The phylogeny of the genus Nannochloropsis (Monodopsidaceae, Eustigmatophyceae), with descriptions of N. australis sp. nov. and Microchloropsis gen. nov.

REFERENCES

• Andersen R.A., Brett R.W., Potter D. & Sexton J.P. 1998. Phylogeny of the Eustigmatophyceae based upon the 18S rRNA gene, with emphasis on Nannochloropsis. Protist 149: 61–74.
   PubMed Web of Science ®Google Scholar
• Apt K.E. & Behrens P.W. 1999. Commercial developments in microalgal biotechnology. Journal of Phycology 35: 215–226.
   Web of Science ®Google Scholar
• Blackburn S.I., Bolch C.J.S., Haskard K.A. & Hallegraeff G.M. 2001. Reproductive compatibility among four global populations of the toxic dinoflagellate Gymnodinium catenatum (Dinophyceae). Phycologia 40: 78–87.
   Web of Science ®Google Scholar
• Bongiovani N., Sanchez-Puerta M.V., Popovich C. & Leonardi P. 2014. Identificación molecular y filogenética de una cepa oleaginosa de Nannochloropsis oceanica (Eustigmatophyceae) aislada de la costa Atlántica suroeste (Argentina). Revista de Biología Marina y Oceanografía 49: 615–623.
   Google Scholar
• Bourrelly P. 1958. Note systématique sur quelques algues microscopiques des cuvettes supralittorales de la région de Dinard. Bulletin du Laboratoire Maritime de Dinard 43: 111–118.
   Google Scholar
• Brown M.R., Jeffrey S.W., Volkman J.K. & Dunstan G.A. 1997. Nutritional properties of microalgae for mariculture. Aquaculture 151: 315–331.
   Web of Science ®Google Scholar
• Brown M.R., Frampton D.M.F., Dunstan G.A. & Blackburn S.I. 2014. Assessing near-infrared reflectance spectroscopy for the rapid detection of lipid and biomass in microalgae cultures. Journal of Applied Phycology 26: 191–198.
   Web of Science ®Google Scholar
• Cao S., Zhang X., Fan X., Qiao H., Liang C., Xu D., Mou S., Wang W. & Ye N. 2013. Phylogeny and characterisation of Nannochloropsis oceanica var. sinensis var. nov. (Eustigmatophyceae), a new oleaginous alga from China. Phycologia 52: 573–577.
   Web of Science ®Google Scholar
• Carpinelli C.E., Telatin A., Vitulo N., Forcato C., D'angelo M., Schiavon R., Vezzi A., Giacometti G.M., Morosinotto T. & Valle G. 2014. Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion. Molecular Plant 7: 323–335.
   Web of Science ®Google Scholar
• Decelle J., Romac S., Stern R.F., Bendif E.M., 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 rRNA gene of photosynthetic eukaryotes with curated taxonomy. Molecular Ecology Resources DOI: 10.1111/1755-0998.12401.
   Google Scholar
• Edgar R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792–1797.
   PubMed Web of Science ®Google Scholar
• Fawley K.P. & Fawley M.W. 2007. Observations on the diversity and ecology of freshwater Nannochloropsis (Eustigmatophyceae), with descriptions of new taxa. Protist 158: 325–336.
   PubMed Web of Science ®Google Scholar
• Fawley K.P., Eliáš M. & Fawley M.W. 2014. The diversity and phylogeny of the commercially important algal class Eustigmatophyceae, including the new clade Goniochloridales. Journal of Applied Phycology 26: 1773–1782.
   Web of Science ®Google Scholar
• Fawley M.W. & Fawley K.P. 2004. A simple and rapid technique for the isolation of DNA from microalgae. Journal of Phycology 40: 223–225.
   Web of Science ®Google Scholar
• Guillard R.R.L. 1975. Culture of phytoplankton for feeding marine invertebrates. In: Culture of marine invertebrate animals (Ed. by W.L. Smith & M.H. Chanley), pp. 29–60. Plenum Press, New York.
