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2. Coxiella burnetii

Author

Frangoulidis, Dimitrios, Walter, Mathias C., Fasemore, Akinyemi M., Cutler, Sally J., and de Filippis, Ivano, editor

Published
2022
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3. Author Correction: Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

Author

Sipos, György, Prasanna, Arun N, Walter, Mathias C, O’Connor, Eoin, Bálint, Balázs, Krizsán, Krisztina, Kiss, Brigitta, Hess, Jaqueline, Varga, Torda, Slot, Jason, Riley, Robert, Bóka, Bettina, Rigling, Daniel, Barry, Kerrie, Lee, Juna, Mihaltcheva, Sirma, LaButti, Kurt, Lipzen, Anna, Waldron, Rose, Moloney, Nicola M, Sperisen, Christoph, Kredics, László, Vágvölgyi, Csaba, Patrignani, Andrea, Fitzpatrick, David, Nagy, István, Doyle, Sean, Anderson, James B, Grigoriev, Igor V, Güldener, Ulrich, Münsterkötter, Martin, and Nagy, László G

Subjects
Biological Sciences, Genetics, Ecology, Evolutionary biology, Environmental management
Abstract

In the version of this Article originally published, it was incorrectly stated that "16,687 protein-coding genes were inferred for the most recent common ancestor (MRCA) of Armillaria"; the value was incorrect and it should have read "15,787". This has now been corrected.

Published
2018

4. Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

Author

Sipos, György, Prasanna, Arun N, Walter, Mathias C, O’Connor, Eoin, Bálint, Balázs, Krizsán, Krisztina, Kiss, Brigitta, Hess, Jaqueline, Varga, Torda, Slot, Jason, Riley, Robert, Bóka, Bettina, Rigling, Daniel, Barry, Kerrie, Lee, Juna, Mihaltcheva, Sirma, LaButti, Kurt, Lipzen, Anna, Waldron, Rose, Moloney, Nicola M, Sperisen, Christoph, Kredics, László, Vágvölgyi, Csaba, Patrignani, Andrea, Fitzpatrick, David, Nagy, István, Doyle, Sean, Anderson, James B, Grigoriev, Igor V, Güldener, Ulrich, Münsterkötter, Martin, and Nagy, László G

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Armillaria, Fungal Proteins, Genome, Fungal, Proteomics, Sequence Analysis, RNA, Species Specificity, Transcriptome, Ecology, Evolutionary biology, Environmental management
Abstract

Armillaria species are both devastating forest pathogens and some of the largest terrestrial organisms on Earth. They forage for hosts and achieve immense colony sizes via rhizomorphs, root-like multicellular structures of clonal dispersal. Here, we sequenced and analysed the genomes of four Armillaria species and performed RNA sequencing and quantitative proteomic analysis on the invasive and reproductive developmental stages of A. ostoyae. Comparison with 22 related fungi revealed a significant genome expansion in Armillaria, affecting several pathogenicity-related genes, lignocellulose-degrading enzymes and lineage-specific genes expressed during rhizomorph development. Rhizomorphs express an evolutionarily young transcriptome that shares features with the transcriptomes of both fruiting bodies and vegetative mycelia. Several genes show concomitant upregulation in rhizomorphs and fruiting bodies and share cis-regulatory signatures in their promoters, providing genetic and regulatory insights into complex multicellularity in fungi. Our results suggest that the evolution of the unique dispersal and pathogenicity mechanisms of Armillaria might have drawn upon ancestral genetic toolkits for wood-decay, morphogenesis and complex multicellularity.

