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52. Comparative genomics and the nature of placozoan species

Author

Eitel, Michael, primary, Francis, Warren R., additional, Varoqueaux, Frédérique, additional, Daraspe, Jean, additional, Osigus, Hans-Jürgen, additional, Krebs, Stefan, additional, Vargas, Sergio, additional, Blum, Helmut, additional, Williams, Gray A., additional, Schierwater, Bernd, additional, and Wörheide, Gert, additional

Published
2018
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53. Structural Optimization of a Pyridinylimidazole Scaffold: Shifting the Selectivity from p38α Mitogen-Activated Protein Kinase to c-Jun N-Terminal Kinase 3

Author

Ansideri, Francesco, primary, Macedo, Joana T., additional, Eitel, Michael, additional, El-Gokha, Ahmed, additional, Zinad, Dhafer S., additional, Scarpellini, Camilla, additional, Kudolo, Mark, additional, Schollmeyer, Dieter, additional, Boeckler, Frank M., additional, Blaum, Bärbel S., additional, Laufer, Stefan A., additional, and Koch, Pierre, additional

Published
2018
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59. Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA)

Author

Voolstra, Christian CR, Coddington, Jonathan, Collins, Timothy, Crandall, Keith, Dahl, Mikael, Distel, Daniel, Dunn, Casey, Eitel, Michael, Flot, Jean-François, Giribet, Gonzalo, Ghiselli, Fabrizio, Adamski, Marcin, Haddock, Steven, Kocot, Kevin, Liew, Yi Jin, Majeske, Audrey, Misof, Bernhard, Mungal, Christopher, O'Brien, Stephen J., Ravasi, Timothy, de Freitas Rebelo, Mauro, Riesgo, Ana, Agrawal, Shobhit, Schnitzler, Christine, Schulze, Anja, Swalla, Billie, Tagu, Denis, Toonen, Robert, da Silva, Marcela Uliano, Vargas, Sergio, Zhou, Xin, Wörheide, Gert, Lopez, Jose J.V., Antunes, Agostinho, Aranda, Manuel, Baxevanis, Andy, Blaxter, Mark, Bosch, Thomas, Bracken-Grissom, Heather, Voolstra, Christian CR, Coddington, Jonathan, Collins, Timothy, Crandall, Keith, Dahl, Mikael, Distel, Daniel, Dunn, Casey, Eitel, Michael, Flot, Jean-François, Giribet, Gonzalo, Ghiselli, Fabrizio, Adamski, Marcin, Haddock, Steven, Kocot, Kevin, Liew, Yi Jin, Majeske, Audrey, Misof, Bernhard, Mungal, Christopher, O'Brien, Stephen J., Ravasi, Timothy, de Freitas Rebelo, Mauro, Riesgo, Ana, Agrawal, Shobhit, Schnitzler, Christine, Schulze, Anja, Swalla, Billie, Tagu, Denis, Toonen, Robert, da Silva, Marcela Uliano, Vargas, Sergio, Zhou, Xin, Wörheide, Gert, Lopez, Jose J.V., Antunes, Agostinho, Aranda, Manuel, Baxevanis, Andy, Blaxter, Mark, Bosch, Thomas, and Bracken-Grissom, Heather

Abstract

The Global Invertebrate Genomics Alliance (GIGA), a collaborative network of diverse scientists, marked its second anniversary with a workshop in Munich, Germany in 2015, where international attendees focused on discussing current progress, milestones and bioinformatics resources. The community determined the recruitment and training of talented researchers as one of the most pressing future needs and identified opportunities for network funding. GIGA also promotes future research efforts to prioritise taxonomic diversity and create new synergies. Here, we announce the generation of a central and simple data repository portal with a wide coverage of available sequence data, via the compagen platform, in parallel with more focused and specialised organism databases to globally advance invertebrate genomics. This article serves the objectives of GIGA by disseminating current progress and future prospects in the science of invertebrate genomics with the aim of promotion and facilitation of interdisciplinary and international research., SCOPUS: er.j, SCOPUS: re.j, info:eu-repo/semantics/published