   Google Scholar
• Hibberd D.J. 1981. Notes on the taxonomy and nomenclature of the algal classes Eustigmatophyceae and Tribophyceae (synonym Xanthophyceae). Journal of the Linnean Society of London, Botany 82: 93–119.
   Web of Science ®Google Scholar
• Jinkerson R.E., Radakovits R. & Posewitz M.C. 2013. Genomic insights from the oleaginous model alga Nannochloropsis gaditana. Bioengineered 4: 37–43.
   PubMed Web of Science ®Google Scholar
• Karlson B., Potter D., Kuylenstierna M. & Andersen R.A. 1996. Ultrastructure, pigment composition, and 18S rRNA gene sequence for Nannochloropsis granulata sp. nov. (Monodopsidaceae, Eustigmatophyceae), a marine ultraplankter isolated from the Skagerrak, northeast Atlantic Ocean. Phycologia 35: 253–260.
   Web of Science ®Google Scholar
• Khozin-Goldberg I. & Boussiba S. 2011. Concerns over the reporting of inconsistent data on fatty acid composition for microalgae of the genus Nannochloropsis (Eustigmatophyceae). Journal of Applied Phycology 23: 933–934.
   Web of Science ®Google Scholar
• Kilian O., Benemann C.S.E., Niyogi K.K. & Vick B. 2011. High-efficiency homologous recombination in the oil-producing alga Nannochloropsis sp. Proceedings of the National Academy of Science of the United States of America 108: 21265–21269.
   PubMed Web of Science ®Google Scholar
• Krienitz L., Hepperle D., Stich H.-B. & Weile W. 2000. Nannochloropsis limnetica (Eustigmatophyceae), a new species of picoplankton from freshwater. Phycologia 39: 219–227.
   Web of Science ®Google Scholar
• Leliaert F., Vergruggen H., Vanormelingen P., Steen F., López-Bautista J.M., Zuccarello G.C. & de Clerck O. 2014. DNA-based species delimitation in algae. European Journal of Phycology 49: 179–196.
   Web of Science ®Google Scholar
• Liang C., Cao S., Zhan X., Zhu B., Su Z., Xu D., Guang X. & Ye N. 2013. De novo sequencing and global transcriptome analysis of Nannochloropsis sp. (Eustigmatophyceae) following nitrogen starvation. BioEnergy Research 6: 494–505
   Web of Science ®Google Scholar
• Lubián L.M. 1982. Nannochloropsis gaditana sp. nov., una nueva Eustigmatophyceae marina. Lazaroa 4: 287–293.
   Google Scholar
• Neustupa J., Nemcová Y., Veselá J., Steinová J. & Škaloud P. 2013. 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.
   PubMed Web of Science ®Google Scholar
• Pan K., Qin J., Li S., Dai W., Zhu B., Jin Y., Yu W., Yang G. & Li D. 2011. Nuclear monoploidy and asexual propagation of Nannochloropsis oceanica (Eustigmatophyceae) as revealed by its genome sequence. Journal of Phycology 47: 1425–1432.
   Web of Science ®Google Scholar
• Pawlowski J., Audic S., Adl S., Bass D., Belbahri L., Berney C., Bowser S.S., Cepicka I., Decelle J., Dunthorn M., Fiore-Donno A.M., Gile G.H., Holzmann M., Jahn R., Jirků M., Keeling P.J., Kostka M., Kudryavtsev A., Lara E., Lukeš J., Mann D.G., Mitchell E.A.D., Nitsche F., Romeralo M., Saunders G.W., Simpson A.G.B., Smirnov A.V., Spouge J.L., Stern R.F., Stoeck T, Zimmermann J., Schindel D. & de Vargas C. 2012. CBOL Protist Working Group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biology 10 (11): e1001419. DOI:10.1371/journal.pbio.1001419
   PubMed Web of Science ®Google Scholar
• Radakovits R., Jinkerson R.E., Fuerstenberg S.I., Tae H., Settlage R.E., Boore J.L. & Posewitz M.C. 2012. Draft genome sequence and genetic transformation of the oleaginous alga: Nannochloropsis gaditana. Nature Communications 3: 686. DOI: 10.1038/ncomms1688.
