The genome of the foraminiferan reticulomyxa filosa

Current Biology

Volumn 24, Issue 1, 2014, Pages 11-18

  Glöckner, Gernot ^a,b   Hülsmann, Norbert ^c   Schleicher, Michael ^d   Noegel, Angelika A ^a   Eichinger, Ludwig ^a   Gallinger, Christoph ^d   Pawlowski, Jan ^e   Sierra, Roberto ^e   Euteneuer, Ursula ^d   Pillet, Loic ^e   Moustafa, Ahmed ^f   Platzer, Matthias ^g   Groth, Marco ^g   Szafranski, Karol ^g   Schliwa, Manfred ^d  

^a UNIVERSITY OF COLOGNE   (Germany)

^b LEIBNIZ INSTITUTE OF FRESHWATER ECOLOGY AND INLAND FISHERIES   (Germany)

^c FREIE UNIVERSITÄT BERLIN   (Germany)

^d UNIVERSITY OF MUNICH   (Germany)

^e UNIVERSITY OF GENEVA   (Switzerland)

^f AMERICAN UNIVERSITY IN CAIRO   (Egypt)

^g FRITZ LIPMANN INSTITUTE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGAE; BACTERIA (MICROORGANISMS); BIGELOWIELLA; BIGELOWIELLA NATANS; CHLORARACHNIOPHYCEAE; EUKARYOTA; FORAMINIFERA; PLASMODIUM (APICOMPLEXA); PROTISTA; RETICULOMYXA FILOSA; RHIZARIA;

TRANSCRIPTION FACTOR;

ARTICLE; CYTOLOGY; CYTOSKELETON; GENETICS; GENOME; HORIZONTAL GENE TRANSFER; MEIOSIS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; RHIZARIA;

CYTOSKELETON; GENE TRANSFER, HORIZONTAL; GENOME, PROTOZOAN; MEIOSIS; MOLECULAR SEQUENCE DATA; RHIZARIA; TRANSCRIPTION FACTORS;

EID: 84891829045     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2013.11.027     Document Type: Article

References (56)

