Single cell genome analysis of an uncultured heterotrophic stramenopile

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Roy, Rajat S ^a,b   Price, Dana C ^b   Schliep, Alexander ^a,c   Cai, Guohong ^d   Korobeynikov, Anton ^e,f   Yoon, Hwan Su ^g   Yang, Eun Chan ^h   Bhattacharya, Debashish ^b  

^a RUTGERS UNIVERSITY   (United States)

^b The State University of New Jersey   (United States)

^c RUTGERS UNIVERSITY   (United States)

^d RUTGERS UNIVERSITY   (United States)

^e ST PETERSBURG STATE UNIVERSITY   (Russian Federation)

^f ST PETERSBURG ACADEMIC UNIVERSITY   (Russian Federation)

^g Sungkyunkwan University   (South Korea)

^h Korea Research Institute of Ships and Ocean Engineering   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; RNA 18S; SEA WATER;

ARTICLE; BIODIVERSITY; BIOLOGY; CLASSIFICATION; GENETICS; GENOMICS; METABOLISM; PHYLOGENY; PROTEOMICS; SINGLE CELL ANALYSIS; STRAMENOPILE;

BIODIVERSITY; COMPUTATIONAL BIOLOGY; GENOMICS; PHYLOGENY; PROTEOME; PROTEOMICS; RNA, RIBOSOMAL, 18S; SEAWATER; SINGLE-CELL ANALYSIS; STRAMENOPILES;

EID: 84899477000     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep04780     Document Type: Article

References (54)

