Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids

Dagan T, Roettger M, Stucken K, Landan G, Koch R, Major P, Gould SB, Goremykin VV, Rippka R, de Marsac NT, Gugger M, et al. (2013)
Genome Biology And Evolution 5(1): 31-44.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Dagan, Tal; Roettger, Mayo; Stucken, Karina; Landan, Giddy; Koch, Robin; Major, Peter; Gould, Sven B.; Goremykin, Vadim V.; Rippka, Rosmarie; de Marsac, Nicole Tandeau; Gugger, Muriel; Lockhart, Peter J.
Alle
Abstract / Bemerkung
Cyanobacteria forged two major evolutionary transitions with the invention of oxygenic photosynthesis and the bestowal of photosynthetic lifestyle upon eukaryotes through endosymbiosis. Information germane to understanding those transitions is imprinted in cyanobacterial genomes, but deciphering it is complicated by lateral gene transfer (LGT). Here, we report genome sequences for the morphologically most complex true-branching cyanobacteria, and for Scytonema hofmanni PCC 7110, which with 12,356 proteins is the most gene-rich prokaryote currently known. We investigated components of cyanobacterial evolution that have been vertically inherited, horizontally transferred, and donated to eukaryotes at plastid origin. The vertical component indicates a freshwater origin for water-splitting photosynthesis. Networks of the horizontal component reveal that 60% of cyanobacterial gene families have been affected by LGT. Plant nuclear genes acquired from cyanobacteria define a lower bound frequency of 611 multigene families that, in turn, specify diazotrophic cyanobacterial lineages as having a gene collection most similar to that possessed by the plastid ancestor.
Stichworte
cyanobacteria; true-branching; phylogenomics; plastid evolution; endosymbiosis; nitrogen fixation
Erscheinungsjahr
2013
Zeitschriftentitel
Genome Biology And Evolution
Band
5
Ausgabe
1
Seite(n)
31-44
ISSN
1759-6653
eISSN
1759-6653
Page URI
https://pub.uni-bielefeld.de/record/2565642

Zitieren

Dagan T, Roettger M, Stucken K, et al. Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids. Genome Biology And Evolution. 2013;5(1):31-44.
Dagan, T., Roettger, M., Stucken, K., Landan, G., Koch, R., Major, P., Gould, S. B., et al. (2013). Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids. Genome Biology And Evolution, 5(1), 31-44. doi:10.1093/gbe/evs117
Dagan, Tal, Roettger, Mayo, Stucken, Karina, Landan, Giddy, Koch, Robin, Major, Peter, Gould, Sven B., et al. 2013. “Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids”. Genome Biology And Evolution 5 (1): 31-44.
Dagan, T., Roettger, M., Stucken, K., Landan, G., Koch, R., Major, P., Gould, S. B., Goremykin, V. V., Rippka, R., de Marsac, N. T., et al. (2013). Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids. Genome Biology And Evolution 5, 31-44.
Dagan, T., et al., 2013. Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids. Genome Biology And Evolution, 5(1), p 31-44.
T. Dagan, et al., “Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids”, Genome Biology And Evolution, vol. 5, 2013, pp. 31-44.
Dagan, T., Roettger, M., Stucken, K., Landan, G., Koch, R., Major, P., Gould, S.B., Goremykin, V.V., Rippka, R., de Marsac, N.T., Gugger, M., Lockhart, P.J., Allen, J.F., Brune, I., Maus, I., Pühler, A., Martin, W.F.: Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids. Genome Biology And Evolution. 5, 31-44 (2013).
Dagan, Tal, Roettger, Mayo, Stucken, Karina, Landan, Giddy, Koch, Robin, Major, Peter, Gould, Sven B., Goremykin, Vadim V., Rippka, Rosmarie, de Marsac, Nicole Tandeau, Gugger, Muriel, Lockhart, Peter J., Allen, John F., Brune, Iris, Maus, Irena, Pühler, Alfred, and Martin, William F. “Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids”. Genome Biology And Evolution 5.1 (2013): 31-44.

88 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Genome and pan-genome analysis to classify emerging bacteria.
Caputo A, Fournier PE, Raoult D., Biol Direct 14(1), 2019
PMID: 30808378
Timing the Evolutionary Advent of Cyanobacteria and the Later Great Oxidation Event Using Gene Phylogenies of a Sunscreen.
Garcia-Pichel F, Lombard J, Soule T, Dunaj S, Wu SH, Wojciechowski MF., MBio 10(3), 2019
PMID: 31113897
An Expanded Ribosomal Phylogeny of Cyanobacteria Supports a Deep Placement of Plastids.