Published
2017

5. A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem.

Author

Rabe, Franziska, Bosch, Jason, Stirnberg, Alexandra, Guse, Tilo, Bauer, Lisa, Seitner, Denise, Rabanal, Fernando A, Czedik-Eysenberg, Angelika, Uhse, Simon, Bindics, Janos, Genenncher, Bianca, Navarrete, Fernando, Kellner, Ronny, Ekker, Heinz, Kumlehn, Jochen, Vogel, John P, Gordon, Sean P, Marcel, Thierry C, Münsterkötter, Martin, Walter, Mathias C, Sieber, Christian Mk, Mannhaupt, Gertrud, Güldener, Ulrich, Kahmann, Regine, and Djamei, Armin

Subjects
Ustilago, Molecular Biology, Genes, Mating Type, Fungal, Host-Pathogen Interactions, Brachypodium, Brachypodium distachyon, Ustilago bromivora, biotrophic interaction, effector, grass, infectious disease, microbiology, plant biology, plant pathogen, Genes, Mating Type, Fungal, Infectious Diseases, Infection, Biochemistry and Cell Biology
Abstract

Due to their economic relevance, the study of plant pathogen interactions is of importance. However, elucidating these interactions and their underlying molecular mechanisms remains challenging since both host and pathogen need to be fully genetically accessible organisms. Here we present milestones in the establishment of a new biotrophic model pathosystem: Ustilago bromivora and Brachypodium sp. We provide a complete toolset, including an annotated fungal genome and methods for genetic manipulation of the fungus and its host plant. This toolset will enable researchers to easily study biotrophic interactions at the molecular level on both the pathogen and the host side. Moreover, our research on the fungal life cycle revealed a mating type bias phenomenon. U. bromivora harbors a haplo-lethal allele that is linked to one mating type region. As a result, the identified mating type bias strongly promotes inbreeding, which we consider to be a potential speciation driver.

Published
2016

10. Machine Learning Algorithms for Classification of MALDI-TOF MS Spectra from Phylogenetically Closely Related Species Brucella melitensis, Brucella abortus and Brucella suis

Author

Dematheis, Flavia, primary, Walter, Mathias C., additional, Lang, Daniel, additional, Antwerpen, Markus, additional, Scholz, Holger C., additional, Pfalzgraf, Marie-Theres, additional, Mantel, Enrico, additional, Hinz, Christin, additional, Wölfel, Roman, additional, and Zange, Sabine, additional

Published
2022
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14. FlexTaxD: flexible modification of taxonomy databases for improved sequence classification

Author

Sundell, David, primary, Öhrman, Caroline, additional, Svensson, Daniel, additional, Karlsson, Edvin, additional, Brindefalk, Björn, additional, Myrtennäs, Kerstin, additional, Ahlinder, Jon, additional, Antwerpen, Markus H, additional, Walter, Mathias C, additional, Forsman, Mats, additional, Stenberg, Per, additional, and Sjödin, Andreas, additional

Published
2021
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17. FlexTaxD : flexible modification of taxonomy databases for improved sequence classification

Author

Sundell, David, Öhrman, Caroline, Svensson, Daniel, Karlsson, Edvin, Brindefalk, Björn, Myrtennäs, Kerstin, Ahlinder, Jon, Antwerpen, Markus H, Walter, Mathias C, Forsman, Mats, Stenberg, Per, Sjödin, Andreas, Sundell, David, Öhrman, Caroline, Svensson, Daniel, Karlsson, Edvin, Brindefalk, Björn, Myrtennäs, Kerstin, Ahlinder, Jon, Antwerpen, Markus H, Walter, Mathias C, Forsman, Mats, Stenberg, Per, and Sjödin, Andreas

Abstract

The Flexible Taxonomy Database framework provides a method for modification and merging official and custom taxonomic databases to create improved databases. Using such databases will increase accuracy and precision of existing methods to classify sequence reads.

Published
2021
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21. First Phylogenetic Analysis of Malian SARS-CoV-2 Sequences Provides Molecular Insights into the Genomic Diversity of the Sahel Region

Author

Kouriba, Bourema, primary, Dürr, Angela, additional, Rehn, Alexandra, additional, Sangaré, Abdoul Karim, additional, Traoré, Brehima Y., additional, Bestehorn-Willmann, Malena S., additional, Ouedraogo, Judicael, additional, Heitzer, Asli, additional, Sogodogo, Elisabeth, additional, Maiga, Abderrhamane, additional, Walter, Mathias C., additional, Zimmermann, Fee, additional, Wölfel, Roman, additional, and Antwerpen, Markus H., additional

Published
2020
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22. PEDANT covers all complete RefSeq genomes