1. S.M. Adl, A.G. Simpson, C.E. Lane, J. Lukeš, D. Bass, S.S. Bowser, M.W. Brown, F. Burki, M. Dunthorn, and V. Hampl et al. The revised classification of eukaryotes J. Eukaryot. Microbiol. 59 2012 429 493
2. S.I. Nikolaev, C. Berney, J.F. Fahrni, I. Bolivar, S. Polet, A.P. Mylnikov, V.V. Aleshin, N.B. Petrov, and J. Pawlowski The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes Proc. Natl. Acad. Sci. USA 101 2004 8066 8071
3. B.A. Curtis, G. Tanifuji, F. Burki, A. Gruber, M. Irimia, S. Maruyama, M.C. Arias, S.G. Ball, G.H. Gile, and Y. Hirakawa et al. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs Nature 492 2012 59 65
4. J. Murray Ecology and Applications of Benthic Foraminifera 2006 Cambridge University Press Cambridge
5. J.F. Travis, and S.S. Bowser The motility of Foraminifera J.J. Lee, R.O. Anderson, Biology of Foraminifera 1991 Academic Press London 91 156
6. A. Habura, L. Wegener, J.L. Travis, and S.S. Bowser Structural and functional implications of an unusual foraminiferal beta-tubulin Mol. Biol. Evol. 22 2005 2000 2009
7. S.S. Bowser, A. Habura, and J. Pawlowski Molecular evolution of Foraminifera L.A. Katz, D. Bhattacharya, Genomics and Evolution of Microbial Eukaryotes 2006 Oxford University Press New York 78 93
8. N. Hülsmann Biology of the genus Reticulomyxa (Rhizopoda) J. Protozool. 34 1984 55a
9. M.P. Koonce, U. Euteneuer, K.L. McDonald, D. Menzel, and M. Schliwa Cytoskeletal architecture and motility in a giant freshwater amoeba, Reticulomyxa Cell Motil. Cytoskeleton 6 1986 521 533
10. R.N. Nauss Reticulomyxa filosa gen. et spec. nov., a new primitive plasmodium Bull. Torrey Bot. Club 76 1949 161 173
11. Hülsmann, N. (2006). Bewegung, Nahrungsaufnahme und Fortpflanzung bei Reticulomyxa filosa (Rhizopoda), Begleitpublikation zum Film C 1639 (Göttingen: IWF Wissen und Medien gGmbH). http://www.filmarchives-online. eu.
12. A. Ashkin, K. Schütze, J.M. Dziedzic, U. Euteneuer, and M. Schliwa Force generation of organelle transport measured in vivo by an infrared laser trap Nature 348 1990 346 348
13. U. Euteneuer, M.P. Koonce, K.K. Pfister, and M. Schliwa An ATPase with properties expected for the organelle motor of the giant amoeba, Reticulomyxa Nature 332 1988 176 178
14. M.P. Koonce, J. Tong, U. Euteneuer, and M. Schliwa Active sliding between cytoplasmic microtubules Nature 328 1987 737 739
15. L.W. Parfrey, and L.A. Katz Genome dynamics are influenced by food source in Allogromia laticollaris strain CSH (Foraminifera) Genome Biol. Evol. 2 2010 678 685
16. F. Burki, K. Shalchian-Tabrizi, and J. Pawlowski Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes Biol. Lett. 4 2008 366 369
17. J.P. Aris, and G. Blobel Isolation of yeast nuclei Methods Enzymol. 194 1991 735 749
18. G. Parra, K. Bradnam, and I. Korf CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes Bioinformatics 23 2007 1061 1067
19. K.F. Aoki-Kinoshita, and M. Kanehisa Gene annotation and pathway mapping in KEGG Methods Mol. Biol. 396 2007 71 91
20. Y. Moriya, M. Itoh, S. Okuda, A.C. Yoshizawa, and M. Kanehisa KAAS: an automatic genome annotation and pathway reconstruction server Nucleic Acids Res. 35 Web Server issue 2007 W182 W185
21. W. Burgdorfer, R.L. Anacker, R.G. Bird, and D.S. Bertram Intranuclear growth of Rickettsia rickettsii J. Bacteriol. 96 1968 1415 1418
22. M. Punta, P.C. Coggill, R.Y. Eberhardt, J. Mistry, J. Tate, C. Boursnell, N. Pang, K. Forslund, G. Ceric, and J. Clements et al. The Pfam protein families database Nucleic Acids Res. 40 Database issue 2012 D290 D301
23. K. Szafranski, R. Lehmann, G. Parra, R. Guigo, and G. Glöckner Gene organization features in A/T-rich organisms J. Mol. Evol. 60 2005 90 98
24. A.J. Heidel, H.M. Lawal, M. Felder, C. Schilde, N.R. Helps, B. Tunggal, F. Rivero, U. John, M. Schleicher, and L. Eichinger et al. Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication Genome Res. 21 2011 1882 1891
25. L. Li, C.J. Stoeckert Jr., and D.S. Roos OrthoMCL: identification of ortholog groups for eukaryotic genomes Genome Res. 13 2003 2178 2189
26. L.K. Fritz-Laylin, S.E. Prochnik, M.L. Ginger, J.B. Dacks, M.L. Carpenter, M.C. Field, A. Kuo, A. Paredez, J. Chapman, and J. Pham et al. The genome of Naegleria gruberi illuminates early eukaryotic versatility Cell 140 2010 631 642
27. D.D. Orokos, and J.L. Travis Cell surface and organelle transport share the same enzymatic properties in Reticulomyxa Cell Motil. Cytoskeleton 38 1997 270 277
