Publications

Publications 2020

  • Hülter NF, Wein T, Effe J, Garoña A, Dagan T.  2020. Intracellular competitions reveal determinants of plasmid evolutionary success. Front. Microbiol.:1–12. doi: 10.3389/fmicb.2020.02062. Link
  • Wein T, Wang Y, Hülter NF, Hammerschmidt K, Dagan T. 2020. Antibiotics interfere with the evolution of plasmid stability. Curr Biol 30:1–7. doi: 10.1016/j.cub.2020.07.019 Link
  • Glock N, Romero D, Roy AS, Woehle C, Dale AW, Schönfeld J, Wein T, Weissenbach J, Dagan T. 2020. A hidden sedimentary phosphate pool inside benthic foraminifera from the Peruvian upwelling region might nucleate phosphogenesis. Geochim. Cosmochim. Acta 289:14–32.  doi: 10.1016/j.gca.2020.08.002 Link
  • Svetlitsky D, Dagan T, Ziv-Ukelson M. 2020. Discovery of multi-operon colinear syntenic blocks in microbial genomes. Bioinformatics 36:i21–i29.  doi: 10.1093/bioinformatics/btaa503 Link
  • Springstein BL,  Arévalo S, Helbig AO, Herrero A, Stucken K,  Flores E,  Dagan T. 2020. A nov el septal protein of multicellular heterocystous cyanobacteria is associated with the divisome. Mol Microbiol 113(6):1140-1154. doi: 10.1111/mmi.14483. link
  • Springstein BL, Nies F, Dagan T. 2020. Natural competence in Chlorogloeospis fritschii PCC 6912 and other ramified caynaobacteria. bioRxiv. doi: 10.1101/2020.06.19.162503. link
  • Springstein BL, Nürnberg DJ, Kieninger A, Woehle C, Weissenbach J, Theune M, Helbig AO, Tholey A, Maldener I, Dagan T, Stucken K. 2020. A cytoskeletal network maintains filament shape in the multicellular cyanobacterium Anabaena sp. PCC 7120. bioRxiv. doi: https://doi.org/10.1101/553073 . link
  • Yu Y,  Boström C, Franzenburg S, Bayer T, Dagan T, Reusch TBH. 2020. Somatic genetic drift and multilevel selection a clonal seagrass. Nature Ecology & Evolution. doi: 10.1038/s41559-020-1196-4. link
  • Springstein BL, Woehle C, Weissenbach J, Dagan T, Stucken K. 2020. Identification and characterization of novel filament-forming proteins in cyanobacteria. Sci Rep 10 (1), 1894. doi: 10.1038/s41598-020-58726-9. link
  • Godfroid M, Dagan T, Merker M, Kohl TA, Diel R, Maurer FP, Niemann S, Kupczok A. 2020. Insertion and deletion evolution reflects antibiotics selection pressure in a Mycobacterium tuberculosis outbreak. bioRxiv:2020.01.28.922765. link

 

Publications 2019

  • Wein T, Stücker FT, Hülter NF, Dagan T. 2019. Quantification of plasmid-mediated antibiotic resistance in an expeimental evolution approch. J Vis Exp 14 (154). doi: 10.3791/60749. link
    Video

  • Rausch P, Rühlemann M, Hermes BM, Doms S, Dagan T, Dierking K, Domin H, Fraune S, von Frieling, J, Hentschel U, Heinsen FA, Höppner M, Jahn MT, Jaspers C, Kissoyan KAB, Langfeldt D, Rehman A, H. Reusch TBH, Roeder T, Schmitz RA, Schulenburg H, Soluch R, Sommer F, Stukenbrock E, Weiland-Bräuer N, Rosenstiel P, Franke A, Bosch T, Baines JF. 2019. Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms. Microbiome 7 (1):133. doi: 10.1186/s40168-019-0743-1. link

  • T Wein, T Dagan. 2019. The effect of population bottleneck size and selective regime on genetic diversity and evolvability in bacteria. Genome Biol Evol 11 (11), 3283-3290. doi: 10.1093/gbe/evz243. link
     
  • Ansorge R, Romano S, Sayavedra L, Porras MÁG, Kupczok A, Tegetmeyer HE, Dubilier N, Petersen J. 2019. Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels. Nature Microbiology. link
    Behind the paper
    Press release

  • Jahn MT, Arkhipova K, Markert SM, Stigloher C, Lachnit T, Pita L, Kupczok A, Ribes M, Stengel ST, Rosenstiel P, et al. 2019. A Phage Protein Aids Bacterial Symbionts in Eukaryote Immune Evasion. Cell Host & Microbe. link
    Press release

  • Romero Picazo D, Dagan T, Ansorge R, Petersen JM, Dubilier N, Kupczok A. 2019. Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated. ISME J link
    Behind the paper