Author

Walter, Mathias C., Rattei, Thomas, Arnold, Roland, Güldener, Ulrich, Münsterkötter, Martin, Nenova, Karamfilka, Kastenmüller, Gabi, Tischler, Patrick, Wölling, Andreas, Volz, Andreas, Pongratz, Norbert, Jost, Ralf, Mewes, Hans-Werner, and Frishman, Dmitrij

Published
2009

25. Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

Author

Sipos, György; https://orcid.org/0000-0002-6666-1384, Prasanna, Arun N; https://orcid.org/0000-0001-6995-9293, Walter, Mathias C; https://orcid.org/0000-0003-3012-2626, O'Connor, Eoin, Bálint, Balázs, Krizsán, Krisztina, Kiss, Brigitta, Hess, Jaqueline, Varga, Torda, Slot, Jason, Riley, Robert, Bóka, Bettina, Rigling, Daniel, Barry, Kerrie, Lee, Juna, Mihaltcheva, Sirma, LaButti, Kurt, Lipzen, Anna, Waldron, Rose, Moloney, Nicola M, Sperisen, Christoph, Kredics, László, Vágvölgyi, Csaba; https://orcid.org/0000-0003-0009-7773, Patrignani, Andrea, Fitzpatrick, David, Nagy, István, Doyle, Sean, Anderson, James B, Grigoriev, Igor V, Güldener, Ulrich, et al, Sipos, György; https://orcid.org/0000-0002-6666-1384, Prasanna, Arun N; https://orcid.org/0000-0001-6995-9293, Walter, Mathias C; https://orcid.org/0000-0003-3012-2626, O'Connor, Eoin, Bálint, Balázs, Krizsán, Krisztina, Kiss, Brigitta, Hess, Jaqueline, Varga, Torda, Slot, Jason, Riley, Robert, Bóka, Bettina, Rigling, Daniel, Barry, Kerrie, Lee, Juna, Mihaltcheva, Sirma, LaButti, Kurt, Lipzen, Anna, Waldron, Rose, Moloney, Nicola M, Sperisen, Christoph, Kredics, László, Vágvölgyi, Csaba; https://orcid.org/0000-0003-0009-7773, Patrignani, Andrea, Fitzpatrick, David, Nagy, István, Doyle, Sean, Anderson, James B, Grigoriev, Igor V, Güldener, Ulrich, and et al

Abstract

Armillaria species are both devastating forest pathogens and some of the largest terrestrial organisms on Earth. They forage for hosts and achieve immense colony sizes via rhizomorphs, root-like multicellular structures of clonal dispersal. Here, we sequenced and analysed the genomes of four Armillaria species and performed RNA sequencing and quantitative proteomic analysis on the invasive and reproductive developmental stages of A. ostoyae. Comparison with 22 related fungi revealed a significant genome expansion in Armillaria, affecting several pathogenicity-related genes, lignocellulose-degrading enzymes and lineage-specific genes expressed during rhizomorph development. Rhizomorphs express an evolutionarily young transcriptome that shares features with the transcriptomes of both fruiting bodies and vegetative mycelia. Several genes show concomitant upregulation in rhizomorphs and fruiting bodies and share cis-regulatory signatures in their promoters, providing genetic and regulatory insights into complex multicellularity in fungi. Our results suggest that the evolution of the unique dispersal and pathogenicity mechanisms of Armillaria might have drawn upon ancestral genetic toolkits for wood-decay, morphogenesis and complex multicellularity.

Published
2017

29. eggNOG 4.5:a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

Author

Huerta-Cepas, Jaime, Szklarczyk, Damian, Forslund, Kristoffer, Cook, Helen, Heller, Davide, Walter, Mathias C, Rattei, Thomas, Mende, Daniel R, Sunagawa, Shinichi, Kuhn, Michael, Jensen, Lars Juhl, von Mering, Christian, Bork, Peer, Huerta-Cepas, Jaime, Szklarczyk, Damian, Forslund, Kristoffer, Cook, Helen, Heller, Davide, Walter, Mathias C, Rattei, Thomas, Mende, Daniel R, Sunagawa, Shinichi, Kuhn, Michael, Jensen, Lars Juhl, von Mering, Christian, and Bork, Peer