Moore KR, Magnabosco C, Momper L, Gold DA, Bosak T, Fournier GP., Front Microbiol 10(), 2019
PMID: 31354692
Emerging and evolving concepts in gene essentiality.
Rancati G, Moffat J, Typas A, Pavelka N., Nat Rev Genet 19(1), 2018
PMID: 29033457
Ancient balancing selection on heterocyst function in a cosmopolitan cyanobacterium.
Sano EB, Wall CA, Hutchins PR, Miller SR., Nat Ecol Evol 2(3), 2018
PMID: 29335576
The monoplastidic bottleneck in algae and plant evolution.
de Vries J, Gould SB., J Cell Sci 131(2), 2018
PMID: 28893840
Complete chloroplast genome sequence and comparative analysis of loblolly pine (Pinus taeda L.) with related species.
Asaf S, Khan AL, Khan MA, Shahzad R, Lubna, Kang SM, Al-Harrasi A, Al-Rawahi A, Lee IJ., PLoS One 13(3), 2018
PMID: 29596414
The future of genomics in polar and alpine cyanobacteria.
Chrismas NAM, Anesio AM, Sánchez-Baracaldo P., FEMS Microbiol Ecol 94(4), 2018
PMID: 29506259
Determination of the Role of Microcystis aeruginosa in Toxin Generation Based on Phosphoproteomic Profiles.
Qu J, Shen L, Zhao M, Li W, Jia C, Zhu H, Zhang Q., Toxins (Basel) 10(7), 2018
PMID: 30041444
Host-pathogen biotic interactions shaped vitamin K metabolism in Archaeplastida.
Cenci U, Qiu H, Pillonel T, Cardol P, Remacle C, Colleoni C, Kadouche D, Chabi M, Greub G, Bhattacharya D, Ball SG., Sci Rep 8(1), 2018
PMID: 30323231
Concerted Up-regulation of Aldehyde/Alcohol Dehydrogenase (ADHE) and Starch in Chlamydomonas reinhardtii Increases Survival under Dark Anoxia.
van Lis R, Popek M, Couté Y, Kosta A, Drapier D, Nitschke W, Atteia A., J Biol Chem 292(6), 2017
PMID: 28007962
Evolution of Chaperonin Gene Duplication in Stigonematalean Cyanobacteria (Subsection V).
Weissenbach J, Ilhan J, Bogumil D, Hülter N, Stucken K, Dagan T., Genome Biol Evol 9(1), 2017
PMID: 28082600
Biotic Host-Pathogen Interactions As Major Drivers of Plastid Endosymbiosis.
Cenci U, Bhattacharya D, Weber APM, Colleoni C, Subtil A, Ball SG., Trends Plant Sci 22(4), 2017
PMID: 28089380
An Early-Branching Freshwater Cyanobacterium at the Origin of Plastids.
Ponce-Toledo RI, Deschamps P, López-García P, Zivanovic Y, Benzerara K, Moreira D., Curr Biol 27(3), 2017
PMID: 28132810
The Carboxy Terminus of YCF1 Contains a Motif Conserved throughout >500 Myr of Streptophyte Evolution.
de Vries J, Archibald JM, Gould SB., Genome Biol Evol 9(2), 2017
PMID: 28164224
Endosymbiosis: Did Plastids Evolve from a Freshwater Cyanobacterium?
de Vries J, Archibald JM., Curr Biol 27(3), 2017
PMID: 28171752
How Embryophytic is the Biosynthesis of Phenylpropanoids and their Derivatives in Streptophyte Algae?
de Vries J, de Vries S, Slamovits CH, Rose LE, Archibald JM., Plant Cell Physiol 58(5), 2017
PMID: 28340089
A Metagenomic Approach to Cyanobacterial Genomics.
Alvarenga DO, Fiore MF, Varani AM., Front Microbiol 8(), 2017
PMID: 28536564
The Physiology of Phagocytosis in the Context of Mitochondrial Origin.
Martin WF, Tielens AGM, Mentel M, Garg SG, Gould SB., Microbiol Mol Biol Rev 81(3), 2017
PMID: 28615286
Early photosynthetic eukaryotes inhabited low-salinity habitats.
Sánchez-Baracaldo P, Raven JA, Pisani D, Knoll AH., Proc Natl Acad Sci U S A 114(37), 2017
PMID: 28808007
Biotic interactions as drivers of algal origin and evolution.
Brodie J, Ball SG, Bouget FY, Chan CX, De Clerck O, Cock JM, Gachon C, Grossman AR, Mock T, Raven JA, Saha M, Smith AG, Vardi A, Yoon HS, Bhattacharya D., New Phytol 216(3), 2017
PMID: 28857164
Plasticity first: molecular signatures of a complex morphological trait in filamentous cyanobacteria.
