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1. Metagenomics untangles potential adaptations of Antarctic endolithic bacteria at the fringe of habitability

Author

European Commission, Programma Nazionale di Ricerche in Antartide, Museo Nazionale dell'Antartide, Università degli Studi della Tuscia, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Junta de Andalucía, Australian Research Council, Joint Genome Institute (US), Coleine, Claudia [0000-0002-9289-6179], Albanese, Davide [0000-0002-9493-3850], Ray, Angelique E. [0000-0003-0051-1938], Delgado-Baquerizo, Manuel [0000-0002-6499-576X], Stajich, Jason E. [0000-0002-7591-0020], Selbmann, Laura [0000-0002-8967-3329], Coleine, Claudia, Albanese, Davide, Ray, Angelique E., Delgado-Baquerizo, Manuel, Stajich, Jason E., Williams, Timothy J., Larsen, Stefano, Tringe, Susannah G., Pennacchio, Christa, Ferrari, Belinda C., Donati, Claudio, Selbmann, Laura, European Commission, Programma Nazionale di Ricerche in Antartide, Museo Nazionale dell'Antartide, Università degli Studi della Tuscia, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Junta de Andalucía, Australian Research Council, Joint Genome Institute (US), Coleine, Claudia [0000-0002-9289-6179], Albanese, Davide [0000-0002-9493-3850], Ray, Angelique E. [0000-0003-0051-1938], Delgado-Baquerizo, Manuel [0000-0002-6499-576X], Stajich, Jason E. [0000-0002-7591-0020], Selbmann, Laura [0000-0002-8967-3329], Coleine, Claudia, Albanese, Davide, Ray, Angelique E., Delgado-Baquerizo, Manuel, Stajich, Jason E., Williams, Timothy J., Larsen, Stefano, Tringe, Susannah G., Pennacchio, Christa, Ferrari, Belinda C., Donati, Claudio, and Selbmann, Laura

Abstract

Survival and growth strategies of Antarctic endolithic microbes residing in Earth's driest and coldest desert remain virtually unknown. From 109 endolithic microbiomes, 4539 metagenome-assembled genomes were generated, 49.3 % of which were novel candidate bacterial species. We present evidence that trace gas oxidation and atmospheric chemosynthesis may be the prevalent strategies supporting metabolic activity and persistence of these ecosystems at the fringe of life and the limits of habitability.

Published
2024

2. Deciphering the molecular components of the quorum sensing system in the fungus Ophiostoma piceae

Author

Ministerio de Ciencia e Innovación (España), Consejo Superior de Investigaciones Científicas (España), Joint Genome Institute (US), Department of Energy (US), Santos-Pascual, Rodrigo [0000-0002-7982-4963], Martínez, María Jesús [0000-0003-2166-1097], Prieto Orzanco, Alicia [0000-0002-5075-4025], Barriuso, Jorge [0000-0003-0916-6560], Santos-Pascual, Rodrigo, Campoy, Iván, Sanz, David, Martínez, María Jesús, Prieto Orzanco, Alicia, Barriuso, Jorge, Ministerio de Ciencia e Innovación (España), Consejo Superior de Investigaciones Científicas (España), Joint Genome Institute (US), Department of Energy (US), Santos-Pascual, Rodrigo [0000-0002-7982-4963], Martínez, María Jesús [0000-0003-2166-1097], Prieto Orzanco, Alicia [0000-0002-5075-4025], Barriuso, Jorge [0000-0003-0916-6560], Santos-Pascual, Rodrigo, Campoy, Iván, Sanz, David, Martínez, María Jesús, Prieto Orzanco, Alicia, and Barriuso, Jorge

