Published October 10, 2018
| Version v1
Journal article
Restricted
The polyphasic approach revealed new species of Chloroidium (Trebouxiophyceae, Chlorophyta)
Authors/Creators
- 1. University of Göttingen, Experimental Phycology and Culture Collection of Algae, D-37073 Göttingen, Germany & M.G. Kholodny Institute of Botany, National Academy Science of Ukraine, Kyiv 01601, Ukraine
- 2. Biology Centre, Czech Academy of Sciences, Institute of Soil Biology, 37005 České Budějovice, Czech Republic
- 3. University of Innsbruck, Research Institute for Limnology, A-5310 Mondsee, Austria
Description
Darienko, Tatyana, Lukešová, Alena, Pröschold, Thomas (2018): The polyphasic approach revealed new species of Chloroidium (Trebouxiophyceae, Chlorophyta). Phytotaxa 372 (1): 51-66, DOI: 10.11646/phytotaxa.372.1.4, URL: http://dx.doi.org/10.11646/phytotaxa.372.1.4
Files
Restricted
The record is publicly accessible, but files are restricted. <a href="https://zenodo.org/account/settings/login?next=https://zenodo.org/records/13728682">Log in</a> to check if you have access.
Linked records
Additional details
Identifiers
- LSID
- urn:lsid:plazi.org:pub:CC670913FFABEA39D1159D0F164EFF8C
- URL
- http://publication.plazi.org/id/CC670913FFABEA39D1159D0F164EFF8C
References
- Aboal, M. & Werner, O. (2011) Morphology, fine structure, life cycle and phylogenetic analysis of Phyllosiphon arisari, a siphonous parasitic green alga. European Journal of Phycology 46: 181-192. https://doi.org/10.1080/09670262.2011.590902
- Akaike, H. (1974) A new look at the statistical model identification. IEEE Transactions on Automatic Control 19: 716-723. https://doi.org/10.1109/TAC.1974.1100705
- Albertano, P., Pollio, A. & Taddei, R. (1991) Viridiella fridericiana (Chlorococcales, Chlorophyta), a new genus and species isolated from extremely acid environments. Phycologia 30: 346-354. https://doi.org/10.2216/i0031-8884-30-4-346.1
- Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) Basic local alignment search tool. Journal of Molecular Biology 215: 403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
- Andreyva, V.M. (1975) Rod Chlorella. Morphologiya, sistematika, princypy klassifikatsii [The genus Chlorella. Morphology, systematics, principal classification]. Nauka, Leningrad, 86 pp. [in Russian]
- Chodat, R. (1913) Monographies d'Algues en culture pure. Materiaux pour la Flore cryptogamique Suisse 4: 1-266.
- Clement, M., Posada, D. & Crandall, K.A. (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology 9: 1657- 1659. https://doi.org/10.1046/j.1365-294x.2000.01020.x
- Clement, M., Snell, Q., Walker, P., Posada, D. & Crandall, K. (2002) TCS: Estimating gene genealogies. Parallel and Distributed Processing Symposium, International Proceedings 2: 184. https://doi.org/10.1021/ja012036c
- Coleman, A.W. (2000) The significance of a coincidence between evolutionary landmarks found in mating affinity and a DNA sequence. Protist 151: 1-9. https://doi.org/10.1078/1434-4610-00002
- Coleman, A.W. (2003) ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends in Genetics 19: 370-375. https://doi.org/10.1016/S0168-9525(03)00118-5