Koch R, Kupczok A, Stucken K, Ilhan J, Hammerschmidt K, Dagan T., BMC Evol Biol 17(1), 2017
PMID: 28859625
The complete chloroplast genome sequence of Amentotaxus argotaenia (Taxaceae).
Li J, Gao L, Tao K, Su Y, Wang T., Mitochondrial DNA A DNA Mapp Seq Anal 27(4), 2016
PMID: 26119122
Complete genome sequence of cyanobacterium Fischerella sp. NIES-3754, providing thermoresistant optogenetic tools.
Hirose Y, Fujisawa T, Ohtsubo Y, Katayama M, Misawa N, Wakazuki S, Shimura Y, Nakamura Y, Kawachi M, Yoshikawa H, Eki T, Kanesaki Y., J Biotechnol 220(), 2016
PMID: 26784989
Advances in genomics, transcriptomics and proteomics of toxin-producing cyanobacteria.
D'Agostino PM, Woodhouse JN, Makower AK, Yeung AC, Ongley SE, Micallef ML, Moffitt MC, Neilan BA., Environ Microbiol Rep 8(1), 2016
PMID: 26663762
Reconstructing the complex evolutionary history of mobile plasmids in red algal genomes.
Lee J, Kim KM, Yang EC, Miller KA, Boo SM, Bhattacharya D, Yoon HS., Sci Rep 6(), 2016
PMID: 27030297
Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss.
Zamani-Dahaj SA, Okasha M, Kosakowski J, Higgs PG., Mol Biol Evol 33(7), 2016
PMID: 27189546
Aliterella atlantica gen. nov., sp. nov., and Aliterella antarctica sp. nov., novel members of coccoid Cyanobacteria.
Rigonato J, Gama WA, Alvarenga DO, Branco LH, Brandini FP, Genuário DB, Fiore MF., Int J Syst Evol Microbiol 66(8), 2016
PMID: 27054834
Fluorescence in situ hybridization of Microcystis strains producing microcystin using specific mRNA probes.
Zeller P, Méjean A, Biegala I, Contremoulins V, Ploux O., Lett Appl Microbiol 63(5), 2016
PMID: 27538762
Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora.
Nowack EC, Price DC, Bhattacharya D, Singer A, Melkonian M, Grossman AR., Proc Natl Acad Sci U S A 113(43), 2016
PMID: 27791007
The multicellular nature of filamentous heterocyst-forming cyanobacteria.
Herrero A, Stavans J, Flores E., FEMS Microbiol Rev 40(6), 2016
PMID: 28204529
Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications.
Cassier-Chauvat C, Veaudor T, Chauvat F., Front Microbiol 7(), 2016
PMID: 27881980
Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins.
Ramírez-Sánchez O, Pérez-Rodríguez P, Delaye L, Tiessen A., Genomics Proteomics Bioinformatics 14(6), 2016
PMID: 27998811
Exploring cyanobacterial genomes for natural product biosynthesis pathways.
Micallef ML, D'Agostino PM, Al-Sinawi B, Neilan BA, Moffitt MC., Mar Genomics 21(), 2015
PMID: 25482899
NpR3784 is the prototype for a distinctive group of red/green cyanobacteriochromes using alternative Phe residues for photoproduct tuning.
Rockwell NC, Martin SS, Gan F, Bryant DA, Lagarias JC., Photochem Photobiol Sci 14(2), 2015
PMID: 25342233
Origin and Evolution of Water Oxidation before the Last Common Ancestor of the Cyanobacteria.
Cardona T, Murray JW, Rutherford AW., Mol Biol Evol 32(5), 2015
PMID: 25657330
Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes.
Ku C, Nelson-Sathi S, Roettger M, Garg S, Hazkani-Covo E, Martin WF., Proc Natl Acad Sci U S A 112(33), 2015
PMID: 25733873
Plastid establishment did not require a chlamydial partner.
Domman D, Horn M, Embley TM, Williams TA., Nat Commun 6(), 2015
PMID: 25758953
YCF1: A Green TIC?
de Vries J, Sousa FL, Bölter B, Soll J, Gould SB., Plant Cell 27(7), 2015
PMID: 25818624
Cyanobacteria: the bright and dark sides of a charming group
Sciuto K, Moro I., Biodivers Conserv 24(4), 2015
PMID: IND601243589
Genomic perspectives on the birth and spread of plastids.
Archibald JM., Proc Natl Acad Sci U S A 112(33), 2015
PMID: 25902528
Regulatory RNAs in photosynthetic cyanobacteria.
Kopf M, Hess WR., FEMS Microbiol Rev 39(3), 2015
PMID: 25934122
Identification of DXCF cyanobacteriochrome lineages with predictable photocycles.
