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Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned? 

A. P. Grygansky, J. Golan, A. Muszewska, A. Idnurm, S. Dolatabadi, S. J. Mondo, V. B. Kutovenko, V. O. Kutovenko, M. T. Gajdeczka, I. M. Anishchenko, J. Pawlowska, N. V. Tran, I. Ebersberger, K. Voigt, Y. Wang, Y. Chang, T. E. Pawlowska, J. Heitman, R. Vilgalys, G. Bonito, G. L. Benny, M. E. Smith, N. Reynolds, T. Y. James, I. V. Grigoriev, J. W. Spatafora, J. E. Stajich

Microorganisms 2023, 11(7), 1830; https://doi.org/10.3390/microorganisms11071830

FUBP1 is a general splicing factor facilitating 3' splice site recognition and splicing of long introns

S. Ebersberger, C. Hipp, M. M. Mulorz, A. Buchbender, D. Hubrich, H. Kang, S. Martinez-Lumbreras, P. Kristofori, R. Sutandy, L. Llacsahuanga Allcca, J. Schönfeld, C. Bakisoglu, A. Busch, H. Hänel, K. Tretow, M. Welzel, A. Di Liddo, M. M. Möckel, K. Zarnack, I. Ebersberger, S. Legewie, K. Luck, M. Sattler, J. König

Molecular Cell (2023), https://doi.org/10.1016/j.molcel.2023.07.002

Better integration of chemical pollution research will further our understanding of biodiversity loss

F. Sylvester, F. G. Weichert, V. L. Lozano, K. J. Groh, M. Bálint, L. Baumann, C. Bässler, W. Brack, B. Brandl, J. Curtius, P. Dierkes, P. Döll, I. Ebersberger, S. Fragkostefanakis, E. J. N. Helfrich, T. Hickler, S. Johann, J. Jourdan, S. Klimpel, H. Kminek, F. Liquin, D. Möllendorf, T. Mueller, J. Oehlmann, R. Ottermanns, S. U. Pauls, M. Piepenbring, J. Pfefferle, G. J. Schenk, J. F. Scheepens, M. Scheringer, S. Schiwy, A. Schlottmann, F. Schneider, L. M. Schulte, M. Schulze-Sylvester, E. Stelzer, F. Strobl, A. Sundermann, K. Tockner, T. Tröger, A. Vilcinskas, C. Völker, R. Winkelmann, H. Hollert

nature ecology & evolution, June 2023, https://doi.org/10.1038/s41559-023-02117-6

Feature architecture aware phylogenetic profiling indicates a functional diversification of type IVa pili in the nosocomial pathogen Acinetobacter baumannii

R. Iruegas, K. Pfefferle, S. Goettig, B. Averhoff, I. Ebersberger

PLOS Genetics, July 27, 2023, https://doi.org/10.1371/journal.pgen.1010646

ncOrtho: Efficient and reliable identification of miRNA orthologs

F. Langschied, M. Leisegang, R. Brandes, I. Ebersberger

Nucleic Acids Research, June 2023, gkad467, https://doi.org/10.1093/nar/gkad467

FAS: Assessing the similarity between proteins using multi-layered feature architectures 

J. Dosch, H. Bergmann, V. Tran, I. Ebersberger

Bioinformatics, April 2023, btad226, https://doi.org/10.1093/bioinformatics/btad226

Endothelial versus pronephron fate decision is modulated by the transcription factors Cloche/Npas4l, Tal1, and Lmo2.

Mattonet, K.; Riemslagh, FW.; Guenther, S.; Prummel, KD.; Kesavan, G.; Hans, S.; Ebersberger, I.; Brand, M.; Burger, A.; Reischauer, S.; Mosimann, C.; Stainier, DYR.

Sci Adv. 2022 Sep 2;8(35):eabn2082. doi: 10.1126/sciadv.abn2082. Epub 2022 Aug 31.

InvL, an Invasin-Like Adhesin, Is a Type II Secretion System Substrate Required for Acinetobacter baumannii Uropathogenesis. 

Jackson-Litteken, CD.; Di Venanzio, G.; Le, NH.; Scott, NE.; Djahanschiri, B.; Distel, JS.; Pardue, EJ.; Ebersberger, I.; Feldman, MF. 

mBio. 2022 Jun 28;13(3):e0025822. doi: 10.1128/mbio.00258-22. Epub 2022 May 31.

Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex

Djahanschiri, B.; Di Venanzio, G.; Distel, J.S.; Breisch, J.; Dieckmann, M. A.; Goesmann, A.; Averhoff, B.; Göttig, S.; Wilharm, G.; Feldman, M.F.; Ebersberger, I.;

PLOS Genetics 2022

doi: https://doi.org/10.1101/2022.01.10.475602

Assembly and Functional Role of PACE Transporter PA2880 from Pseudomonas aeruginosa

Zhao, J.; Hellwig, N.; Djahanschiri, B.; Khera R.; Morgner N.; Ebersberger, I.; Wang , J.; Michel, H.

Microbiol Spectr 2022 Apr 4;e0145321. doi: 10.1128/spectrum.01453-21

The structure of the Aquifex aeolicus MATE family multidrug resistance transporter and sequence comparisons suggest the existence of a new subfamily

Zhao, J.; Xie, H.; Mehdipour, A. R.; Safarian, S.; Ermler, U.; Münke, C.; Thielmann, C.; Hummer, G.; Ebersberger, I.; Wang, J.; Michel, H.

PNAS November 16, 2021 118 (46) e2107335118; https://doi.org/10.1073/pnas.2107335118

Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity

Birikmen, M.; Bohnsack, K. E.; Tran, V.; Somayaji, S.; Bohnsack, M. T.; Ebersberger, I.

Front. Microbiol., 16 September 2021 | https://doi.org/10.3389/fmicb.2021.739000

Ten years of collaborative progress in the Quest for Ortholog

Linard, B.; Ebersberger, I.; McGlynn, S. E.; Glover, N.; Mochizuki, T.; Patricio, M.; Lecompte, O.; Nevers, Y.; QFO Consortium; Thomas, P.D.; Gabaldón, T.; Sonnhammer, E.; Dessimoz, C.; Uchiyama, I.

Molecular Biology and Evolution 2021, msab098, https://doi.org/10.1093/molbev/msab098

Minimized combinatorial CRISPR screens identify genetic interactions in autophagy

Diehl, V.; Wegner, M.; Grumati, P.; Husnjak, K.; Schaubeck, S.; Gubas, A.; Jayeshkumar Shah, V.; Polat, I. H.; Langschied, F.; Prieto-Garcia, C.; Müller, K.; Kalousi, A.; Ebersberger, I.; Brandts, C. H.; Dikic, I.; Kaulich, M.

Nucleic Acids Research, Volume 49, Issue 10, 4 June 2021, Pages 5684–5704, https://doi.org/10.1093/nar/gkab309

Bacterial and Fungal Toll-Like Receptor Activation Elicits Type I IFN Responses in Mast Cells

Kornstädt, L.; Pierre, S.; Weigert, A.; Ebersberger, S.; Schäufele, T. J.; Kolbinger, A.; Schmid, T.; Cohnen, J.; Thomas, D.; Ferreirós, N.; Brüne, B.; Ebersberger, I., Scholich, K.

Front. Immunol. 2021, https://doi.org/10.3389/fimmu.2020.607048

Immune challenge reduces gut microbial diversity and triggers fertility-dependent gene expression changes in a social insect

Negroni, M. A.; Segers, F. H. I. D.; Vogelweith, F.; Foitzik, S.

BMC Genomics volume 21, Article number: 816 (2020)

https://doi.org/10.1186/s12864-020-07191-9

Peptidoglycanediting provides immunity to Acinetobacter baumannii during bacterial warfare

Nguyen, H. L.; Peters, K.; Espaillat, A.; Sheldon, J. R.; Gray, J.; Di Venanzio, G.; Lopez, J.; Djahanschiri, B.; Mueller, E. A.; Hennon, S. W.; Levin, P.-A.; Ebersberger, I.; Skaar, E. P.; Cava, F.; Vollmer, W.; Feldman M. F.;

Sci Adv . 2020 Jul 22;6(30):eabb5614. doi: 10.1126/sciadv.abb5614. eCollection 2020 Jul.

Tek/Tie2 is not required for cardiovascular development in zebrafish

Jiang, Z.; Carlantoni, C.; Allanki, S.; Ebersberger, I.; Stainier, D. Y. R. ;

Development 2020 : dev.193029 doi: 10.1242/dev.193029 Published 14 September 2020

Comparative transcriptomics reveal insights into the drought response of the three Panicum species P. bisulcatum, P. laetum and P. turgidum

Kotrade, P.; Werner, A.; Ebersberger, I.; Brüggemann, W.;

Plant Gene Volume 23, September 2020, https://doi.org/10.1016/j.plgene.2020.100232

Adjustment of photosynthetic activity to drought and fluctuating light in wheat

Grieco, M.; Roustan, R.; Dermendjiev, G.; Rantala, S.;Jain, J.; Leonardelli, M.; Neumann, K.; Berger, V.; Engelmeier, D.; Bachmann, B.; Ebersberger, I.; Aro, E.-M.; Weckwerth, W.; Teige, M.;