Abstract

Quorum sensing (QS) is a complex cell-cell communication mechanism that coordinates population-level behaviors in microbes. In eukaryotes, this phenomenon has been extensively described in the dimorphic yeast Candida albicans as its main QS molecule, the sesquiterpene alcohol farnesol, is responsible for various phenotypic (i.e., inhibition of yeast-to-hyphae transition, biofilm formation, and, hence, pathogenesis) and metabolic (i.e., induction of oxidative stress and apoptosis) changes. Ophiostoma piceae CECT 20416 is a dimorphic saprotrophic ascomycete with biotechnological interest that also produces farnesol as QS molecule, but in this case, the alcohol promotes the morphological transition to the mycelial form, biofilm formation, enzyme secretion, and melanin production. Here, we characterized the physiological response of Ophiostoma piceae to farnesol, the molecular components of the QS system of this fungus have been investigated using a “multiomics” approach that involved genomic, transcriptomic, and proteomic analyses. Some genes identified in this work are proposed as key factors in farnesol transport and signaling. We have also cataloged the genes undergoing major transcriptional changes triggered by the presence of the autoinducer, such as cell-wall remodeling, reactive oxygen species (ROS) protection, and melanin biosynthesis, using self-organizing maps. This analysis could be useful for applications in the forestry industry, for enzymes production, and for the valorization of residues. Furthermore, it might as well help to investigate the QS mechanisms of clinically relevant fungi phylogenetically related to Ophiostoma.

Published
2023

3. Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium

Author

Department of Energy (US), Joint Genome Institute (US), John Templeton Foundation, Gordon and Betty Moore Foundation, Generalitat Valenciana, Ministerio de Universidades (España), Džunková, Mária, La Clair, James J., Tyml, Tomáš, Doud, Devin, Schulz, Frederik, Piquer-Esteban, Samuel, Porcel Sanchis, Dafne, Osborn, Andrew, Robinson, David, Louie, Katherine B., Bowen, Benjamin P., Bowers, Robert M., Lee, Janey, Arnau, Vicente, Díaz-Villanueva, Wladimiro, Stepanauskas, Ramunas, Gosliner, Terrence, Date, Shailesh V., Northen, Trent R., Cheng, Jan-Fang, Burkart, Michael D., Woyke, Tanja, Department of Energy (US), Joint Genome Institute (US), John Templeton Foundation, Gordon and Betty Moore Foundation, Generalitat Valenciana, Ministerio de Universidades (España), Džunková, Mária, La Clair, James J., Tyml, Tomáš, Doud, Devin, Schulz, Frederik, Piquer-Esteban, Samuel, Porcel Sanchis, Dafne, Osborn, Andrew, Robinson, David, Louie, Katherine B., Bowen, Benjamin P., Bowers, Robert M., Lee, Janey, Arnau, Vicente, Díaz-Villanueva, Wladimiro, Stepanauskas, Ramunas, Gosliner, Terrence, Date, Shailesh V., Northen, Trent R., Cheng, Jan-Fang, Burkart, Michael D., and Woyke, Tanja

Abstract

[Background] Nudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiotic microbes are responsible for their synthesis remains unexplored. Another issue in searching for undiscovered natural products is that computational analysis of genomes of uncultured microbes can result in detection of novel biosynthetic gene clusters; however, their in vivo functionality is not guaranteed which limits further exploration of their pharmaceutical or industrial potential. To overcome these challenges, we used a fluorescent pantetheine probe, which produces a fluorescent CoA-analog employed in biosynthesis of secondary metabolites, to label and capture bacterial symbionts actively producing these compounds in the mantle of the nudibranch Doriopsilla fulva., [Results] We recovered the genome of Candidatus Doriopsillibacter californiensis from the Ca. Tethybacterales order, an uncultured lineage of sponge symbionts not found in nudibranchs previously. It forms part of the core skin microbiome of D. fulva and is nearly absent in its internal organs. We showed that crude extracts of D. fulva contained secondary metabolites that were consistent with the presence of a beta-lactone encoded in Ca. D. californiensis genome. Beta-lactones represent an underexplored group of secondary metabolites with pharmaceutical potential that have not been reported in nudibranchs previously., [Conclusions] Altogether, this study shows how probe-based, targeted sorting approaches can capture bacterial symbionts producing secondary metabolites in vivo.