Rockwell NC, Martin SS, Lagarias JC., Photochem Photobiol Sci 14(5), 2015
PMID: 25738434
Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils.
Schirrmeister BE, Gugger M, Donoghue PC., Palaeontology 58(5), 2015
PMID: 26924853
Endosymbiotic theories for eukaryote origin.
Martin WF, Garg S, Zimorski V., Philos Trans R Soc Lond B Biol Sci 370(1678), 2015
PMID: 26323761
Genome mining for natural product biosynthetic gene clusters in the Subsection V cyanobacteria.
Micallef ML, D'Agostino PM, Sharma D, Viswanathan R, Moffitt MC., BMC Genomics 16(), 2015
PMID: 26335778
Endosymbiosis and Eukaryotic Cell Evolution.
Archibald JM., Curr Biol 25(19), 2015
PMID: 26439354
Comparison of the terrestrial cyanobacterium Leptolyngbya sp. NIES-2104 and the freshwater Leptolyngbya boryana PCC 6306 genomes.
Shimura Y, Hirose Y, Misawa N, Osana Y, Katoh H, Yamaguchi H, Kawachi M., DNA Res 22(6), 2015
PMID: 26494835
Origin of marine planktonic cyanobacteria.
Sánchez-Baracaldo P., Sci Rep 5(), 2015
PMID: 26621203
Distribution of long chain heterocyst glycolipids in N2-fixing cyanobacteria of the order Stigonematales.
Bauersachs T, Mudimu O, Schulz R, Schwark L., Phytochemistry 98(), 2014
PMID: 24361292
Branching and intercellular communication in the Section V cyanobacterium Mastigocladus laminosus, a complex multicellular prokaryote.
Nürnberg DJ, Mariscal V, Parker J, Mastroianni G, Flores E, Mullineaux CW., Mol Microbiol 91(5), 2014
PMID: 24383541
Evolutionary development of redox regulation in chloroplasts.
Balsera M, Uberegui E, Schürmann P, Buchanan BB., Antioxid Redox Signal 21(9), 2014
PMID: 24483204
Origin and evolution of plastids and photosynthesis in eukaryotes.
McFadden GI., Cold Spring Harb Perspect Biol 6(4), 2014
PMID: 24691960
Gene transfers shaped the evolution of de novo NAD+ biosynthesis in eukaryotes.
Ternes CM, Schönknecht G., Genome Biol Evol 6(9), 2014
PMID: 25169983
The plastid ancestor originated among one of the major cyanobacterial lineages.
Ochoa de Alda JA, Esteban R, Diago ML, Houmard J., Nat Commun 5(), 2014
PMID: 25222494
All1371 is a polyphosphate-dependent glucokinase in Anabaena sp. PCC 7120.
Klemke F, Beyer G, Sawade L, Saitov A, Korte T, Maldener I, Lockau W, Nürnberg DJ, Volkmer T., Microbiology 160(pt 12), 2014
PMID: 25320362
Evolutionary rewiring: a modified prokaryotic gene-regulatory pathway in chloroplasts.
Puthiyaveetil S, Ibrahim IM, Allen JF., Philos Trans R Soc Lond B Biol Sci 368(1622), 2013
PMID: 23754813
Interactions of photosynthesis with genome size and function.
Raven JA, Beardall J, Larkum AW, Sánchez-Baracaldo P., Philos Trans R Soc Lond B Biol Sci 368(1622), 2013
PMID: 23754816
Evolutionary origins of the photosynthetic water oxidation cluster: bicarbonate permits Mn(2+) photo-oxidation by anoxygenic bacterial reaction centers.
Khorobrykh A, Dasgupta J, Kolling DR, Terentyev V, Klimov VV, Dismukes GC., Chembiochem 14(14), 2013
PMID: 24006214
Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes.
Qiu H, Yoon HS, Bhattacharya D., Front Plant Sci 4(), 2013
PMID: 24065973
Assessing the bacterial contribution to the plastid proteome.
Qiu H, Price DC, Weber AP, Facchinelli F, Yoon HS, Bhattacharya D., Trends Plant Sci 18(12), 2013
PMID: 24139901

107 References

Daten bereitgestellt von Europe PubMed Central.

ProtTest: selection of best-fit models of protein evolution.
Abascal F, Zardoya R, Posada D., Bioinformatics 21(9), 2005
PMID: 15647292
Evolutionary biology: out of thin air.
Allen JF, Martin W., Nature 445(7128), 2007
PMID: 17287803
Light-driven oxygen production from superoxide by Mn-binding bacterial reaction centers.
Allen JP, Olson TL, Oyala P, Lee WJ, Tufts AA, Williams JC., Proc. Natl. Acad. Sci. U.S.A. 109(7), 2012
PMID: 22308385
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
Proterozoic ocean chemistry and evolution: a bioinorganic bridge?