28. M. Schliwa, T. Shimizu, R.D. Vale, and U. Euteneuer Nucleotide specificities of anterograde and retrograde organelle transport in Reticulomyxa are indistinguishable J. Cell Biol. 112 1991 1199 1203
29. B. Wickstead, and K. Gull Dyneins across eukaryotes: a comparative genomic analysis Traffic 8 2007 1708 1721
30. M. Kollmar Thirteen is enough: the myosins of Dictyostelium discoideum and their light chains BMC Genomics 7 2006 183
31. M. Kollmar, and G. Glöckner Identification and phylogenetic analysis of Dictyostelium discoideum kinesin proteins BMC Genomics 4 2003 47
32. J.M. Joseph, P. Fey, N. Ramalingam, X.I. Liu, M. Rohlfs, A.A. Noegel, A. Müller-Taubenberger, G. Glöckner, and M. Schleicher The actinome of Dictyostelium discoideum in comparison to actins and actin-related proteins from other organisms PLoS ONE 3 2008 e2654
33. E.M. Myers Observations on the origin and fate of flagellated gametes in multiple tests of discorbis (Foraminifera) J. Mar. Biol. Assoc. U. K. 24 1940 201 225
34. I. Barrantes, G. Glöckner, S. Meyer, and W. Marwan Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum BMC Genomics 11 2010 115
35. G. Glöckner, G. Golderer, G. Werner-Felmayer, S. Meyer, and W. Marwan A first glimpse at the transcriptome of Physarum polycephalum BMC Genomics 9 2008 6
36. P. Lorenz, S. Dietmann, T. Wilhelm, D. Koczan, S. Autran, S. Gad, G. Wen, G. Ding, Y. Li, M.F. Rousseau-Merck, and H.J. Thiesen The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues BMC Genomics 11 2010 206
37. E.M. Zdobnov, and R. Apweiler InterProScan - an integration platform for the signature-recognition methods in InterPro Bioinformatics 17 2001 847 848
38. F. Burki, A. Kudryavtsev, M.V. Matz, G.V. Aglyamova, S. Bulman, M. Fiers, P.J. Keeling, and J. Pawlowski Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists BMC Evol. Biol. 10 2010 377
39. F. Burki, N. Okamoto, J.F. Pombert, and P.J. Keeling The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins Proc. Biol. Sci. 279 2012 2246 2254
40. P.J. Keeling, and J.D. Palmer Horizontal gene transfer in eukaryotic evolution Nat. Rev. Genet. 9 2008 605 618
41. A. Moustafa, B. Beszteri, U.G. Maier, C. Bowler, K. Valentin, and D. Bhattacharya Genomic footprints of a cryptic plastid endosymbiosis in diatoms Science 324 2009 1724 1726
42. th Cairo International, 103-107.
43. K.D. Pruitt, T. Tatusova, and D.R. Maglott NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins Nucleic Acids Res. 35 Database issue 2007 D61 D65
44. I.V. Grigoriev, H. Nordberg, I. Shabalov, A. Aerts, M. Cantor, D. Goodstein, A. Kuo, S. Minovitsky, R. Nikitin, and R.A. Ohm et al. The genome portal of the Department of Energy Joint Genome Institute Nucleic Acids Res. 40 Database issue 2012 D26 D32
45. M.S. Boguski, T.M. Lowe, and C.M. Tolstoshev dbEST - database for "expressed sequence tags" Nat. Genet. 4 1993 332 333
46. R.C. Edgar MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 32 2004 1792 1797
47. S. Capella-Gutiérrez, J.M. Silla-Martínez, and T. Gabaldón trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Bioinformatics 25 2009 1972 1973
48. S. Whelan, and N. Goldman A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach Mol. Biol. Evol. 18 2001 691 699
49. M.N. Price, P.S. Dehal, and A.P. Arkin FastTree: computing large minimum evolution trees with profiles instead of a distance matrix Mol. Biol. Evol. 26 2009 1641 1650
50. H. Shimodaira, and M. Hasegawa Multiple comparisons of log-likelihoods with applications to phylogenetic inference Mol. Biol. Evol. 16 1999 1114
51. A. Moustafa, and D. Bhattacharya 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 2008 6
52. M. Clarke, A.J. Lohan, B. Liu, I. Lagkouvardos, S. Roy, N. Zafar, C. Bertelli, C. Schilde, A. Kianianmomeni, and T.R. Bürglin et al. Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling Genome Biol. 14 2013 R11
53. P.J. Keeling The endosymbiotic origin, diversification and fate of plastids Philos. Trans. R. Soc. Lond. B Biol. Sci. 365 2010 729 748
54. E.C. Nowack, H. Vogel, M. Groth, A.R. Grossman, M. Melkonian, and G. Glöckner Endosymbiotic gene transfer and transcriptional regulation of transferred genes in Paulinella chromatophora Mol. Biol. Evol. 28 2011 407 422
55. L. Pillet, and J. Pawlowski Transcriptome analysis of foraminiferan Elphidium margaritaceum questions the role of gene transfer in kleptoplastidy Mol. Biol. Evol. 30 2013 66 69
56. E. Blanco, G. Parra, and R. Guigo Using Geneid to identify genes Curr. Protoc. Bioinfomatics 4 2007 4.3 10.1002/0471250953.bi0403s18