Coccolithophores have influenced the global climate for over 200 million years1. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems2. 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 space3. 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 ocean4. 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.
At a glance
- A review of the coccolithophorid Emiliania huxleyi (Prymnesiophyceae), with particular reference to growth, coccolith formation, and calcification-photosynthesis interactions. Phycologia 40, 503–529 (2001)
- Relating coccolithophore calcification rates to phytoplankton community dynamics: regional differences and implications for carbon export. Deep-Sea Res. II 54, 538–557 (2007) , , &
- Satellite and ship studies of coccolithophore production along a continental shelf edge. Nature 304, 339–342 (1983) , , , &
- 99–125 (Springer, 2004) & in Coccolithophores: From Molecular Processes to Global Impact (eds & )
- Assessing the gene space in draft genomes. Nucleic Acids Res. 37, 289–297 (2009) , , , &
- The ecoresponsive genome of Daphnia pulex. Science 331, 555–561 (2011) et al.
- The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins. Proc. R. Soc. B 279, 2246–2254 (2012) , , &
- Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proc. Natl Acad. Sci. USA 107, 14679–14684 (2010) et al.
- Structural and regulatory genes required to make the gas dimethyl sulfide in bacteria. Science 315, 666–669 (2007) et al.
- Identification and functional characterisation of genes encoding the omega-3 polyunsaturated biosynthetic pathway from the coccolithophore Emiliania huxleyi. Phytochemistry 72, 594–600 (2011) et al.
- Candida albicans sphingolipid C9-methyltransferase in involved in hyphal elongation. Microbiology 156, 1234–1243 (2010) &
- Long-chain alkenones and alkyl alkenoates as palaeotemperature indicators: their production, flux, and early sedimentary diagenesis in the Eastern North Atlantic. Advances in Organic Chemistry 19, 287–298 (1992) , &
- Liquid-saturated hydrocarbons resulting from pyrolysis of the marine Coccolithophores Emiliania huxleyi and Gephyrocapsa oceanica. Mar. Biotechnol. 1, 346–352 (1999) , , , &
- 351–356 (Springer, 1991) & in The Carbonic Anhydrases (eds , , & ) Ch. 32,
- Genomic fluidity: an integrative view of gene diversity within microbial populations. BMC Genomics 12, 32 (2011) , , &
- Importance of light for the formation of algal blooms by Emiliania huxleyi. Mar. Ecol. Prog. Ser. 136, 195–203 (1996) &
- Vitamin B6 deficient plants display increased sensitivity to high light and photo-oxidative stress. BMC Plant Biol. 9, 130 (2009) et al.
- Photoprotection in the diatom Thalassiosira pseudonana: role of LI818-like proteins in response to high light stress. Biochim. Biophys. Acta 1797, 1449–1457 (2010) &
- A novel alkaline phosphatase in the coccolithophore Emiliania huxleyi (Prymnesiophyceae) and its regulation by phosphorus. J. Phycol. 42, 835–844 (2006) , , , &
- 249–348 (Elsevier Science, 2002) & Dynamics of DOP in Biogeochemistry of Marine Dissolved Organic Matter (eds & ) Ch. 6,
- Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity. Nature 458, 69–72 (2009) et al.
- Coccolithophores: functional biodiversity, enzymes and bioprospecting. Mar. Drugs 9, 586–602 (2011) et al.
- Nitrate:phosphate ratios and Emiliania huxleyi blooms. Limnol. Oceanogr. 50, 1020–1024 (2005) , &
- 1–7 (John Wiley & Sons, 2001) , & The Biogeochemistry of Iron in Seawater Vol. 7, Ch. 1,
- Ferredoxin and flavodoxin as biochemical indicators of iron limitation during open-ocean iron enrichment. Limnol. Oceanogr. 44, 1609–1615 (1999) &
- Effect of trace metal availability on coccolithophorid calcification. Nature 430, 673–676 (2004) et al.
- The requirement of selenium for the growth of marine coccolithophorids, Emiliania huxleyi, Gephyrocapsa oceanica and Helladosphaera sp. (Prymnesiophyceae). Plant Cell Physiol. 40, 762–766 (1999) &
- Feedback interactions between zinc and phytoplankton in seawater. Limnol. Oceanogr. 37, 25–40 (1992) &
- Supplementary Information (3 MB)
This file contains Supplementary Text and Data in 5 sections – see contents for details.
- Supplementary Information (478 KB)
This file contains Supplementary Figures 1-6 and Supplementary Tables 1-15.
- Supplementary Data 1 (765 KB)
This file contains refined gene models validated by Sanger ESTs.
- Supplementary Data 2 (210 KB)
This file contains refined gene models validated by tiling arrays.
- Supplementary Data 3 (236 KB)
This file contains refined gene models validated by RNAseq.
- Supplementary Data 4 (230 KB)
This file contains a phylogenomic gene list.
- Supplementary Data 5 (384 KB)
This file contains core and variable genes identified by direct mapping of Illumina reads based on 50% gene coverage.
- Supplementary Data 6 (643 KB)
This file contains core genes identified by comparative genomic hybridization.
- Supplementary Data 7 (64 KB)
This file contains conserved eukaryotic genes mapping approach (CEGMA) list.
- Supplementary Data 8 (50 KB)
This file contains genes encoding putative metal binding proteins.