Anbar AD, Knoll AH., Science 297(5584), 2002
PMID: 12183619
CRITICA: coding region identification tool invoking comparative analysis.
Badger JH, Olsen GJ, Woese CR., Mol. Biol. Evol. 16(4), 1999
PMID: 10331277
Daddy, where did (PS)I come from?
Baymann F, Brugna M, Muhlenhoff U, Nitschke W., Biochim. Biophys. Acta 1507(1-3), 2001
PMID: 11687221
Dating the rise of atmospheric oxygen.
Bekker A, Holland HD, Wang PL, Rumble D 3rd, Stein HJ, Hannah JL, Coetzee LL, Beukes NJ., Nature 427(6970), 2004
PMID: 14712267
Xenbase: a Xenopus biology and genomics resource.
Bowes JB, Snyder KA, Segerdell E, Gibb R, Jarabek C, Noumen E, Pollet N, Vize PD., Nucleic Acids Res. 36(Database issue), 2007
PMID: 17984085
Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast.
Brinkman FS, Blanchard JL, Cherkasov A, Av-Gay Y, Brunham RC, Fernandez RC, Finlay BB, Otto SP, Ouellette BF, Keeling PJ, Rose AM, Hancock RE, Jones SJ, Greberg H., Genome Res. 12(8), 2002
PMID: 12176923
Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the mesoproterozoic/neoproterozoic radiation of eukaryotes
Butterfield NJ., 2000
Nitrogen deprivation stimulates symbiotic gland development in Gunnera manicata.
Chiu WL, Peters GA, Levieille G, Still PC, Cousins S, Osborne B, Elhai J., Plant Physiol. 139(1), 2005
PMID: 16113217
Sequence based data supports a single Nostoc strain in individual coralloid roots of cycads.
Costa JL, Romero EM, Lindblad P., FEMS Microbiol. Ecol. 49(3), 2004
PMID: 19712296
Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution.
Dagan T, Artzy-Randrup Y, Martin W., Proc. Natl. Acad. Sci. U.S.A. 105(29), 2008
PMID: 18632554
Exocellular polysaccharides from cyanobacteria and their possible applications
De R, Vincenzini M., 1998
Improved microbial gene identification with GLIMMER.
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL., Nucleic Acids Res. 27(23), 1999
PMID: 10556321
Metabolic symbiosis and the birth of the plant kingdom.
Deschamps P, Colleoni C, Nakamura Y, Suzuki E, Putaux JL, Buleon A, Haebel S, Ritte G, Steup M, Falcon LI, Moreira D, Loffelhardt W, Raj JN, Plancke C, d'Hulst C, Dauvillee D, Ball S., Mol. Biol. Evol. 25(3), 2007
PMID: 18093994
Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor.
Deusch O, Landan G, Roettger M, Gruenheit N, Kowallik KV, Allen JF, Martin W, Dagan T., Mol. Biol. Evol. 25(4), 2008
PMID: 18222943
Revolutionary concepts in evolutionary biology
Doolittle WF., 1980
Pattern pluralism and the Tree of Life hypothesis.
Doolittle WF, Bapteste E., Proc. Natl. Acad. Sci. U.S.A. 104(7), 2007
PMID: 17261804
Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria.
Dufresne A, Ostrowski M, Scanlan DJ, Garczarek L, Mazard S, Palenik BP, Paulsen IT, de Marsac NT, Wincker P, Dossat C, Ferriera S, Johnson J, Post AF, Hess WR, Partensky F., Genome Biol. 9(5), 2008
PMID: 18507822
An efficient algorithm for large-scale detection of protein families.
Enright AJ, Van Dongen S, Ouzounis CA., Nucleic Acids Res. 30(7), 2002
PMID: 11917018
The origin of mitochondria in light of a fluid prokaryotic chromosome model.
Esser C, Martin W, Dagan T., Biol. Lett. 3(2), 2007
PMID: 17251118
The microbial engines that drive Earth's biogeochemical cycles.
Falkowski PG, Fenchel T, Delong EF., Science 320(5879), 2008
PMID: 18497287
PHYLIP (phylogeny inference package). Version 3.5c
Felsenstein J., 1993
Test on nif probes and DNA hybridizations
Franche C, Damerval T., 1988
Consed: a graphical tool for sequence finishing.
Gordon D, Abajian C, Green P., Genome Res. 8(3), 1998
PMID: 9521923
Plastid evolution.
Gould SB, Waller RF, McFadden GI., Annu Rev Plant Biol 59(), 2008
PMID: 18315522
Mitochondrial and plastid evolution in eukaryotes: an outsiders' perspective.