   PubMed Web of Science ®Google Scholar
• Starkenburg S.R., Kwon K.J., Jha R.K., McKay C., Jacobs M., Chertkov O., Twary S., Rocap G. & Cattolico R.A. 2014. A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes. BMC Genomics 15: 212. DOI: 10.1186/1471-2164-15-212.
   Web of Science ®Google Scholar
• Suda S., Atsumi M., & Miyashita H. 2002. Taxonomic characterization of a marine Nannochloropsis species, N. oceanica sp. nov. (Eustigmatophyceae). Phycologia: 41: 273–279.
   Web of Science ®Google Scholar
• Swofford D.L. 2002. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
   Google Scholar
• Tamura K., Peterson D., Peterson N., Stecher G., Nei M. & Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731–2739.
   PubMed Web of Science ®Google Scholar
• Tavaré S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. In: Some mathematical questions in biology—DNA sequence analysis (Ed. by Miura R.M.), pp. 57–86. American Mathematical Society, Providence, RI.
   Google Scholar
• Taylor H.R. & Harris W.E. 2012. An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Molecular Ecology Resources 12: 377–388.
   PubMed Web of Science ®Google Scholar
• Vieler A., Wu G., Tsai C.-H., Bullard B., Cornish A.J., Harvey C., Reca I.-B., Thornburg C., Achawanantakun R., Buehl C.J., Campbell M.S., Cavalier D., Childs K.L., Clark T.J., Deshpande R., Erickson E., Ferguson A.A., Handee W., Kong Q., Li X., Liu B., Lundback S., Peng C., Roston R.L., Sanjaya, Simpson J.P., TerBush A., Warakanont J., Zäuner S., Farre E.M., Hegg E.L., Jiang N., Kuo M.-H., Lu Y., Niyogi K.K., Ohlrogge J., Osteryoung K.W., Shachar-Hill Y., Sears B.B., Sun Y., Takahashi H., Yandell M., Shiu S.-H. & Benning C. 2012. Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779. PLoS Genetics 8: e1003064. DOI: 10.1371/journal.pgen.1003064.
   PubMed Web of Science ®Google Scholar
• Wang D., Ning K., Li J., Hu J., Han D., Wang H., Zeng X., Jing X., Zhou Q., Su X., Chang X., Wang A., Wang W., Jia J., Wei L., Xin Y., Qiao Y., Huang R., Chen J., Han B., Yoon, K. Hill R.T., Zohar Y., Chen F., Hu Q. & Xu J. 2014. Nannochloropsis genomes reveal evolution of microalgal oleaginous traits. PLOS Genetics 10: e1004094. DOI:10.1371/journal.pgen.1004094.
   PubMed Web of Science ®Google Scholar
• Wei L., Xin Y., Wang D., Jing X., Zhou Q., Su X., Jia J., Ning K., Chen F., Hu Q. & Xu J. 2013. Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae. BMC Genomics 14: 534. DOI: 10.1186/1471-2164-14-534.
   PubMed Web of Science ®Google Scholar
• White T.J., Bruns T., Lee S. & Taylor J.W. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR protocols: a guide to methods and applications (Ed. by M.A. Innis, D. H. Gelfand, J.J. Sninsky & T.J. White), pp. 315–322. Academic Press, New York.
   Google Scholar
• Zheng M., Tian J., Yang G., Zheng L., Chen G., Chen J. & Wang B. 2013. Transcriptome sequencing, annotation and expression analysis of Nannochloropsis sp. at different growth phases. Gene 523: 117–121.
   Web of Science ®Google Scholar
• Zwickl D.J. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD thesis. The University of Texas at Austin. 125 pp.
   Google Scholar