Plant Cell Environ. 2020;1–17; https://doi.org/10.1111/pce.13756

What is in Umbilicaria pustulata? A metagenomic approach to reconstruct the holo-genome of a lichen 

Greshake Tzovaras, B.; Segers, F.; Bicker,  A.; Dal Grande, F.; Otte, J.; Yahya Anvar, S.; Hankeln, T.; Schmitt, I.; Ebersberger, I.;

Genome Biology and Evolution 2020, eva0049, https://doi.org/10.1093/gbe/evaa049

The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation

Hildebrandt, A.; Brüggemann, M.; Rücklé, C.; Boerner, S.; Heidelberger, J. B.; Busch, A.; Hänel, H.; Voigt, A.; Möckel, M. M.; Ebersberger, S.; Scholz, A.; Dold, A.; Schmid, T.; Ebersberger, I.; Roignant, J.Y.; Zarnack, K.; König, J.; Beli, P.

Genome Biology volume 20, Article number: 216 (2019)

Advances and Applications in the Quest for Orthologs.

Glover N.; Dessimoz C.; Ebersberger I.; Forslund SK.; Gabaldón T.; Huerta-Cepas J.; Martin MJ.; Muffato M.; Patricio M.; Pereira C.; Sousa da Silva A.; Wang Y.; Sonnhammer E.; Thomas PD.; Quest for Orthologs Consortium.

Mol Biol Evol. 2019 Oct 1;36(10):2157-2164. doi: 10.1093/molbev/msz150.#

Identification of the novel class D β-lactamase OXA-679 involved in carbapenem resistance in Acinetobacter calcoaceticus

Tietgen, M.; Kramer, JS.; Brunst, S.; Djahanschiri, B.; Wohra, S.; Higgins, PG.; Weidensdorfer, M.; Riedel-Christ, S.; Pos, KM.; Gonzaga, A.; Steglich, M.; Nübel, U.; Ebersberger, I.; Proschak, E.; Göttig, S.

J Antimicrob Chemother. 2019 Jun 1;74(6):1494-1502. doi: 10.1093/jac/dkz080.

Apoptotic tumor cell-derived microRNA-375 uses CD36 to alter the tumor-associated macrophage phenotype

Frank, AC.; Ebersberger, S.; Fink, AF.; Lampe, S.; Weigert, A.; Schmid, T.; Ebersberger, I.; Syed, SN.; Brüne, B.

Nat Commun. 2019 Mar 8;10(1):1135. doi: 10.1038/s41467-019-08989-2.

Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

Linker, SM.; Urban, L.; Clark, SJ.; Chhatriwala, M.; Amatya, S.; McCarthy, DJ.; Ebersberger, I.; Vallier, L.; Reik, W.; Stegle, O1.;, Bonder, MJ.

Genome Biol. 2019 Feb 11;20(1):30. doi: 10.1186/s13059-019-1644-0.

The Acinetobacter trimeric autotransporter adhesin Ata controls key virulence traits of Acinetobacter baumannii

Weidensdorfer, M.; Ishikawa, M.; Hori, K.; Linke, D.; Djahanschiri, B.; Iruegas, R.; Ebersberger, I.; Riedel-Christ, S.; Enders, G.; Leukert, L.; Kraiczy, P.; Rothweiler, F.; Cinatl, J.; Berger, J.; Hipp, K.; Kempf, V. A. J.; Göttig, S.

Virulence 2019, Jan, Pages 68-81, doi.org/10.1080/21505594.2018.1558693

The evolutionary traceability of a protein

Jain, A.; Persia, D.; Fliedner, F.; von Haesseler, A.; Ebersberger, I.

Genome Biol Evol. 2019 Feb 1;11(2):531-545. doi: 10.1093/gbe/evz008.

HEATSTER: A Database and Web Server for Identification and Classification of Heat Stress Transcription Factors in Plants.

Berz, J.; Simm, S.; Schuster, S.; Scharf, K.D.; Schleiff, E.; Ebersberger, I.

Bioinform Biol Insights. 2019 Jan 7;13:1177932218821365. doi: 10.1177/1177932218821365. eCollection 2019.