- Cote, C.A., Greer, C.L. & Peculis, B.A. (2002) Dynamic conformational model for the role of ITS2 in pre-rRNA processing in yeast. RNA 8: 786-797. https://doi.org/10.1017/S1355838202023063
- Darienko, T., Gustavs, L., Mudimu, O., Rad Menendez, C., Schumann, R., Karsten, U., Friedl, T. & Proschold, T. (2010) Chloroidium, a common terrestrial coccoid green alga previously assigned to Chlorella (Trebouxiophyceae, Chlorophyta). European Journal of Phycology 45: 79-95. https://doi.org/10.1080/09670260903362820
- Darienko, T., Gustavs, L., Eggert, A., Wolf, W. & Proschold, T. (2015a) Evaluating the species boundaries of green microalgae (Coccomyxa, Trebouxiophyceae, Chlorophyta) using integrative taxonomy and DNA barcoding with further implications for the species identification in environmental samples. PLOS One 10: e0127838. https://doi.org/10.1371/journal.pone.0127838
- Darienko, T. & Proschold, T. (2015b) Genetic variability and taxonomic revision of the genus Auxenochlorella (Shihira et Krauss) Kalina et Puncocharova (Trebouxiophyceae, Chlorophyta). Journal of Phycology 51: 394-400. https://doi.org/10.1111/jpy.12279
- Darienko, T., Gustavs, L. & Proschold, T. (2016) Species concept and nomenclatural changes within the genera Elliptochloris and Pseudochlorella (Trebouxiophyceae) based on an integrative approach. Journal of Phycology 52: 1125-1145. https://doi.org/10.1111/jpy.12481
- Demchenko, E., Mikhailyuk, T., Coleman, A.W. & Proschold, T. (2012) Generic and species concepts in Microglena (previously the Chlamydomonas monadina group) revised using an integrative approach. European Journal of Phycology 47: 264-290. https://doi.org/10.1080/09670262.2012.678388
- Do, C.B., Woods, D.A. & Batzoglou, S. (2006) CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics 22: e90-e98. https://doi.org/10.1093/bioinformatics/btl246
- Ettl, H. & Gartner, G. (1995) Syllabus der Boden-, Luft- und Flechtenalgen. Stuttgart, Jena and Heidelberg: Gustav Fischer, 721 pp.
- Ettl, H. & Gartner, G. (2014) Syllabus der Boden-, Luft- und Flechtenalgen. Berlin and Heidelberg: Springer, 773 pp. https://doi.org/10.1007/978-3-642-39462-1
- Fott, B. & Novakova, M. (1969) A monograph of the genus Chlorella. The fresh water species. In: Fott, B. (Ed.) Studies in Phycology. Academia, Prague, pp. 10-74.
- Fucikova, K., Lewis, P.O. & Lewis, L.A. (2014) Widespread desert affiliation of trebouxiophycean algae (Trebouxiophyceae, Chlorophyta) including discovering of three new desert genera. Phycological Research 62: 294-305. https://doi.org/10.1111/pre.12062
- Gibson, A., Gowri-Shankar, V., Higgs, P. & Rattray, M. (2005) A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods. Molecular Biology and Evolution 22: 251-264. https://doi.org/10.1093/molbev/msi012
- Hallmann, C., Hoppert, M., Mudimu, O. & Friedl, T. (2016) Biodiversity of green algae covering artificial hard substrate surfaces in a suburban environment: A case study using molecular approaches. Journal of Phycology 52: 732-744. https://doi.org/10.1111/jpy.12437
- Hanagata, N., Karube, I. & Chihara, M. (1997) Bark-inhabiting green algae in Japan (3) Chlorella trebouxioides and Ch. angustoellipsoidea, sp. nov, (Chlorelloidea, Chlorellaceae, Chlorococcales). Japanese Journal of Botany 72: 36-43.