Published
2017

62. High-Quality Draft Genome Sequence of the Actinobacterium Nocardia terpenica IFM 0406, Producer of the Immunosuppressant Brasilicardins, Using Illumina and PacBio Technologies

Author

Buchmann, Anina, primary, Eitel, Michael, additional, Koch, Pierre, additional, Schwarz, Paul N., additional, Stegmann, Evi, additional, Wohlleben, Wolfgang, additional, Wolański, Marcin, additional, Krawiec, Michał, additional, Zakrzewska-Czerwińska, Jolanta, additional, Méndez, Carmen, additional, Botas, Alma, additional, Núñez, Luz Elena, additional, Morís, Francisco, additional, Cortés, Jesus, additional, and Gross, Harald, additional

Published
2016
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65. Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, CandidatusAquarickettsia rohweri, gen. nov., sp. nov

Author

Klinges, J Grace, Rosales, Stephanie M, McMinds, Ryan, Shaver, Elizabeth C, Shantz, Andrew A, Peters, Esther C, Eitel, Michael, Wörheide, Gert, Sharp, Koty H, Burkepile, Deron E, Silliman, Brian R, and Vega Thurber, Rebecca L

Abstract

Bacterial symbionts are integral to the health and homeostasis of invertebrate hosts. Notably, members of the Rickettsiales genus Wolbachiainfluence several aspects of the fitness and evolution of their terrestrial hosts, but few analogous partnerships have been found in marine systems. We report here the genome, phylogenetics, and biogeography of a ubiquitous and novel Rickettsiales species that primarily associates with marine organisms. We previously showed that this bacterium was found in scleractinian corals, responds to nutrient exposure, and is associated with reduced host growth and increased mortality. This bacterium, like other Rickettsiales, has a reduced genome indicative of a parasitic lifestyle. Phylogenetic analysis places this Rickettsiales within a new genus we define as “CandidatusAquarickettsia.” Using data from the Earth Microbiome Project and SRA databases, we also demonstrate that members of “Ca. Aquarickettsia” are found globally in dozens of invertebrate lineages. The coral-associated “CandidatusA. rohweri” is the first finished genome in this new clade. “Ca. A. rohweri” lacks genes to synthesize most sugars and amino acids but possesses several genes linked to pathogenicity including Tlc, an antiporter that exchanges host ATP for ADP, and a complete Type IV secretion system. Despite its inability to metabolize nitrogen, “Ca. A. rohweri” possesses the NtrY-NtrX two-component system involved in sensing and responding to extracellular nitrogen. Given these data, along with visualization of the parasite in host tissues, we hypothesize that “Ca. A. rohweri” reduces coral health by consuming host nutrients and energy, thus weakening and eventually killing host cells. Last, we hypothesize that nutrient enrichment, which is increasingly common on coral reefs, encourages unrestricted growth of “Ca. A. rohweri” in its host by providing abundant N-rich metabolites to be scavenged.

Published
2019
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78. Correction: Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov (The ISME Journal, (2019), 13, 12, (2938-2953), 10.1038/s41396-019-0482-0)

Author

Klinges, J. Grace, Rosales, Stephanie M., McMinds, Ryan, Shaver, Elizabeth C., Shantz, Andrew A., Peters, Esther C., Eitel, Michael, Wörheide, Gert, Sharp, Koty H., Burkepile, Deron E., Silliman, Brian R., Thurber, Rebecca L.Vega, Klinges, J. Grace, Rosales, Stephanie M., McMinds, Ryan, Shaver, Elizabeth C., Shantz, Andrew A., Peters, Esther C., Eitel, Michael, Wörheide, Gert, Sharp, Koty H., Burkepile, Deron E., Silliman, Brian R., and Thurber, Rebecca L.Vega

79. Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov

Author

Klinges, J. Grace, Rosales, Stephanie M., McMinds, Ryan, Shaver, Elizabeth C., Shantz, Andrew A., Peters, Esther C., Eitel, Michael, Wörheide, Gert, Sharp, Koty H., Burkepile, Deron E., Silliman, Brian R., Vega Thurber, Rebecca L., Klinges, J. Grace, Rosales, Stephanie M., McMinds, Ryan, Shaver, Elizabeth C., Shantz, Andrew A., Peters, Esther C., Eitel, Michael, Wörheide, Gert, Sharp, Koty H., Burkepile, Deron E., Silliman, Brian R., and Vega Thurber, Rebecca L.

80. Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov

Author

Klinges, J. Grace, Rosales, Stephanie M., McMinds, Ryan, Shaver, Elizabeth C., Shantz, Andrew A., Peters, Esther C., Eitel, Michael, Wörheide, Gert, Sharp, Koty H., Burkepile, Deron E., Silliman, Brian R., Vega Thurber, Rebecca L., Klinges, J. Grace, Rosales, Stephanie M., McMinds, Ryan, Shaver, Elizabeth C., Shantz, Andrew A., Peters, Esther C., Eitel, Michael, Wörheide, Gert, Sharp, Koty H., Burkepile, Deron E., Silliman, Brian R., and Vega Thurber, Rebecca L.

81. Correction: Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov (The ISME Journal, (2019), 13, 12, (2938-2953), 10.1038/s41396-019-0482-0)

Author

Klinges, J. Grace, Rosales, Stephanie M., McMinds, Ryan, Shaver, Elizabeth C., Shantz, Andrew A., Peters, Esther C., Eitel, Michael, Wörheide, Gert, Sharp, Koty H., Burkepile, Deron E., Silliman, Brian R., Thurber, Rebecca L.Vega, Klinges, J. Grace, Rosales, Stephanie M., McMinds, Ryan, Shaver, Elizabeth C., Shantz, Andrew A., Peters, Esther C., Eitel, Michael, Wörheide, Gert, Sharp, Koty H., Burkepile, Deron E., Silliman, Brian R., and Thurber, Rebecca L.Vega

88. Improving genome assemblies of non-model non-vertebrate animals with long reads and Hi-C

Author

Guiglielmoni, Nadege, Flot, Jean-François, Koszul, Romain, Mardulyn, Patrick, Smits, Guillaume, Eitel, Michael, and McCartney, Ann

Subjects
Genome assembly, Non-vertebrate animals, Hi-C, Sciences bio-médicales et agricoles, Long reads
Abstract

The corpus of reference genomes is rapidly expanding as more and more genome assemblies are released for a wide variety of species. The constant progress in sequencing technologies has led to the release in 2021 of a first complete, telomere-to-telomere, gap-less assembly of a human genome, yet a myriad of eukaryote species still lack genomic resources. For animals, genomic projects have focused on species closely related to humans (vertebrates) and those with an impact on health and agriculture. By contrast, there is still a dearth of non-vertebrate genomes that poorly represents their tremendous diversity (about 95% of animal diversity).Haploid chromosome-level genome assemblies using long reads and chromosome conformation capture (such as Hi-C) have become a standard in recent publications. To provide a haploid representation of diploid and polyploid genomes, assemblers collapse haplotypes into a single sequence, yet they are sensitive to high levels of heterozygosity and often yield fragmented assemblies with artefactual duplications. I tackled these shortcomings with two strategies: improving collapsed assemblies with a comprehensive long-read assembly methodology tuned for highly heterozygous genomes; and separating haplotypes to obtain phased assemblies using long reads and Hi-C. The assemblies were finally brought to chromosome-level scaffolds with a new Hi-C scaffolder, which demonstrated its efficiency on genomes of non-model organisms.These methods were applied to generate chromosome-level assemblies of three species for which none or few assemblies of closely related species were available: the bdelloid rotifer Adineta vaga, the coral Astrangia poculata, and the chaetognath Flaccisagitta enflata. These high-quality assemblies contribute to filling the current gaps in non-vertebrate genomics and pave the way for future sequencing initiatives aiming to generate such reference assemblies for all the species on Earth., Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Published
2021