1. Parfrey, L. W. et al. Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life. Syst. Biol. 59, 518-533 (2010
2. Pawlowski, J. et al. CBOL protist working group: Barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol. 10, e1001419 (2012
3. Guiry, M. D.Howmany species of algae are there J. Phycol. 48, 1057-1063 (2012
4. Boo, S. M. et al. Complex phylogeographic patterns in the freshwater alga Synura provide new insights on ubiquity versus endemism in microbial eukaryotes. Mol. Ecol. 19, 4328-4338 (2010
5. Moustafa, A. et al. Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science 324, 1724-1726 (2009
6. Curtis, B. A. et al. Cryptophyte and chlorarachniophyte nuclear genomes reveal evolutionarymosaicism and the fate of nucleomorphs. Nature 492, 59-65 (2012
7. Keeling, P. J.&Palmer, J. D. Horizontal gene transfer in eukaryotic evolution. Nat. Rev. Genet. 9, 605-618 (2008
8. Chan, C. X. et al. Analysis of dinoflagellate genes reveals the remarkably complex evolutionary history of a microbial eukaryote. J. Phycol. 48, 1130-1142 (2012
9. Bhattacharya, D. et al. Genome of the red alga Porphyridium purpureum. Nat. Commun. 4, 1941 (2013
10. Behnke, A. et al. Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions. Environ. Microbiol. 13, 340-349 (2011
11. Cuvelier, M. L. et al. Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proc. Natl. Acad. Sci. U.S.A. 107, 14679-14684 (2010
12. Lepere, C. et al. Whole-genome amplification (WGA) of marine photosynthetic eukaryote populations. FEMS Microbiol. Ecol. 76, 513-523 (2011
13. Worden, A. Z., Dupont, C. & Allen, A. E. Genomes of uncultured eukaryotes: Sorting FACS from fiction. Genome Biol. 12, 117 (2011
14. Yoon, H. S. et al. Single-cell genomics reveals organismal interactions in uncultivated marine protists. Science 332, 714-717 (2011
15. Bhattacharya, D. et al. Single cell genome analysis supports a link between phagotrophy and primary plastid endosymbiosis. Sci. Rep. 2, 356 (2012
16. Stepanauskas, R. Single cell genomics: An individual look at microbes. Curr. Opin. Microbiol. 15, 613-620 (2012
17. Vaulot, D. et al. Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling. PLoS One 7, e39648 (2012
18. Massana, R. et al. Phylogenetic and ecological analysis of novel marine stramenopiles. Appl. Environ. Microbiol. 70, 3528-3534 (2004
19. Rodr?guez-Mart?nez, R., Rocap, G., Logares, R., Romac, S. & Massana, R. Low evolutionary diversification in a widespread and abundant uncultured protist (MAST-4). Mol. Biol. Evol. 29, 1393-1406 (2012
20. Logares, R. et al. Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing. ISME J. 6, 1823-1833 (2012
21. Anderson, R., Wylezich, C., Glaubitz, S., Labrenz, M. & Ju?rgens, K. Impact of protist grazing on a key bacterial group for biogeochemical cycling in Baltic Sea pelagic oxic/anoxic interfaces. Environ. Microbiol. 15, 1580-1594 (2013
22. Massana, R., Terrado, R., Forn, I., Lovejoy, C. & Pedro?s-Alio?, C. Distribution and abundance of uncultured heterotrophic flagellates in the world oceans. Environ. Microbiol. 8, 1515-1522 (2006
23. Massana, R. et al. Phylogenetic and ecological analysis of novel marine stramenopiles. Appl. Environ. Microbiol. 70, 3528-3534 (2004
24. Lin, Y. C. et al. Distribution patterns and phylogeny of marine stramenopiles in the North Pacific Ocean. Appl. Environ. Microbiol. 78, 3387-3399 (2012
25. Bankevich, A. et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477 (2012
26. Parra, G., Bradnam, K. & Korf, I. CEGMA: A pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23, 1061-1067 (2007
27. Stanke, M. & Morgenstern, B. Augustus: A web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res. 33, W465-W467 (2005
28. Bhattacharya, D. et al. Identification of amarine cyanophage in a protist single cell metagenome assembly. J. Phycol. 49, 207-212 (2013
29. Qiu, H. et al. Adaptation through horizontal gene transfer in the cryptoendolithic red alga Galdieria phlegrea. Curr. Biol. 23, R865-R866 (2013
30. Hackett, J. D. et al. Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates. Mol. Biol. Evol. 24, 1702-1713 (2007
31. Burki, F., Okamoto, N., Pombert, J. F. & Keeling, P. J. The evolutionary history of haptophytes and cryptophytes: Phylogenomic evidence for separate origins. Proc. Biol. Sci. 279, 2246-2254 (2012
32. Armbrust, E. V. et al. The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science 306, 79-86 (2004
33. Lloyd, K. G. et al. Predominant archaea in marine sediments degrade detrital proteins. Nature 496, 215-218 (2013
34. Ellegaard, K. M., Klasson, L. & Andersson, S. G. Testing the reproducibility of multiple displacement amplification on genomes of clonal endosymbiont populations. PLoS One 8, e82319 (2013
35. Rodrigue, S. et al. Whole genome amplification and de novo assembly of single bacterial cells. PLoS One 4, e6864 (2009
36. Chitsaz, H. et al. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat. Biotechnol. 29, 915-921 (2011
37. Palenik, B. et al. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc. Natl. Acad. Sci. U.S.A. 104, 7705-7710 (2007
38. Tyler, B. M. et al. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313, 1261-1266 (2006
39. Stiller, J. W., Huang, J., Ding, Q., Tian, J. & Goodwillie, C. Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses BMC Genomics 10, 484 (2009
40. Frommolt, R. et al. Ancient recruitment by chromists of green algal genes encoding enzymes for carotenoid biosynthesis. Mol. Biol. Evol. 25, 2653-2567 (2008
41. Archibald, J. M. et al. Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans. Proc. Natl. Acad. Sci. U.S.A. 100, 7678-7683 (2003
42. Andersson, J. O. Gene transfer and diversification of microbial eukaryotes. Annu. Rev. Microbiol. 63, 177-93 (2009
43. Rose, J. M., Caron, D. A., Sieracki, M. E. & Poulton, N. Counting heterotrophic nanoplanktonic protists in cultures and aquatic communities by flow cytometry. Aquat. Microbial Ecol. 34, 263-277 (2004
44. Stepanauskas, R. & Sieracki, M. E. Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proc. Natl. Acad. Sci. U.S.A. 104, 9052-9057 (2007
45. Raghunathan, A. et al. Genomic DNA amplification from a single bacterium. Appl. Environ. Microbiol. 71, 3342-3347 (2005
46. Dean, F. B. et al. Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. U.S.A. 99, 5261-5266 (2002
47. Zong, C., Lu, S., Chapman, A. R. & Xie, X. S. Genome-wide detection of singlenucleotide and copy-number variations of a single human cell. Science 338, 1622-1626 (2012
48. Woyke, T. et al. Assembling themarine metagenome, one cell at a time. PLoS One 4, e5299 (2009
49. Peng, Y. et al. IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420-1428 (2012
50. Price, D. C. et al. Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science 335, 843-847 (2012
51. Stamatakis, A. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa andmixed models. Bioinformatics 22, 2688-2690 (2006
52. Moustafa, A. & Bhattacharya, D. PhyloSort: A user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas. BMC Evol. Biol. 8, 6 (2008
53. Edgar, R. C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004
54. Talavera, G. & Castresana, J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564-577 (2007).