IL-6 augments IL-4-induced polarization of primary human macrophages through synergy of STAT3, STAT6 and BATF transcription factors

Conserved Gene Microsynteny Unveils Functional Interaction Between Protein Disulfide Isomerase and Rho Guanine-Dissociation Inhibitor Families

Moretti, A. I. S.; Pavanelli, J. C.; Nolasco, P.; Leisegang, M. S.; Tanaka, L. Y.; Fernandes, C. G.; Wosniak Jr, J.; Kajihara, D.; Dias, M. H.; Fernandes, D. C.; Jo, H.; Tran, N. V.; Ebersberger, I.; Brandes, R. P.; Bonatto, D.; Laurindo, F. R. M.

Scientific Reports 2017 Dec 8;7(1):17262. doi: 10.1038/s41598-017-16947-5.

Gearing up to handle the mosaic nature of life in the quest for orthologs

Forslund, K.; Pereira, C.; Capella-Gutierrez, S.; Sousa da Silva, A.; Altenhoff, A.; Huerta-Cepas, J.; Muffato, M.; Patricio, M.; Vandepoele, K.; Ebersberger, I.; Blake, J.; Breis, J.T.F.

The Quest for Orthologs Consortium: Boeckmann, B.; Gabaldón, T.; Sonnhammer, E.; Dessimoz, C.; Lewis, S.

Bioinformatics. 2018 Jan 15;34(2):323-329. doi: 10.1093/bioinformatics/btx542.

Natural product diversity associated with the nematode symbionts Photorhabdus and Xenorhabdus

Tobias, N.;  Wolff, H.;  Djahanschiri, B.;  Grundmann, F.;  Kronenwerth, M.;  Shi, Y.;  Simonyi, S.;  Grün, P.;  Shapiro-Ilan, D.;  Pidot, S.;  Stinear, T.;  Ebersberger, I.;  Bode, H.

Nat Microbiol. 2017 Dec;2(12):1676-1685. doi: 10.1038/s41564-017-0039-9. Epub 2017 Oct 9.

The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet.

Liu, H.; Chen, C.; Gao, Z.; Min, J.; Gu, Y.; Jian, J.; Jiang, X.; Cai, H.; Ebersberger, I.; Xu, M.; Zhang, X.; Chen, J.; Luo, W.; Chen, B.; Chen, J.; Liu, H.; Li, J.; Lai, R.; Bai, M.; Wei, J.; Yi, S.; Wang, H.; Cao, X.; Zhou, X.; Zhao, Y.; Wei, K.; Yang, R.; Liu, B.; Zhao, S.; Fang, X.; Schartl, M.; Qian, X.; Wang, W.

Gigascience. 2017 Jul 1;6(7):1-13. doi: 10.1093/gigascience/gix039.

An annotated draft genome for Radix auricularia (Gastropoda, Mollusca)

Schell, T.; Feldmeyer, B.; Schmidt, H.; Greshake, B.; Tills, O.; Truebano, M.; Rundle, SD.; Paule, J.; Ebersberger, I.; Pfenninger, M.;

Genome Biology and Evolution, Volume 9, Issue 3, March 2017, Pages 585–592, https://doi.org/10.1093/gbe/evx032

Characterization of microsatellite loci in the lichen-forming fungus Cetraria aculeata (Parmeliaceae, Ascomycota).

Lutsak, T.; Fernández-Mendoza, F.; Greshake, B.; Dal Grande, F.; Ebersberger, I.; Ott, S.; Printzen, C.

Appl Plant Sci. 2016 Sep 19;4(9). pii: apps.1600047. doi: 10.3732/apps.1600047.

An evolutionary perspective of AMPK-TOR signaling in the three domains of life

Roustan, V.; Jain, A.; Teige, M.; Ebersberger, I.; Weckwerth, W.;

Acinetobacter equi sp. nov. isolated from horse faeces

Poppel, M.T.; Skiebe, E.; Laue, M.; Bergmann, H.; Ebersberger, I.; Garn, T.; Fruth, A.; Baumgardt, S.; Busse, H.J.; Wilharm, G.;

Int J Syst Evol Microbiol. 2015 Nov 30. doi: 10.1099/ijsem.0.000806

Acinetobacter baumannii Virulence Is Mediated by the Concerted Action of Three Phospholipases D

Stahl, J.; Bergmann, H.; Göttig, S.; Ebersberger, I.; Averhoff, B.;

PLoS One. 2015; 10(9): e0138360

Potential and pitfalls of eukaryotic metagenome skimming: A test case for lichens.

Greshake, B.; Zehr, S.; Dal Grande, F.; Meiser, A.; Schmitt, I.; Ebersberger, I.;

Mol Ecol Resour. 2015 Sep 8. doi: 10.1111/1755-0998.12463

The association of late-acting snoRNPs with human pre-ribosomal complexes requires the RNA helicase DDX21

Sloan, K. E.; Leisegang, M. S.; Doebele, C.; Ramírez, A. S.; Simm, S.; Safferthal, C.; Kretschmer, J.; Schorge, T.; Markoutsa, S.; Haag, S.; Karas, M.; Ebersberger, I.; Schleiff, E.; Watkins, N. J.; T. Bohnsack, M. T.