  • Kupczok A, Dagan T. 2019. Rates of Molecular Evolution in a Marine Synechococcus Phage Lineage. Viruses 11:720. link

  • Ashkenazy H, Sela I, Levy Karin E, Landan G, Pupko T. 2019. Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction. Syst Biol. 68(1):117-130. link

  • Kaminski Strauss S, Schirman D, Jona G, Brooks AN, Kunjapur AM, Nguyen Ba AN, Flint A, Solt A, Mershin A, Dixit A, Yona AH, Csörgő B, Busby BP, Hennig BP, Pál C, Schraivogel D, Schultz D, Wernick DG, Agashe D, Levi D, Zabezhinsky D, Russ D, Sass E, Tamar E, Herz E, Levy ED, Church GM, Yelin I, Nachman I, Gerst JE, Georgeson JM, Adamala KP, Steinmetz LM, Rübsam M, Ralser M, Klutstein M, Desai MM, Walunjkar N, Yin N, Aharon Hefetz N, Jakimo N, Snitser O, Adini O, Kumar P, Soo Hoo Smith R, Zeidan R, Hazan R, Rak R, Kishony R, Johnson S, Nouriel S, Vonesch SC, Foster S, Dagan T, Wein T, Karydis T, Wannier TM, Stiles T, Olin-Sandoval V, Mueller WF, Bar-On YM, Dahan O, Pilpel Y. Evolthon: A community endeavor to evolve lab evolution. PLoS Biol. 2019. 17(3):e3000182. link

  • Johnsen U, Reinhardt A, Landan G, Tria FDK, Turner JM, Davies C, Schönheit P. 2019. New views on an old enzyme: allosteric regulation and evolution of archaeal pyruvate kinases. FEBS J. 286(13):2471-2489. link
    Journal cover

  • Wein T, Hülter NF, Mizrahi I, Dagan T. 2019. Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance. Nat Commun. 10(1):2595. link

  • Wein T, Romero Picazo D, Blow F, Woehle C, Jami E, Reusch TBH, Martin WF, Dagan T. Currency, exchange, and inheritance in the evolution of symbiosis.
    Trends Microbiol. 2019. doi:10.1016/j.tim.2019.05.010. link

  • Hassani MA, Özkurt E, Seybold H, Dagan T, Stukenbrock EH. Interactions and coadaptation in plant metaorganisms. Annu Rev Phytopathol. 2019. doi:10.1146/annurev-phyto-082718-100008. link

  • Hammerschmidt K, Landan G, Tria FDK, Dagan T. 2019. A chronology of multicellularity evolution in cyanobacteria. bioRxiv: 570788. link

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  • Glock N, Roy A-S, Romero D, Wein T, Weissenbach J, Revsbech NP, Høgslund S, Clemens D, Sommer S, Dagan T. 2019. Metabolic preference of nitrate over oxygen as an electron acceptor in Foraminifera from the Peruvian oxygen minimum zone. PNAS link
    Pressemitteilung
    Press release

  • Ilhan J, Kupczok A, Woehle C, Wein T, Hülter NF, Rosenstiel P, Landan G, Mizrahi I, Dagan T. 2019. Segregational drift and the interplay between plasmid copy number and evolvability, Mol Biol Evol 36(3):472–486. link

  • Svetlitsky D, Dagan T, Chalifa-Caspi V, Ziv-Ukelson M. 2019. CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes. Bioinformatics 265:11436. link

  • Wolf S, Fischer MA, Kupczok A, Reetz J, Kern T, Schmitz RA, Rother M. 2019. Characterization of the lytic archaeal virus Drs3 infecting Methanobacterium formicicum. Arch Virol. 164:667–674. link

Publications 2018

  • Godfroid M, Dagan T, Kupczok A. 2018. Recombination signal in Mycobacterium tuberculosis stems from reference-guided assemblies and alignment artefacts. Genome Biol Evol 10:1920–1926. link

  • Wöhle C, Roy AS, Glock N, Wein T, Weissenbach J, Rosenstiel P, Hiebenthal C, Michels J, Schönfeld J, Dagan T. 2018. A novel eukaryotic denitrification pathway in foraminifera. Curr Biol, 28:2536–2543.e5. link
    Pressemitteilung
    Press release

  • Bang C, Dagan T, Deines P, Dubilier N, Duschl WJ, Fraune S, Hentschel U, Hirt H, Hülter N, Lachnit T, Picazo D, Pita L, Pogoreutz C, Rädecker N, Saad MM, Schmitz RA, Schulenburg H, Voolstra CR, Weiland-Bräuer N, Ziegler M, Bosch TCG. 2018. Metaorganisms in extreme environments: do microbes play a role in organismal adaptation? Zoology (Jena) 127:1–19. link