Published
2023

4. Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability

Author

National Science Foundation (US), European Commission, Museo Nazionale dell'Antartide, Università degli Studi della Tuscia, Ministerio de Ciencia e Innovación (España), Junta de Andalucía, University of California, Riverside, Joint Genome Institute (US), National Institutes of Health (US), Department of Energy (US), Canadian Institute for Advanced Research, Ettinger, Cassandra L. [0000-0001-7334-403X], Delgado-Baquerizo, Manuel [0000-0002-6499-576X], Donati, Claudio [0000-0001-8688-1651], Albanese, Davide [0000-0002-9493-3850], Stajich, Jason E. [0000-0002-7591-0020], Coleine, Claudia [0000-0002-9289-6179], Ettinger, Cassandra L., Saunders, Morgan, Selbmann, Laura, Delgado-Baquerizo, Manuel, Donati, Claudio, Albanese, Davide, Roux, Simon, Tringe, Susannah G., Pennacchio, Christa, del Rio, Tijana G., Stajich, Jason E., Coleine, Claudia, National Science Foundation (US), European Commission, Museo Nazionale dell'Antartide, Università degli Studi della Tuscia, Ministerio de Ciencia e Innovación (España), Junta de Andalucía, University of California, Riverside, Joint Genome Institute (US), National Institutes of Health (US), Department of Energy (US), Canadian Institute for Advanced Research, Ettinger, Cassandra L. [0000-0001-7334-403X], Delgado-Baquerizo, Manuel [0000-0002-6499-576X], Donati, Claudio [0000-0001-8688-1651], Albanese, Davide [0000-0002-9493-3850], Stajich, Jason E. [0000-0002-7591-0020], Coleine, Claudia [0000-0002-9289-6179], Ettinger, Cassandra L., Saunders, Morgan, Selbmann, Laura, Delgado-Baquerizo, Manuel, Donati, Claudio, Albanese, Davide, Roux, Simon, Tringe, Susannah G., Pennacchio, Christa, del Rio, Tijana G., Stajich, Jason E., and Coleine, Claudia

Abstract

Background: Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have been largely unexplored despite important roles related to host metabolism and nutrient cycling. To begin to address this, we present a large-scale viral catalog from Antarctic rock microbial communities. Results: We performed metagenomic analyses on rocks from across Antarctica representing a broad range of environmental and spatial conditions, and which resulted in a predicted viral catalog comprising > 75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities which had predicted auxiliary metabolic genes (AMGs) with functions indicating that they may be potentially influencing bacterial adaptation and biogeochemistry. Conclusion: This catalog lays the foundation for expanding knowledge of virosphere diversity, function, spatial ecology, and dynamics in extreme environments. This work serves as a step towards exploring adaptability of microbial communities in the face of a changing climate. [MediaObject not available: see fulltext.] © 2023, The Author(s)

Published
2023

5. IMA genome-F18 : The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicillium biforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1

Author

Ministry of Education, Youth and Sports (Czech Republic), Mendel University, Department of Energy (US), Joint Genome Institute (US), Bioenergy Research Center (US), Department of Science and Innovation (South Africa), National Research Foundation (South Africa), Visagie, Cobus M., Magistà, Donato, Ferrara, Massimo, Balocchi, Felipe, Duong, Tuan A., Eichmeier, Ales, Gramaje, David, Aylward, Janneke, Baker, Scott E., Barnes, Irene, Calhoun, Sara, Angelis, Maria de, Frisvad, Jens C., Hakalova, Eliska, Hayes, Richard D., Houbraken, Jos, Grigoriev, Igor V., LaButti, Kurt, Leal, Catarina, Lipzen, Anna, Ng, Vivian, Pangilinan, Jasmyn, Pecenka, Jakub, Perrone, Giancarlo, Piso, Anja, Savage, Emily, Spetik, Milan, Wingfield, Michael J., Zhang, Yu, Wingfield, Brenda D., Ministry of Education, Youth and Sports (Czech Republic), Mendel University, Department of Energy (US), Joint Genome Institute (US), Bioenergy Research Center (US), Department of Science and Innovation (South Africa), National Research Foundation (South Africa), Visagie, Cobus M., Magistà, Donato, Ferrara, Massimo, Balocchi, Felipe, Duong, Tuan A., Eichmeier, Ales, Gramaje, David, Aylward, Janneke, Baker, Scott E., Barnes, Irene, Calhoun, Sara, Angelis, Maria de, Frisvad, Jens C., Hakalova, Eliska, Hayes, Richard D., Houbraken, Jos, Grigoriev, Igor V., LaButti, Kurt, Leal, Catarina, Lipzen, Anna, Ng, Vivian, Pangilinan, Jasmyn, Pecenka, Jakub, Perrone, Giancarlo, Piso, Anja, Savage, Emily, Spetik, Milan, Wingfield, Michael J., Zhang, Yu, and Wingfield, Brenda D.

