chloroplast; nucleoid; evolution; endosymbiosis
Strain(s): 2285
PubMed: 26608058
DOI: 10.1093/gbe/evv233

Ohtaka,K., Hori, K., Kanno, Y., Seo, M., Ohta, H. 2017 Primitive Auxin Response without TIR1 and Aux/IAA in the Charophyte Alga Klebsormidium nitens. Plant Physiol., 174, 1621-1632.
Strain(s): 2285
PubMed: 28533212
DOI: 10.1104/pp.17.00274

de Mendoza, A., Bonnet, A., Vargas-Landin, D. B., Ji, N., Li, H., Yang, F., Li, L., Hori, K., Pflueger, J., Buckberry, S., Ohta, H., Rosic, N., Lesage, P., Lin, S., Lister, R. 2018 Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons. Nat. Commun., 9, 1341 (article ID).
Keywords: DNA methylation; Epigenomics; Molecular evolution; Transposition
Strain(s): 2285
PubMed: 29632298
DOI: 10.1038/s41467-018-03724-9

Yokono, M., Takabayashi, A., Kishimoto, J., Fujita, T., Iwai, M., Murakami, A., Akimoto, S., Tanaka, A. 2019 The PSI-PSII megacomplex in green plants. Plant Cell Physiol., 60, 1098–1108.
Keywords: Energy transfer; Nonphotochemical quenching; Photosystem
Strain(s): 144, 296, 303, 2285, 2541
PubMed: 30753722
DOI: 10.1093/pcp/pcz026

Mojzeš, P., Gao, L., Ismagulova, T., Pilátová, J., Moudříková, Š., Gorelova, O., Solovchenko, A., Nedbal, L., Salih, A. 2020 Guanine, a high-capacity and rapid-turnover nitrogen reserve in microalgal cells. Proc. Natl. Acad. Sci. U. S. A., 117, 32722-32730.
Strain(s): 2285, 2587, 2860
PubMed: 33293415
DOI: 10.1073/pnas.2005460117

Rosas-Santiago, P., Zechinelli Pérez, K., Gómez Méndez, M. F., Vera López Portillo, F., Ruiz Salas, J. L., Cordoba Martínez, E., Acosta Maspon, A., Pantoja, O. 2021 A differential subcellular localization of two copper transporters from the COPT family suggests distinct roles in copper homeostasis in Physcomitrium patens. Plant Physiol. Biochem., 167, 459-469.
Keywords: Copper transport; Copper uptake; COPT; Physcomitrium patens
Strain(s): 2285
PubMed: 34418592
DOI: 10.1016/j.plaphy.2021.08.023

Takano, H., Tsunefuka, T., Takio, S., Ishikawa, H., Takechi, K. 2018 Visualization of plastid peptidoglycan in the charophyte alga Klebsormidium nitens using a metabolic labeling method. Cytologia, 83, 375-380.
Keywords: charophyte; Evolution; Klebsormidium nitens; Plastid peptidoglycan; Streptophyte
Strain(s): 2285
DOI: 10.1508/cytologia.83.375

Pilátová, J., Pánek, T., Oborník, M., Čepička, I., Mojzeš, P. 2022 Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes. ISME J., 16, 2290-2294.
Strain(s): 67, 303, 995, 1604, 2146, 2285, 2860
PubMed: 35672454
DOI: 10.1038/s41396-022-01264-1

Chatelain, P., Blanchard, C., Astier, J., Klinguer,A., Wendehenne, D., Jeandroz, S., Rosnoblet, C. 2022 Reliable reference genes and abiotic stress marker genes in Klebsormidium nitens. Sci Rep, 12, 18988 (article ID).
Strain(s): 2285
PubMed: 36348043
DOI: 10.1038/s41598-022-23783-9

Ferrari, C., Proost, S., Janowski, M., Becker, J., Nikoloski, Z., Bhattacharya, D., Price, D., Tohge, T., Bar-Even, A., Fernie, A., Stitt, M., Mutwil, M. 2019 Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida. Nat. Commun., 10, 737 (article ID).
Strain(s): 2285
PubMed: 30760717
DOI: 10.1038/s41467-019-08703-2

Tansley, C., Houghton, J., Rose, A. M. E., Witek, B., Payet, R. D., Wu, T., Miller, J. B. 2023 CIPK-B is essential for salt stress signalling in Marchantia polymorpha. New Phytol., 237, 2210-2223.
Keywords: calcineurin B-like protein; calcium signalling; CBL-interacting protein kinase; evolution; liverwort; Marchantia polymorpha; salt stres
Strain(s): 2285
PubMed: 36660914
DOI: 10.1111/nph.18633

Kondo, S., Hori, K., Sasaki-Sekimoto, Y., Kobayashi, A., Kato, T., Yuno-Ohta, N., Nobusawa, T., Ohtaka, K., Shimojima, M., Ohta, H. 2016 Primitive extracellularlipid components on the surface of the charophytic alga Klebsormidium flaccidum and their possible biosynthetic pathways as deduced from the genome sequence. Front. Plant Sci., 7, 952 (article ID).
Keywords: Klebsormidium flaccidum; Chlamydomonas reinhardtii; Arabidopsis thaliana; extracellular lipids; polyester backbone; wax; cuticle
Strain(s): 2285
PubMed: 27446179
DOI: 10.3389/fpls.2016.00952

Nazipova, A., Makshakova, O., Kozlova, L. 2023 The in silico characterization of monocotyledonous α-L-Arabinofuranosidases on the example of maize. Life-Basel, 13, 266 (article ID).
Keywords: α-L-arabinofuranosidase; arabinoxylan; maize; homology modeling; molecular docking
Strain(s): 2285
PubMed: 36836625
DOI: 10.3390/life13020266

Tounosu, N., Sesoko, K., Hori, K., Shimojima, M., Ohta, H. 2023 Cis‑regulatory elements and transcription factors related to auxin signaling in the streptophyte algae Klebsormidium nitens. Sci Rep, 13, 9635 (article ID).
Strain(s): 2285
PubMed: 37322074
DOI: 10.1038/s41598-023-36500-x

Knosp, S., Kriegshauser, L., Tatsumi, K., Malherbe, L., Erhardt, M., Wiedemann, G., Bakan, B., Kohchi, T., Reski, R., Renault, H. 2024 An ancient role for CYP73 monooxygenases in phenylpropanoid biosynthesis and embryophyte development. Embo J., 43, 4092-4109.
Keywords: Plant Evolution; Bryophytes; Cytochromes P450; Biopolymers; Cinnamic Acid 4-Hydroxylase
Strain(s): 2285
PubMed: 39090438
DOI: 10.1038/s44318-024-00181-7

Dong, Y. T., Krishnamoorthi, S., Tan, G. Z. H., Poh, Z. Y., Urano, D. 2024 Co-option of plant gene regulatory network in nutrient responses during terrestrialization. Nat. Plants, 10, 1955–1968.
Strain(s): 67, 68, 2285
PubMed: 39592744
DOI: 10.1038/s41477-024-01851-4

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