- Hanagata, N., Karube, I., Chihara, M. & Silva, P.C. (1998) Reconsideration of the taxonomy of ellipsoid species of Chlorella (Trebouxiophyceae, Chlorophyta), with establishment of Watanabea gen. nov. Phycological Research 46: 221-229. https://doi.org/10.1111/j.1440-1835.1998.tb00117.x
- Higgs, P., Jameson, D., Jow, H. & Rattray, M. (2003) The evolution of tRNA-Leu genes in animal mitochondrial genomes. Journal of Molecular Evolution 57: 435-445. https://doi.org/10.1007/s00239-003-2494-6
- Hudelot, C., Gowri-Shankar, V., Jow, H., Rattray, M. & Higgs, P. (2003) RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences. Molecular Phylogenetics and Evolution 28: 241-252. https://doi.org/10.1016/S1055-7903(03)00061-7
- Huss, V.A.R., Frank, C., Hartmann, E.C., Hirmer, M., Kloboucek, A., Seidel, B.M., Wenzeler, P. & Kessler, E. (1999) Biochemical taxonomy and molecular phylogeny of the genus Chlorella sensu lato (Chlorophyta). Journal of Phycology 35: 587-598. https://doi.org/10.1046/j.1529-8817.1999.3530587.x
- Jow, H., Hudelot, C., Rattray, M. & Higgs, P. (2002) Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. Molecular Biology and Evolution 19: 1591-1601. https://doi.org/10.1093/oxfordjournals.molbev.a004221
- Krienitz, L. & Bock, C. (2012) Present state of the systematics of planktonic coccoid green algae of inland waters. Hydrobiologia 698: 295-326. https://doi.org/10.1007/s10750-012-1079-z
- Leigh, J.W. & Bryant, D. (2015) POPART: Full-feature software for haplotype network construction. Methods in Ecology and Evolution 6: 1110-1116. https://doi.org/10.1111/2041-210X.12410
- Ma, S., Huss, V.A.R, Tan, D., Sun, X., Chen, J., Xie, Y. & Zhang, J. (2013) A novel species in the genu Heveochlorella (Trebouxiophyceae, Chlorophyta) witnesses the evolution from an epiphytic into an endophytic lifestyle in tree-dwelling green algae. European Journal of Phycology 48: 200-209. https://doi.org/10.1080/09670262.2013.790996
- Marin, B., Palm, A., Klingberg, M. & Melkonian, M. (2003) Phylogeny and taxonomic revision of plastid-containing euglenophytes based on SSU rDNA sequence comparisons and synapomorphic signatures in the SSU rRNA secondary structure. Protist 154: 99-145. https://doi.org/10.1078/143446103764928521
- Neustupa, J., Nemcova, Y., Elias, M. & Skaloud, P. (2009) Kalinella bambusicola gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel coccoid Chlorella -like subaerial alga from Southeast Asia. Phycological Research 57: 159-169. https://doi.org/10.1111/j.1440-1835.2009.00534.x
- Neustupa, J., Nemcova, Y., Vesela, J., Steinova, J. & Skaloud, P. (2013a) Leptochlorella corticola gen. et sp. nov. and Kalinella apyrenoidosa sp. nov.: two novel Chlorella -like green microalgae (Trebouxiophyceae, Chlorophyta) from subaerial habitats. International Journal of Systematic and Evolutionary Microbiology 63: 377-387. https://doi.org/10.1099/ijs.0.047944-0
- Neustupa, J., Nemcova, Y., Vesela, J., Steinova, J. & Skaloud, P. (2013b) Parachloroidium gen. nov. (Trebouxiophyceae, Chlorophyta), a novel genus of coccoid green algae from subaerial corticolous biofilms. Phycologia 52: 411-421. https://doi.org/10.2216/13-142.2
- Nozaki, H., Ito, M., Sano, R., Uchida, H., Watanabe, M.M. & Kuroiwa, T. (1995) Phylogenetic relationship within the colonial Volvocales (Chlorophyta) inferred from rbc L gene sequence data. Journal of Phycology 31: 970-979. https://doi.org/10.1111/j.0022-3646.1995.00970.x
- Posada, D. (2008) ModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25: 1253-1256. https://doi.org/10.1093/molbev/msn083
- Prochazkova, K., Nemcova, Y., Kulichova, J. & Neustupa, J. (2015) Morphology and phylogeny of parasitic and free-living members of the genus Phyllosiphon (Trebouxiophyceae, Chlorophyta). Nova Hedwigia 101: 501-518. https://doi.org/10.1127/nova_hedwigia/2015/0288