Abstract

Sequencing fungal genomes has now become very common and the list of genomes in this manuscript reflects this. Particularly relevant is that the first announcement is a re-identification of Penicillium genomes available on NCBI. The fact that more than 100 of these genomes have been deposited without the correct species names speak volumes to the fact that we must continue training fungal taxonomists and the importance of the International Mycological Association (after which this journal is named). When we started the genome series in 2013, one of the essential aspects was the need to have a phylogenetic tree as part of the manuscript. This came about as the result of a discussion with colleagues in NCBI who were trying to deal with the very many incorrectly identified bacterial genomes (at the time) which had been submitted to NCBI. We are now in the same position with fungal genomes. Sequencing a fungal genome is all too easy but providing a correct species name and ensuring that the fungus has in fact been correctly identified seems to be more difficult. We know that there are thousands of fungi which have not yet been described. The availability of sequence data has made identification of fungi easier but also serves to highlight the need to have a fungal taxonomist in the project to make sure that mistakes are not made.

Published
2023

6. Brachypodium: 20 years as a grass biology model system; the way forward?

Author

National Science Centre (Poland), University of Silesia in Katowice, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Gobierno de Aragón, European Commission, Joint Genome Institute (US), National Science Foundation (US), University of Zurich, Swiss National Science Foundation, Department of Energy (US), National Natural Science Foundation of China, National Key Research and Development Program (China), Biotechnology and Biological Sciences Research Council (UK), Hasterok, Robert, Catalán, Pilar, Hazen, Samuel P., Roulin, Anne C., Vogel, John P., Wang, Kai, Mur, Luis A. J., National Science Centre (Poland), University of Silesia in Katowice, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Gobierno de Aragón, European Commission, Joint Genome Institute (US), National Science Foundation (US), University of Zurich, Swiss National Science Foundation, Department of Energy (US), National Natural Science Foundation of China, National Key Research and Development Program (China), Biotechnology and Biological Sciences Research Council (UK), Hasterok, Robert, Catalán, Pilar, Hazen, Samuel P., Roulin, Anne C., Vogel, John P., Wang, Kai, and Mur, Luis A. J.

Abstract

It has been 20 years since Brachypodium distachyon was suggested as a model grass species, but ongoing research now encompasses the entire genus. Extensive Brachypodium genome sequencing programmes have provided resources to explore the determinants and drivers of population diversity. This has been accompanied by cytomolecular studies to make Brachypodium a platform to investigate speciation, polyploidisation, perenniality, and various aspects of chromosome and interphase nucleus organisation. The value of Brachypodium as a functional genomic platform has been underscored by the identification of key genes for development, biotic and abiotic stress, and cell wall structure and function. While Brachypodium is relevant to the biofuel industry, its impact goes far beyond that as an intriguing model to study climate change and combinatorial stress.

Published
2022

7. Patterns of pan-genome occupancy and gene coexpression under water-deficit in Brachypodium distachyon

Author

Department of Agriculture (US), Ministerio de Ciencia e Innovación (España), Universidad de Zaragoza, Joint Genome Institute (US), Ministerio de Economía y Competitividad (España), Ibercaja, Instituto de Estudios Altoaragoneses, ARAID Foundation, Contreras-Moreira, Bruno [0000-0002-5462-907X], Sancho Cohen, Rubén, Catalán, Pilar, Contreras-Moreira, Bruno, Juenger, Thomas E., Des Marais, David L., Department of Agriculture (US), Ministerio de Ciencia e Innovación (España), Universidad de Zaragoza, Joint Genome Institute (US), Ministerio de Economía y Competitividad (España), Ibercaja, Instituto de Estudios Altoaragoneses, ARAID Foundation, Contreras-Moreira, Bruno [0000-0002-5462-907X], Sancho Cohen, Rubén, Catalán, Pilar, Contreras-Moreira, Bruno, Juenger, Thomas E., and Des Marais, David L.

Abstract

Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequencing complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome. These analyses demonstrate that many genes are absent from the first reference genomes, whose analysis dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analysed weighted gene coexpression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and the differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable “occupancy” in the pan-genome – genes which are either present in all studied genotypes or missing in some genotypes – show different distributions among coexpression modules. Coexpression analysis united genes expressed in drought-stressed plants into nine modules covering 72 hub genes (87 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 190 hub genes (251 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.