89. Long-Term Culturing of Placozoans (Trichoplax and Hoilungia).

Author

Romanova DY, Varoqueaux F, Eitel M, Yoshida MA, Nikitin MA, and Moroz LL

Subjects
Animals, Placozoa genetics
Abstract

The phylum Placozoa remains one of the least explored among early-branching metazoan lineages. For over 130 years, this phylum had been represented by the single species Trichoplax adhaerens-an animal with the simplest known body plan (three cell layers without any organs) but complex behaviors. Recently, extensive sampling of placozoans across the globe and their subsequent genetic analysis have revealed incredible biodiversity with numerous cryptic species worldwide. However, only a few culture protocols are available to date, and all are for one species only. Here, we describe the breeding of four different species representing two placozoan genera: Trichoplax adhaerens, Trichoplax sp. H2, Hoilungia sp. H4, and Hoilungia hongkongensis originating from diverse biotopes. Our protocols allow to culture all species under comparable conditions. Next, we outlined various food sources and optimized strain-specific parameters enabling long-term culturing. These protocols can facilitate comparative analyses of placozoan biology and behaviors, which together will contribute to deciphering general principles of animal organization., (© 2024. Springer Science+Business Media, LLC, part of Springer Nature.)

Published
2024
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90. The genome of the reef-building glass sponge Aphrocallistes vastus provides insights into silica biomineralization.

Author

Francis WR, Eitel M, Vargas S, Garcia-Escudero CA, Conci N, Deister F, Mah JL, Guiglielmoni N, Krebs S, Blum H, Leys SP, and Wörheide G

Abstract

Well-annotated and contiguous genomes are an indispensable resource for understanding the evolution, development, and metabolic capacities of organisms. Sponges, an ecologically important non-bilaterian group of primarily filter-feeding sessile aquatic organisms, are underrepresented with respect to available genomic resources. Here we provide a high-quality and well-annotated genome of Aphrocallistes vastus , a glass sponge (Porifera: Hexactinellida) that forms large reef structures off the coast of British Columbia (Canada). We show that its genome is approximately 80 Mb, small compared to most other metazoans, and contains nearly 2500 nested genes, more than other genomes. Hexactinellida is characterized by a unique skeletal architecture made of amorphous silicon dioxide (SiO 2 ), and we identified 419 differentially expressed genes between the osculum, i.e. the vertical growth zone of the sponge, and the main body. Among the upregulated ones, mineralization-related genes such as glassin, as well as collagens and actins, dominate the expression profile during growth. Silicateins, suggested being involved in silica mineralization, especially in demosponges, were not found at all in the A. vastus genome and suggests that the underlying mechanisms of SiO 2 deposition in the Silicea sensu stricto (Hexactinellida + Demospongiae) may not be homologous., Competing Interests: We declare we have no competing interests., (© 2023 The Authors.)

Published
2023
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91. Studying Placozoa WBR in the Simplest Metazoan Animal, Trichoplax adhaerens.

Author

Osigus HJ, Eitel M, Horn K, Kamm K, Kosubek-Langer J, Schmidt MJ, Hadrys H, and Schierwater B

Subjects
Animals, Placozoa genetics
Abstract

Placozoans are a promising model system to study fundamental regeneration processes in a morphologically and genetically very simple animal. We here provide a brief introduction to the enigmatic Placozoa and summarize the state of the art of animal handling and experimental manipulation possibilities., (© 2022. The Author(s).)

Published
2022
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