Gross J, Bhattacharya D., Nat. Rev. Genet. 10(7), 2009
PMID: 19506574
Evidence of a chimeric genome in the cyanobacterial ancestor of plastids.
Gross J, Meurer J, Bhattacharya D., BMC Evol. Biol. 8(), 2008
PMID: 18433492
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O., Syst. Biol. 59(3), 2010
PMID: 20525638
Evolution of photosynthesis.
Hohmann-Marriott MF, Blankenship RE., Annu Rev Plant Biol 62(), 2011
PMID: 21438681
Application of phylogenetic networks in evolutionary studies.
Huson DH, Bryant D., Mol. Biol. Evol. 23(2), 2005
PMID: 16221896
Anoxygenic photosynthesis modulated Proterozoic oxygen and sustained Earth's middle age.
Johnston DT, Wolfe-Simon F, Pearson A, Knoll AH., Proc. Natl. Acad. Sci. U.S.A. 106(40), 2009
PMID: 19805080
The rapid generation of mutation data matrices from protein sequences.
Jones DT, Taylor WR, Thornton JM., Comput. Appl. Biosci. 8(3), 1992
PMID: 1633570
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
Katoh K, Misawa K, Kuma K, Miyata T., Nucleic Acids Res. 30(14), 2002
PMID: 12136088
Exploring cyanobacterial mutualism
Kayley MU, Bergman B, Raven JA., 2007
Nitrogen fixation in eukaryotes--new models for symbiosis.
Kneip C, Lockhart P, Voss C, Maier UG., BMC Evol. Biol. 7(), 2007
PMID: 17408485
GISMO--gene identification using a support vector machine for ORF classification.
Krause L, McHardy AC, Nattkemper TW, Puhler A, Stoye J, Meyer F., Nucleic Acids Res. 35(2), 2006
PMID: 17175534
Cyanobacterial heterocysts.
Kumar K, Mella-Herrera RA, Golden JW., Cold Spring Harb Perspect Biol 2(4), 2010
PMID: 20452939
Heads or tails: a simple reliability check for multiple sequence alignments.
Landan G, Graur D., Mol. Biol. Evol. 24(6), 2007
PMID: 17387100
Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits.
Larsson J, Nylander JA, Bergman B., BMC Evol. Biol. 11(), 2011
PMID: 21718514
The morphogene AmiC2 is pivotal for multicellular development in the cyanobacterium Nostoc punctiforme.
Lehner J, Zhang Y, Berendt S, Rasse TM, Forchhammer K, Maldener I., Mol. Microbiol. 79(6), 2011
PMID: 21244533
Transfer of photosynthesis genes to and from Prochlorococcus viruses.
Lindell D, Sullivan MB, Johnson ZI, Tolonen AC, Rohwer F, Chisholm SW., Proc. Natl. Acad. Sci. U.S.A. 101(30), 2004
PMID: 15256601
Heterotachy and tree building: a case study with plastids and eubacteria.
Lockhart P, Novis P, Milligan BG, Riden J, Rambaut A, Larkum T., Mol. Biol. Evol. 23(1), 2005
PMID: 16151191
Tracking euxinia in the ancient ocean: a multiproxy perspective and Proterozoic case study
Lyons TW, Anbar AD, Severmann S, Scott C, Gill BC., 2009
An early productive ocean unfit for aerobics.
Lyons TW, Reinhard CT., Proc. Natl. Acad. Sci. U.S.A. 106(43), 2009
PMID: 19846788
The hydrogen hypothesis for the first eukaryote.
Martin W, Muller M., Nature 392(6671), 1998
PMID: 9510246
Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus.
Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D., Proc. Natl. Acad. Sci. U.S.A. 99(19), 2002
PMID: 12218172
Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D.
Matsuzaki M, Misumi O, Shin-I T, Maruyama S, Takahara M, Miyagishima SY, Mori T, Nishida K, Yagisawa F, Nishida K, Yoshida Y, Nishimura Y, Nakao S, Kobayashi T, Momoyama Y, Higashiyama T, Minoda A, Sano M, Nomoto H, Oishi K, Hayashi H, Ohta F, Nishizaka S, Haga S, Miura S, Morishita T, Kabeya Y, Terasawa K, Suzuki Y, Ishii Y, Asakawa S, Takano H, Ohta N, Kuroiwa H, Tanaka K, Shimizu N, Sugano S, Sato N, Nozaki H, Ogasawara N, Kohara Y, Kuroiwa T., Nature 428(6983), 2004
PMID: 15071595
Über Natur und Ursprung der Chromatophoren im Pflanzenreiche
Mereschkowsky C., 1905
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
Strategy by which nitrogen-fixing unicellular cyanobacteria grow photoautotrophically
Mitsui AS., 1986
Identification of cyanobacterial cell division genes by comparative and mutational analyses.