Published
2022

8. Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives

Author

Joint Genome Institute (US), National Science Foundation (US), Department of Energy (US), Japan Society for the Promotion of Science, Consejo Superior de Investigaciones Científicas (España), Hokkaido University, Gutiérrez Suárez, Ana [0000-0002-8823-9029], Marques, Gisela [0000-0002-6431-8267], Bhatnagar, Jennifer M. [0000-0001-6424-4133], Iwata, Mana, Gutiérrez Suárez, Ana, Marques, Gisela, Sabat, Grzegorz, Kersten, Philip J, Cullen, Daniel, Bhatnagar, Jennifer M., Yadav, Jagjit S., Lipzen, Anna, Yoshinaga, Yuko, Sharma, Aditi, Adam, Catherine, Joint Genome Institute (US), National Science Foundation (US), Department of Energy (US), Japan Society for the Promotion of Science, Consejo Superior de Investigaciones Científicas (España), Hokkaido University, Gutiérrez Suárez, Ana [0000-0002-8823-9029], Marques, Gisela [0000-0002-6431-8267], Bhatnagar, Jennifer M. [0000-0001-6424-4133], Iwata, Mana, Gutiérrez Suárez, Ana, Marques, Gisela, Sabat, Grzegorz, Kersten, Philip J, Cullen, Daniel, Bhatnagar, Jennifer M., Yadav, Jagjit S., Lipzen, Anna, Yoshinaga, Yuko, Sharma, Aditi, and Adam, Catherine

Abstract

Wood extractives, solvent-soluble fractions of woody biomass, are considered to be a factor impeding or excluding fungal colonization on the freshly harvested conifers. Among wood decay fungi, the basidiomycete Phlebiopsis gigantea has evolved a unique enzyme system to efficiently transform or degrade conifer extractives but little is known about the mechanism(s). In this study, to clarify the mechanism(s) of softwood degradation, we examined the transcriptome, proteome, and metabolome of P. gigantea when grown on defined media containing microcrystalline cellulose and pine sapwood extractives. Beyond the conventional enzymes often associated with cellulose, hemicellulose and lignin degradation, an array of enzymes implicated in the metabolism of softwood lipophilic extractives such as fatty and resin acids, steroids and glycerides was significantly up-regulated. Among these, a highly expressed and inducible lipase is likely responsible for lipophilic extractive degradation, based on its extracellular location and our characterization of the recombinant enzyme. Our results provide insight into physiological roles of extractives in the interaction between wood and fungi. © 2021, The Author(s).