Abstract

eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. Developments since the latest public release include changes to the algorithm for creating OGs across taxonomic levels, making nested groups hierarchically consistent. This allows for a better propagation of functional terms across nested OGs and led to the novel annotation of 95 890 previously uncharacterized OGs, increasing overall annotation coverage from 67% to 72%. The functional annotations of OGs have been expanded to also provide Gene Ontology terms, KEGG pathways and SMART/Pfam domains for each group. Moreover, eggNOG now provides pairwise orthology relationships within OGs based on analysis of phylogenetic trees. We have also incorporated a framework for quickly mapping novel sequences to OGs based on precomputed HMM profiles. Finally, eggNOG version 4.5 incorporates a novel data set spanning 2605 viral OGs, covering 5228 proteins from 352 viral proteomes. All data are accessible for bulk downloading, as a web-service, and through a completely redesigned web interface. The new access points provide faster searches and a number of new browsing and visualization capabilities, facilitating the needs of both experts and less experienced users. eggNOG v4.5 is available at http://eggnog.embl.de.

Published
2016

30. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

Author

Huerta-Cepas, Jaime, Szklarczyk, Damian, Forslund, Kristoffer, Cook, Helen, Heller, Davide, Walter, Mathias C, Rattei, Thomas, Mende, Daniel R, Sunagawa, Shinichi, Kuhn, Michael, Jensen, Lars Juhl, von Mering, Christian; https://orcid.org/0000-0001-7734-9102, Bork, Peer, Huerta-Cepas, Jaime, Szklarczyk, Damian, Forslund, Kristoffer, Cook, Helen, Heller, Davide, Walter, Mathias C, Rattei, Thomas, Mende, Daniel R, Sunagawa, Shinichi, Kuhn, Michael, Jensen, Lars Juhl, von Mering, Christian; https://orcid.org/0000-0001-7734-9102, and Bork, Peer

Abstract

eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. Developments since the latest public release include changes to the algorithm for creating OGs across taxonomic levels, making nested groups hierarchically consistent. This allows for a better propagation of functional terms across nested OGs and led to the novel annotation of 95 890 previously uncharacterized OGs, increasing overall annotation coverage from 67% to 72%. The functional annotations of OGs have been expanded to also provide Gene Ontology terms, KEGG pathways and SMART/Pfam domains for each group. Moreover, eggNOG now provides pairwise orthology relationships within OGs based on analysis of phylogenetic trees. We have also incorporated a framework for quickly mapping novel sequences to OGs based on precomputed HMM profiles. Finally, eggNOG version 4.5 incorporates a novel data set spanning 2605 viral OGs, covering 5228 proteins from 352 viral proteomes. All data are accessible for bulk downloading, as a web-service, and through a completely redesigned web interface. The new access points provide faster searches and a number of new browsing and visualization capabilities, facilitating the needs of both experts and less experienced users. eggNOG v4.5 is available at http://eggnog.embl.de.

Published
2016

32. Author response: A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem

Author

Rabe, Franziska, primary, Bosch, Jason, additional, Stirnberg, Alexandra, additional, Guse, Tilo, additional, Bauer, Lisa, additional, Seitner, Denise, additional, Rabanal, Fernando A, additional, Czedik-Eysenberg, Angelika, additional, Uhse, Simon, additional, Bindics, Janos, additional, Genenncher, Bianca, additional, Navarrete, Fernando, additional, Kellner, Ronny, additional, Ekker, Heinz, additional, Kumlehn, Jochen, additional, Vogel, John P, additional, Gordon, Sean P, additional, Marcel, Thierry C, additional, Münsterkötter, Martin, additional, Walter, Mathias C, additional, Sieber, Christian MK, additional, Mannhaupt, Gertrud, additional, Güldener, Ulrich, additional, Kahmann, Regine, additional, and Djamei, Armin, additional

Published
2016
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34. Genome sequence of Coxiella burnetii strain Namibia

Author

Walter, Mathias C, Öhrman, Caroline, Myrtennäs, Kerstin, Sjödin, Andreas, Byström, Mona, Larsson, Pär, Macellaro, Anna, Forsman, Mats, and Frangoulidis, Dimitrios