Nucl. Acids Res. (January 2015) 43 (1): 553-564

Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

Feldmeyer, B.; Greshake, B.; Funke, E.; Patel, S.; Ebersberger, I.; Pfenninger, M.;

BMC Evolutionary Biology 2015, 15:164 doi:10.1186/s12862-015-0434-x

Higher plant proteins of cyanobacterial origin - are they or are they not preferentially targeted to chloroplasts?

Bayer, R.G.; Köstler, T.; Jain, A.; Stael, S.; Ebersberger, I.; Teige, M.;

Mol Plant. 2014 Dec;7(12):1797-800.

A transcriptome approach to ecdysozoan phylogeny

Borner, J.; Rehm, P.; Schill, R. O.; Ebersberger, I.; Burmester, T.;

Mol Phylogenet Evol. 2014 Nov; 80:79-87

The evolution of the ribosome biogenesis pathway from a yeast perspective

Ebersberger, I.: Simm, S.; Leisegang, M. S.; Schmitzberger, P.; Mirus, O.; von Haeseler, A.; Bohnsack, M. T.; Schleiff, E.;

Nucl. Acids Res. 2014 42: 1509-1523

Transcriptome Data Reveal Syndermatan Relationships and Suggest the Evolution of Endoparasitism in Acanthocephala via an Epizoic Stage

Wey-Fabrizius, A. R.; Herlyn, H.; Rieger, B.; Rosenkranz, D.; Witek, A.; Welch, D. B. M. ; Ebersberger, I.; Hankeln, T.;

PLOS ONE February 10, 2014; DOI: 10.1371/journal.pone.0088618

New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias

Nesnidal, M. P.; Helmkampf, M.; Meyer, A.; Witek, A.; Bruchhaus, I.; Ebersberger, I.; Hankeln, T.; Lieb, B.; Struck, T.H. and Hausdorf, B.;

BMC Evolutionary Biology.2013, 13:253; DOI: 10.1186/10.1186/1471-2148-13-253

Decisive Datasets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

Mol Biol Evol 2013; DOI: 10.1093/molbev/mst196

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and othereukaryotes for analysis of environmental sequencingdata

Bengtsson-Palme, J., Ryberg, M.; Hartmann, M.; Branco, S.; Wang, Z.; Godhe, A.; dee Wit, P.; Sánchez-García, M.; Ebersberger, I.; de Sousa, F.; Amend, A.; Jumpponen, A.; Unterseher, M.; Kristiansson, E.; Abarenkov, K.; Bertrand, Y.; Sanli, K.; Eriksson, K. M.; Vik, U.; Veldre, V.; Nilsson, R. H.

Methods in Ecology and Evolution 2013; DOI: 10.1111/2041-210X.12073

REvolver: Modeling sequence evolution under domain constraints.

Mol Biol Evol 2012; 29(9):2133-45

A Consistent Backbone for the Fungi.

Mol Biol Evol 2012; 29:1319-1334.

Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda.

Mol Biol Evol 2012; 29:1031-1045

The plant heat stress transcription factor (Hsf) family: structure, function and evolution.

Scharf, KD.; Berberich, T.; Ebersberger, I. and Nover, L.;

BBA - Gene Regulatory Mechanisms. 2012; 1819(2):104-19, doi.org/10.1016/j.bbagrm.2011.10.002

Phylogenomic analyses of malaria parasites and evolution of their exported proteins.

Zygomycetes, microsporidia, and the evolutionary ancestry of sex determination.

Genome Biology and Evolution. 2011; 3:186-194

FACT: Functional annotation transfer between proteins with similar feature architecture.

Support for the monophyletic origin of Gnathifera from phylogenomics.

Science. 2009; 325(5938):340-343

Centrin4 coordinates cell and nuclear division in T. brucei.

J Cell Sci. 2008; 121(Pt 9):1538-1546

Targeted deletion of AIF decreases mitochondrial oxidative phosphorylation and protects from obesity and diabetes.

Mol Biol Evol. 2007; 24(10):2266-2276

Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae.

Cracks in the shell–zooming in on eggshell formation in the human parasite Schistosoma mansoni.

A neutral explanation for the correlation of diversity with recombination rates in humans.

Genomewide comparison of DNA sequences between humans and chimpanzees.

A variable intron distribution in globin genes of Chironomus: evidence for recent intron gain.