Miyagishima SY, Wolk CP, Osteryoung KW., Mol. Microbiol. 56(1), 2005
PMID: 15773984
Unicellular cyanobacterial distributions broaden the oceanic N2 fixation domain.
Moisander PH, Beinart RA, Hewson I, White AE, Johnson KS, Carlson CA, Montoya JP, Zehr JP., Science 327(5972), 2010
PMID: 20185682
The biogeochemical cycles of trace metals in the oceans.
Morel FM, Price NM., Science 300(5621), 2003
PMID: 12738853
Independence of circadian timing from cell division in cyanobacteria.
Mori T, Johnson CH., J. Bacteriol. 183(8), 2001
PMID: 11274102
Chlamydiae has contributed at least 55 genes to Plantae with predominantly plastid functions.
Moustafa A, Reyes-Prieto A, Bhattacharya D., PLoS ONE 3(5), 2008
PMID: 18493612
The cyanobacterial genome core and the origin of photosynthesis.
Mulkidjanian AY, Koonin EV, Makarova KS, Mekhedov SL, Sorokin A, Wolf YI, Dufresne A, Partensky F, Burd H, Kaznadzey D, Haselkorn R, Galperin MY., Proc. Natl. Acad. Sci. U.S.A. 103(35), 2006
PMID: 16924101
Biochemistry and evolution of anaerobic energy metabolism in eukaryotes.
Muller M, Mentel M, van Hellemond JJ, Henze K, Woehle C, Gould SB, Yu RY, van der Giezen M, Tielens AG, Martin WF., Microbiol. Mol. Biol. Rev. 76(2), 2012
PMID: 22688819
Lateral gene transfer and the nature of bacterial innovation.
Ochman H, Lawrence JG, Groisman EA., Nature 405(6784), 2000
PMID: 10830951
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation.
Palenik B, Grimwood J, Aerts A, Rouze P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, Napoli C, Gendler K, Manuell A, Tai V, Vallon O, Piganeau G, Jancek S, Heijde M, Jabbari K, Bowler C, Lohr M, Robbens S, Werner G, Dubchak I, Pazour GJ, Ren Q, Paulsen I, Delwiche C, Schmutz J, Rokhsar D, Van de Peer Y, Moreau H, Grigoriev IV., Proc. Natl. Acad. Sci. U.S.A. 104(18), 2007
PMID: 17460045
Estimating the timing of early eukaryotic diversification with multigene molecular clocks.
Parfrey LW, Lahr DJ, Knoll AH, Katz LA., Proc. Natl. Acad. Sci. U.S.A. 108(33), 2011
PMID: 21810989
Intracellular spheroid bodies of Rhopalodia gibba have nitrogen-fixing apparatus of cyanobacterial origin.
Prechtl J, Kneip C, Lockhart P, Wenderoth K, Maier UG., Mol. Biol. Evol. 21(8), 2004
PMID: 14963089
Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants.
Price DC, Chan CX, Yoon HS, Yang EC, Qiu H, Weber AP, Schwacke R, Gross J, Blouin NA, Lane C, Reyes-Prieto A, Durnford DG, Neilson JA, Lang BF, Burger G, Steiner JM, Loffelhardt W, Meuser JE, Posewitz MC, Ball S, Arias MC, Henrissat B, Coutinho PM, Rensing SA, Symeonidi A, Doddapaneni H, Green BR, Rajah VD, Boore J, Bhattacharya D., Science 335(6070), 2012
PMID: 22344442
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.
Pruitt KD, Tatusova T, Maglott DR., Nucleic Acids Res. 35(Database issue), 2006
PMID: 17130148
Tansley review no. 116: Cyanobacterium-plant symbioses.
Rai AN, Soderback E, Bergman B., New Phytol. 147(3), 2000
PMID: IND22079133
Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium.
Ran L, Larsson J, Vigil-Stenman T, Nylander JA, Ininbergs K, Zheng WW, Lapidus A, Lowry S, Haselkorn R, Bergman B., PLoS ONE 5(7), 2010
PMID: 20628610
Evolution of cyanobacterial symbioses
Raven JA., 2002
Whole-genome analysis of photosynthetic prokaryotes.
Raymond J, Zhaxybayeva O, Gogarten JP, Gerdes SY, Blankenship RE., Science 298(5598), 2002
PMID: 12446909
Differential gene retention in plastids of common recent origin.
Reyes-Prieto A, Yoon HS, Moustafa A, Yang EC, Andersen RA, Boo SM, Nakayama T, Ishida K, Bhattacharya D., Mol. Biol. Evol. 27(7), 2010
PMID: 20123796
Cell evolution: gene transfer agents and the origin of mitochondria.