Subjects
ddc
Published
2013

35. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

Author

Huerta-Cepas, Jaime, primary, Szklarczyk, Damian, additional, Forslund, Kristoffer, additional, Cook, Helen, additional, Heller, Davide, additional, Walter, Mathias C., additional, Rattei, Thomas, additional, Mende, Daniel R., additional, Sunagawa, Shinichi, additional, Kuhn, Michael, additional, Jensen, Lars Juhl, additional, von Mering, Christian, additional, and Bork, Peer, additional

Published
2015
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36. Genome sequence of Coxiella burnetii strain Namibia

Author

Walter, Mathias C, primary, Öhrman, Caroline, additional, Myrtennäs, Kerstin, additional, Sjödin, Andreas, additional, Byström, Mona, additional, Larsson, Pär, additional, Macellaro, Anna, additional, Forsman, Mats, additional, and Frangoulidis, Dimitrios, additional

Published
2014
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39. Microevolution of the Chromosomal Region of Acute Disease Antigen A (adaA) in the Query (Q) Fever Agent Coxiella burnetii

Author

Frangoulidis, Dimitrios, primary, Splettstoesser, Wolf D., additional, Landt, Olfert, additional, Dehnhardt, Jasmin, additional, Henning, Klaus, additional, Hilbert, Angela, additional, Bauer, Tilman, additional, Antwerpen, Markus, additional, Meyer, Hermann, additional, Walter, Mathias C., additional, and Knobloch, Johannes K.-M., additional

Published
2013
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41. Genome sequence of Coxiella burnetii strain Namibia

Author

Walter, Mathias C, Öhrman, Caroline, Myrtennäs, Kerstin, Sjödin, Andreas, Byström, Mona, Larsson, Pär, Macellaro, Anna, Forsman, Mats, and Frangoulidis, Dimitrios

Subjects
Next generation sequencing (NGS), Coxiella burnetii, Whole genome sequencing, Annotation, Assembly, Q fever, Whole genome amplification, Coxiella Burnetii, Next Generation Sequencing (ngs), Q Fever, Whole Genome Amplification, Whole Genome Sequencing, Short Genome Report
Abstract

We present the whole genome sequence and annotation of the Coxiella burnetii strain Namibia. This strain was isolated from an aborting goat in 1991 in Windhoek, Namibia. The plasmid type QpRS was confirmed in our work. Further genomic typing placed the strain into a unique genomic group. The genome sequence is 2,101,438bp long and contains 1,979 protein-coding and 51 RNA genes, including one rRNA operon. To overcome the poor yield from cell culture systems, an additional DNA enrichment with whole genome amplification (WGA) methods was applied. We describe a bioinformatics pipeline for improved genome assembly including several filters with a special focus on WGA characteristics.

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42. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.

Author

Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, and Bork P

Subjects
Algorithms, Archaeal Proteins chemistry, Bacterial Proteins chemistry, Eukaryota, Phylogeny, Proteome chemistry, Viral Proteins chemistry, Databases, Protein, Molecular Sequence Annotation, Sequence Analysis, Protein
Abstract

eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. Developments since the latest public release include changes to the algorithm for creating OGs across taxonomic levels, making nested groups hierarchically consistent. This allows for a better propagation of functional terms across nested OGs and led to the novel annotation of 95 890 previously uncharacterized OGs, increasing overall annotation coverage from 67% to 72%. The functional annotations of OGs have been expanded to also provide Gene Ontology terms, KEGG pathways and SMART/Pfam domains for each group. Moreover, eggNOG now provides pairwise orthology relationships within OGs based on analysis of phylogenetic trees. We have also incorporated a framework for quickly mapping novel sequences to OGs based on precomputed HMM profiles. Finally, eggNOG version 4.5 incorporates a novel data set spanning 2605 viral OGs, covering 5228 proteins from 352 viral proteomes. All data are accessible for bulk downloading, as a web-service, and through a completely redesigned web interface. The new access points provide faster searches and a number of new browsing and visualization capabilities, facilitating the needs of both experts and less experienced users. eggNOG v4.5 is available at http://eggnog.embl.de., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2016
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