- Prochazkova, K., Nemcova, Y. & Neustupa, J. (2016) Phyllosiphon ari sp. nov. (Watanabea clade, Trebouxiophyceae), a new parasitic species isolated from leaves of Arum italicum (Araceae). Phytotaxa 283: 143-154. https://doi.org/10.11646/phytotaxa.283.2.3
- Prochazkova, K., Nemcova, Y. & Neustupa, J. (2018) Phyllosiphon duini sp. nov. (Trebouxiophyceae, Chlorophyta), a species isolated from a corticolous phototrophic biofilm. Cryptogamie, Algologie 39: 23-34. https://doi.org/10.7872/crya/v39.iss1.2018.23
- Proschold, T., Darienko, T., Krienitz, L. & Coleman, A.W. (2018) Chlamydomonas schloesseri sp. nov. (Chlamydophyceae, Chlorophyta) revealed by morphology, autolysin cross experiments, and multiple gene analyses. Phytotaxa 362: 21-38. https://doi.org/10.11646/phytotaxa.362.1.2
- Ronquist, F., Teslenko, M., Van Der Mark, P., Ayres, D.L., Darling, A., Hohna, S., Larget, B., Liu, L., Suchard, M.A. & Huelsenbeck, J.P. (2012) MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539-542. https://doi.org/10.1093/sysbio/sys029
- Schlosser, U.G. (1997) Additions to the culture collections of algae since 1994. Botanica Acta 110: 424-429. https://doi.org/10.1111/j.1438-8677.1997.tb00659.x
- Song, H., Zhang, Q., Liu, G. & Hu, Z. (2015) Polulichloris henanensis gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccoid green alga. Phytotaxa 218: 137-146. https://doi.org/10.11646/phytotaxa.218.2.3
- Song, H., Hu, Y., Zhu, H., Wang, Q., Liu, G. & Hu, Z. (2016) Three novel species of coccoid green algae within the Watanabea clade (Trebouxiophyceae, Chlorophyta). International Journal of Systematic and Evolutionary Microbiology 66: 5465-5477. https://doi.org/10.1099/ijsem.0.001542
- Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690. https://doi.org/10.1093/bioinformatics/btl446
- Swofford, D.L. (2002) PAUP* Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4.0b10. Sunderland, MA, USA: Sinauer Associates.
- Telford, M.J., Wise, M.J. & Gowri-Shankar, V. (2005) Consideration of RNA secondary structure significantly improves likelihood-based estimates of phylogeny: examples from the bilateria. Molecular Biology and Evolution 22: 1129-1136. https://doi.org/10.1093/molbev/msi099
- Tschermak-Woess, E. (1988) New and known taxa of Chlorella (Chlorophyceae): occurrence as lichen photobionts and observations on living dictyosomes. Plant Systematics and Evolution 159: 123-139. https://doi.org/10.1007/BF00937430
- Xia, X. (2018) DAMBE7: New and improved tools for data analysis in molecular biology and evolution. Molecular Biology and Evolution 35: 1550-1552. https://doi.org/10.1093/molbev/msy073
- Xia, X., Xie, Z., Salemi, M., Chen, L. &Wang, Y. (2003) An index of substitution saturation and its application. Molecular Phylogenetics and Evolution 26: 1-7. https://doi.org/10.1016/S1055-7903(02)00326-3
- Xia, X. & Lemey, P. (2009) Assessing substitution saturation with DAMBE. In: Lemey, P., Salemi, M. & Vandamme, A.-M. (Eds.) The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny. 2nd edition. Cambridge University Press, pp. 615- 630. https://doi.org/10.1017/CBO9780511819049.022
- Yang, Z., Nielsen, R. & Hasegawa, M. (1998) Models of amino acid substitution and applications to mitochondrial protein evolution. Molecular Biology and Evolution 15: 1600-1611. https://doi.org/10.1093/oxfordjournals.molbev.a025888
- Zhang, J., Huss, V.A.R., Sun, X., Chang, K. & Pang, D. (2008) Morphology and phylogenetic position of a trebouxiophycean green alga (Chlorophyta) growing on the rubber tree, Hevea brasiliensis, with the description of a genus and species. European Journal of Phycology 43: 185-193. https://doi.org/10.1080/09670260701718462
- Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acid Research 31: 3406-3615. https://doi.org/10.1093/nar/gkg595