  • Wein T, Dagan T, Fraune S, Bosch TCG, Reusch TBH, Hülter NF. 2018. Carrying Capacity and Colonization Dynamics of Curvibacter in the Hydra Host Habitat. Front. Microbiol. 9:185–10. link

  • Kupczok A, Neve H, Huang KD, Hoeppner MP, Heller KJ, Franz CMAP, Dagan T. 2018. Rates of mutation and recombination in Siphoviridae phage genome evolution over three decades. Mol Biol Evol 35(5): 1147–1159. link
    Pressemitteilung

Publications 2017

  • Weidenbach K, Nickel L, Neve H, Alkhnbashi OS, Künzel S, Kupczok A, Bauersachs T, Cassidy L, Tholey A, Backofen R, Schmitz RA. 2017. MetSV, a novel archaeal lytic virus targeting Methanosarcina strains. J. Virol. 91:e00955-17. Pubmed

  • Koch R, Kupczok A, Stucken K, Ilhan J, Hammerschmidt K, Dagan T. 2017. Plasticity first: molecular signatures of a complex morphological trait in filamentous cyanobacteria. BMC Evolutionary Biology 17:209. Pubmed

  • Tria FDK, Landan G, Dagan T. 2017. Phylogenetic rooting using minimal ancestor deviation. Nat Ecol Evol 1:193. Pubmed
    Pressemitteilung
    Press release

  • Woehle C, Dagan T, Landan G, Vardi A, Rosenwasser S. 2017. Expansion of the redox-sensitive proteome coincides with the plastid endosymbiosis. Nat Plants 3:17066. Pubmed
    Pressemitteilung
    Press release

  • Hülter N, Ilhan J, Wein T, Kadibalban AS, Hammerschmidt K, Dagan T. 2017. An evolutionary perspective on plasmid lifestyle modes. Curr. Opin. Microbiol. 38:74–80. Pubmed

  • Hülter N, Sørum V, Borch-Pedersen K, Liljegren MM, Utnes ALG, Primicerio R, Harms K, Johnsen PJ. 2017. Costs and benefits of natural transformation in Acinetobacter baylyi. BMC Microbiol. 17:34. Pubmed

  • Weissenbach J, Ilhan J, Bogumil D, Hülter N, Stucken K, Dagan T. 2017. Evolution of Chaperonin Gene Duplication in Stigonematalean Cyanobacteria (Subsection V). Genome Biol Evol. evw287. Pubmed

  • Popa O, Landan G, Dagan T. 2017. Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction. The ISME Journal 11:543–554. Pubmed

  • Ribeiro ÂM, Foote AD, Kupczok A, Frazão B, Limborg MT, Piñeiro R, Abalde S, Rocha S, da Fonseca RR. 2017. Marine genomics: News and views. Mar Genomics. 31:1-8. Pubmed

Publications 2016

  • Harms K, Lunnan A, Hülter N, Mourier T, Vinner L, Andam CP, Marttinen P, Fridholm H, Hansen AJ, Hanage WP, Nielsen KM, Willerslev E, Johnsen PJ. 2016. Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms. Proc. Natl. Acad. Sci. 113(52): 15066-15071. Pubmed

  • McLeman A, Sierocinski P, Hesse E, Buckling A, Perron G, Hülter N, Johnsen PJ, Vos M. 2016. No effect of natural transformation on the evolution of resistance to bacteriophages in the Acinetobacter baylyi model system. Sci. Rep. 6:37144. Pubmed

  • Kadibelban AS, Bogumil D, Landan G, Dagan T. 2016 DnaK-dependent accelerated evolutionary rate in prokaryotes, Genome Biol Evol, 8:1590-1599. Pubmed

 

Publications 2015

  • Ku C, Nelson-Sathi S, Roettger M, Sousa FL, Lockhart PJ, Bryant D, Hazkani-Covo E, McInerney JO, Landan G, Martin WF (2015) Endosymbiotic origin and differential loss of eukaryotic genes, Nature, 524(7566):427-32. Pubmed

  • Rauch C, Vries Jd, Rommel S, Rose LE, Woehle C, Christa G, Laetz EM, Wägele H, Tielens AG, Nickelsen J, Schumann T, Jahns P, Gould SB (2015) Why It Is Time to Look Beyond Algal Genes in Photosynthetic Slugs, Genome Biol Evol, 7(9):2602-7. Pubmed

  • Habicht J, Woehle C, Gould SB (2015) Tetrahymena Expresses More than a Hundred Proteins with Lipid-binding MORN Motifs that can Differ in their Subcellular Localisations, J Eukaryot Microbiol, 62(5):694-700. Pubmed

