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Pan genome of the phytoplankton Emiliania underpins its global distribution

(2013) NATURE. 499(7457). p.209-213
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Coccolithophores have influenced the global climate for over 200 million years(1). These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems(2). They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space(3). Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean(4). Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.
Keywords
INDICATORS, STRESS, PHOSPHORUS, CALCIFICATION, HIGH LIGHT, HUXLEYI PRYMNESIOPHYCEAE, GEPHYROCAPSA OCEANICA, BLOOMS, GROWTH

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Chicago
Read, Betsy A, Jessica Kegel, Mary J Klute, Alan Kuo, Stephane C Lefebvre, Florian Maumus, Christoph Mayer, et al. 2013. “Pan Genome of the Phytoplankton Emiliania Underpins Its Global Distribution.” Nature 499 (7457): 209–213.
APA
Read, B. A., Kegel, J., Klute, M. J., Kuo, A., Lefebvre, S. C., Maumus, F., Mayer, C., et al. (2013). Pan genome of the phytoplankton Emiliania underpins its global distribution. NATURE, 499(7457), 209–213.
Vancouver
1.
Read BA, Kegel J, Klute MJ, Kuo A, Lefebvre SC, Maumus F, et al. Pan genome of the phytoplankton Emiliania underpins its global distribution. NATURE. 2013;499(7457):209–13.
MLA
Read, Betsy A, Jessica Kegel, Mary J Klute, et al. “Pan Genome of the Phytoplankton Emiliania Underpins Its Global Distribution.” NATURE 499.7457 (2013): 209–213. Print.
@article{4120924,
  abstract     = {Coccolithophores have influenced the global climate for over 200 million years(1). These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems(2). They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space(3). Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean(4). Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.},
  author       = {Read, Betsy A and Kegel, Jessica and Klute, Mary J and Kuo, Alan and Lefebvre, Stephane C and Maumus, Florian and Mayer, Christoph and Miller, John and Monier, Adam and Salamov, Asaf and Young, Jeremy and Aguilar, Maria and Claverie, Jean-Michel and Frickenhaus, Stephan and Gonzalez, Karina and Herman, Emily K and Lin, Yao-Cheng and Napier, Johnathan and Ogata, Hiroyuki and Sarno, Analissa F and Shmutz, Jeremy and Schroeder, Declan and de Vargas, Colomban and Verret, Frederic and von Dassow, Peter and Valentin, Klaus and Van de Peer, Yves and Wheeler, Glen and Dacks, Joel B and Delwiche, Charles F and Dyhrman, Sonya T and Gl{\"o}ckner, Gernot and John, Uwe and Richards, Thomas and Worden, Alexandra Z and Zhang, Xiaoyu and Grigoriev, Igor V},
  issn         = {0028-0836},
  journal      = {NATURE},
  keyword      = {INDICATORS,STRESS,PHOSPHORUS,CALCIFICATION,HIGH LIGHT,HUXLEYI PRYMNESIOPHYCEAE,GEPHYROCAPSA OCEANICA,BLOOMS,GROWTH},
  language     = {eng},
  number       = {7457},
  pages        = {209--213},
  title        = {Pan genome of the phytoplankton Emiliania underpins its global distribution},
  url          = {http://dx.doi.org/10.1038/nature12221},
  volume       = {499},
  year         = {2013},
}

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