Richards TA, Archibald JM., Curr. Biol. 21(3), 2011
PMID: 21300273
Lichen guilds share related cyanobacterial symbionts.
Rikkinen J, Oksanen I, Lohtander K., Science 297(5580), 2002
PMID: 12130774
Generic assignments, strain histories and properties of pure cultures of cyanobacteria
Rippka R, Deruelles J, Waterbury JB, Herdman M, Stanier RY., 1979

Rippka R, Herdman H., 2002
Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation.
Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER, Chisholm SW., Nature 424(6952), 2003
PMID: 12917642
The SAR11 group of alpha-proteobacteria is not related to the origin of mitochondria.
Rodriguez-Ezpeleta N, Embley TM., PLoS ONE 7(1), 2012
PMID: 22291975
Ocean oxygenation in the wake of the Marinoan glaciation.
Sahoo SK, Planavsky NJ, Kendall B, Wang X, Shi X, Scott C, Anbar AD, Lyons TW, Jiang G., Nature 489(7417), 2012
PMID: 23018964
Morphological and habitat evolution in the Cyanobacteria using a compartmentalization approach
Sánchez-Baracaldo P, Hayes PK, Blank CE., 2005
Diazocyte development in the marine diazotrophic cyanobacterium Trichodesmium.
Sandh G, Xu L, Bergman B., Microbiology (Reading, Engl.) 158(Pt 2), 2011
PMID: 22053003
DNA isolation from dry and fresh samples of polysaccharide-rich plants
Sharma AD, Gill PK, Singh P., 2002
Photosystem I gene cassettes are present in marine virus genomes.
Sharon I, Alperovitch A, Rohwer F, Haynes M, Glaser F, Atamna-Ismaeel N, Pinter RY, Partensky F, Koonin EV, Wolf YI, Nelson N, Beja O., Nature 461(7261), 2009
PMID: 19710652
Genome evolution in cyanobacteria: the stable core and the variable shell.
Shi T, Falkowski PG., Proc. Natl. Acad. Sci. U.S.A. 105(7), 2008
PMID: 18268351
Some aspects of the biology of cells and their possible evolutionary significance
Stanier RY., 1970
Long-branch attraction and the rDNA model of early eukaryotic evolution.
Stiller JW, Hall BD., Mol. Biol. Evol. 16(9), 1999
PMID: 10939894
The smallest known genomes of multicellular and toxic cyanobacteria: comparison, minimal gene sets for linked traits and the evolutionary implications.
Stucken K, John U, Cembella A, Murillo AA, Soto-Liebe K, Fuentes-Valdes JJ, Friedel M, Plominsky AM, Vasquez M, Glockner G., PLoS ONE 5(2), 2010
PMID: 20169071
Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina.
Swingley WD, Chen M, Cheung PC, Conrad AL, Dejesa LC, Hao J, Honchak BM, Karbach LE, Kurdoglu A, Lahiri S, Mastrian SD, Miyashita H, Page L, Ramakrishna P, Satoh S, Sattley WM, Shimada Y, Taylor HL, Tomo T, Tsuchiya T, Wang ZT, Raymond J, Mimuro M, Blankenship RE, Touchman JW., Proc. Natl. Acad. Sci. U.S.A. 105(6), 2008
PMID: 18252824
The COG database: new developments in phylogenetic classification of proteins from complete genomes.
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV., Nucleic Acids Res. 29(1), 2001
PMID: 11125040
Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga.
Thompson AW, Foster RA, Krupke A, Carter BJ, Musat N, Vaulot D, Kuypers MM, Zehr JP., Science 337(6101), 2012
PMID: 22997339
Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity.
Van Mooy BA, Fredricks HF, Pedler BE, Dyhrman ST, Karl DM, Koblizek M, Lomas MW, Mincer TJ, Moore LR, Moutin T, Rappe MS, Webb EA., Nature 458(7234), 2009
PMID: 19182781
Treeness triangles: visualizing the loss of phylogenetic signal.
White WT, Hills SF, Gaddam R, Holland BR, Penny D., Mol. Biol. Evol. 24(9), 2007
PMID: 17630280
The evolution of Photosystem II: insights into the past and future.
Williamson A, Conlan B, Hillier W, Wydrzynski T., Photosyn. Res. 107(1), 2010
PMID: 20512415
Complex evolution of photosynthesis.
Xiong J, Bauer CE., Annu Rev Plant Biol 53(), 2002
PMID: 12221987
Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus.
Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP., Genome Biol Evol 1(), 2009
PMID: 20333202
Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events.
Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT., Genome Res. 16(9), 2006
PMID: 16899658
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 23221676
PubMed | Europe PMC

Suchen in

Google Scholar