  • Kupczok A, Landan G, Dagan T (2015) The Contribution of Genetic Recombination to CRISPR Array Evolution, Genome Biol Evol, 7(7):1925-39. Pubmed

  • Thiergart T, Landan G, Martin WF (2015) Concatenated alignments and the case of the disappearing tree, BMC Evol Biol, 14:266. Pubmed

  • Nelson-Sathi S, Sousa FL, Roettger M, Lozada-Chávez N, Thiergart T, Janssen A, Bryant D, Landan G, Schönheit P, Siebers B, McInerney JO, Martin WF (2015) Origins of major archaeal clades correspond to gene acquisitions from bacteria, Nature, 517(7532):77-80. Pubmed

  • Gophna U, Kristensen DM, Wolf YI, Popa O, Drevet C, Koonin EV (2015) No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales, The ISME Journal, 9:2021–2027. Pubmed

 

Publications 2014

  • Dagan T, Bapteste E, McInerney JO, Martin WF (2014) SMBE Satellite meeting on reticulated microbial evolution 2014--meeting report, Genome Biol Evol, 6(9):2206-9. Pubmed

  • Woehle C, Kusdian G, Radine C, Graur D, Landan G, Gould SB (2014) The parasite Trichomonas vaginalis expresses thousands of pseudogenes and long non-coding RNAs independently from functional neighbouring genes, BMC Genomics, 5:906. Pubmed

  • Stucken K, Koch R, Dagan T (2014) Cyanobacterial defense mechanisms against foreign DNA transfer and their impact on genetic engineering, Biol Res, 46(4):373-82. Pubmed

  • Kupczok A, Bollback JP (2014) Motif depletion in bacteriophages infecting hosts with CRISPR systems, BMC Genomics, 15:663. Pubmed

  • Bogumil D, Alvarez-Ponce D, Landan G, McInerney J, Dagan T (2014) Integration of two ancestral chaperone systems into one: the evolution of molecular chaperones in light of eukaryogenesis, Mol Biol Evol, 31(2):410-418. Pubmed

 

Publications 2013

  • Stucken K, Koch R, Dagan T (2013) Cyanobacterial defense mechanisms against foreign DNA transfer and their impact on genetic engeneering, Biol Res 46(4):373-382. Pubmed

  • Dagan T, Roettger M, Stucken K, Landan G, Koch R, Major P, Gould SB, Goremykin VV, Rippka R, Tandeau de Marsac N, Gugger M, Lockhart PJ, Allen JF, Brune I, Maus I, Pühler A, Martin W (2013) Genomes of stigonematalean cyanobacteria (Subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome Biol Evol, 5:31-44. Pubmed

 

Publications 2012

  • Bogumil D, Dagan T (2012) The cumulative impact of chaperone mediated folding on genome evolution. Biochemistry, 51:9941-9953.Pubmed

  • Nelson-Sathi S, Dagan T, Landan G, Janssen A, Steel M, McInerney J, Deppenmeier U, Martin WF (2012) Acquisition of a thousand eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proc Natl Acad Sci USA, in press.Pubmed

  • Martin WF, Hazkani-Covo E, Shavit-Greivink L, Schmitt V, Händeler K, Gould SB, Landan G, Graur D, Dagan T (2012) Gene transfers from organelles to the nucleus: How much, what happens, and why none in Elysia? J Endocytobiosis Cell Res 23:16-20.

  • Martin WF, Roettger M, Kloesges T, Thiergart T, Woehle C, Gould S, Dagan T(2012)Modern endosymbiotic theory: Getting lateral gene transfer into the equation. J Endocytobiosis Cell Res 23:1-5.

  • Bogumil D, Landan G, Ilhan J, Dagan T (2012) Chaperones divide yeast proteins intoclasses of evolutionary rate and expression level, Genome Biol Evol, 4:618-625.Pubmed

  • Stucken K, Ilhan J, Dagan T, Martin W (2012) Transformation and conjugal transfer of foreign genes into the filamentous multicellular cyanobacteria (Subsection V) Fischerella and Chlorogloeopsis. Current Microbiology, in press. Pubmed

  • Heinz E, Williams T, Nakjang S, Noël CJ, Swan DC, Goldberg AV, Harris SR, Weinmaier T, Markert S, Becher D, Dagan T, Schweder T, Rattei T, Hall N, Hirt RP, Embley TM (2012) Trachipleistophora hominis prodives novel insights into reductive genome evolution in eukaryotes, in press.

  • Külzer S, Charnaud S, Riedel J, Mandal P, Dagan T, Crabb BS, Gilson PR, Przyborski JM (2012) An exported chaperone system in P. falciparum infected erythrocytes, in press.Pubmed

  • Thiergart T, Landan G, Schenk M, Dagan T, Martin WF: An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin. Genome Biol Evol 4:466-85 (2012). Pubmed