Published
2021

9. Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay

Author

Joint Genome Institute (US), Institut Carnot Pasteur MS, l’Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (France), Conseil Régional Provence-Alpes-Côte d'Azur, Centre National de la Recherche Scientifique (France), Labex ARBRE, Conseil Régional de Lorraine, European Commission, Hungarian Academy of Sciences, Ministerio de Economía, Industria y Competitividad (España), Consejo Superior de Investigaciones Científicas (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Czech Science Foundation, Hage, Hayat [0000-0003-4118-1816], Miyauchi, Shingo [0000-0002-0620-5547], Virágh, Máté [0000-0002-2278-1288], Drula, Elodie [0000-0002-9168-5214], Min, Byoungnam [0000-0002-7469-088X], Favel, Anne [0000-0003-2255-3637], Lesage-Meessen, Laurence [0000-0003-2275-2978], Merényi, Z. [0000-0003-1114-3739], Eugenio, Laura I. de [0000-0002-0496-8663], Morin, Emmanuelle [0000-0002-7268-972X], Martínez, Ángel T. [0000-0002-1584-2863], Baldrian, Petr [0000-0002-8983-2721], Stursová, Martina [0000-0003-1387-6426], Martínez, María Jesús [0000-0003-2166-1097], Novotny, Cenek [0000-0003-3274-471X], Maurice, Sundy [0000-0002-5376-0981], Andreopoulos, William [0000-0001-9097-1123], LaButti, Kurt M. [0000-0002-5838-1972], Na, Hyunsoo [0000-0002-4386-017X], Barry, Kerrie [0000-0002-8999-6785], Lipzen, Anna [0000-0003-2293-9329], Henrissat, Bernard [0000-0002-3434-8588], Ahrendt, Steven [0000-0002-3029-2126], Grigoriev, Igor V. [0000-0002-3136-8903], Rosso, Marie-Noëlle [0000-0001-8317-7220], Hage, Hayat, Miyauchi, Shingo, Virágh, Máté, Drula, Elodie, Min, Byoungnam, Chaduli, Delphine, Navarro, David, Favel, Anne, Norest, Manon, Lesage-Meessen, Laurence, Bálint, Balázs, Merényi, Z., Eugenio, Laura I. de, Morin, Emmanuelle, Martínez, Ángel T., Baldrian, Petr, Stursová, Martina, Martínez, María Jesús, Novotny, Cenek, Magnuson, Jon K., Spatafora, Joey W., Maurice, Sundy, Pangilinan, Jasmyn, Andreopoulos, William, LaButti, Kurt M., Hundley, Hope, Na, Hyunsoo, Kuo, Alan, Barry, Kerrie, Lipzen, Anna, Henrissat, Bernard, Riley, Robert, Ahrendt, Steven, Nagy, Lazslo G., Grigoriev, Igor V., Martin, Francis, Rosso, Marie-Noëlle, Joint Genome Institute (US), Institut Carnot Pasteur MS, l’Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (France), Conseil Régional Provence-Alpes-Côte d'Azur, Centre National de la Recherche Scientifique (France), Labex ARBRE, Conseil Régional de Lorraine, European Commission, Hungarian Academy of Sciences, Ministerio de Economía, Industria y Competitividad (España), Consejo Superior de Investigaciones Científicas (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Czech Science Foundation, Hage, Hayat [0000-0003-4118-1816], Miyauchi, Shingo [0000-0002-0620-5547], Virágh, Máté [0000-0002-2278-1288], Drula, Elodie [0000-0002-9168-5214], Min, Byoungnam [0000-0002-7469-088X], Favel, Anne [0000-0003-2255-3637], Lesage-Meessen, Laurence [0000-0003-2275-2978], Merényi, Z. [0000-0003-1114-3739], Eugenio, Laura I. de [0000-0002-0496-8663], Morin, Emmanuelle [0000-0002-7268-972X], Martínez, Ángel T. [0000-0002-1584-2863], Baldrian, Petr [0000-0002-8983-2721], Stursová, Martina [0000-0003-1387-6426], Martínez, María Jesús [0000-0003-2166-1097], Novotny, Cenek [0000-0003-3274-471X], Maurice, Sundy [0000-0002-5376-0981], Andreopoulos, William [0000-0001-9097-1123], LaButti, Kurt M. [0000-0002-5838-1972], Na, Hyunsoo [0000-0002-4386-017X], Barry, Kerrie [0000-0002-8999-6785], Lipzen, Anna [0000-0003-2293-9329], Henrissat, Bernard [0000-0002-3434-8588], Ahrendt, Steven [0000-0002-3029-2126], Grigoriev, Igor V. [0000-0002-3136-8903], Rosso, Marie-Noëlle [0000-0001-8317-7220], Hage, Hayat, Miyauchi, Shingo, Virágh, Máté, Drula, Elodie, Min, Byoungnam, Chaduli, Delphine, Navarro, David, Favel, Anne, Norest, Manon, Lesage-Meessen, Laurence, Bálint, Balázs, Merényi, Z., Eugenio, Laura I. de, Morin, Emmanuelle, Martínez, Ángel T., Baldrian, Petr, Stursová, Martina, Martínez, María Jesús, Novotny, Cenek, Magnuson, Jon K., Spatafora, Joey W., Maurice, Sundy, Pangilinan, Jasmyn, Andreopoulos, William, LaButti, Kurt M., Hundley, Hope, Na, Hyunsoo, Kuo, Alan, Barry, Kerrie, Lipzen, Anna, Henrissat, Bernard, Riley, Robert, Ahrendt, Steven, Nagy, Lazslo G., Grigoriev, Igor V., Martin, Francis, and Rosso, Marie-Noëlle

Abstract

Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. Despite continuous discoveries on the enzymatic machinery involved in wood decomposition, the vision on their evolutionary adaptation to wood decay and genome diversity remains incomplete., We combined the genome sequence information from 50 Polyporales species, including 26 newly sequenced genomes and sought for genomic and functional adaptations to wood decay through the analysis of genome composition and transcriptome responses to different carbon sources.The genomes of Polyporales from different phylogenetic clades showed poor conservation in macrosynteny, indicative of genome rearrangements. We observed different gene family expansion/contraction histories for plant cell wall degrading enzymes in core polyporoids and phlebioids and captured expansions for genes involved in signaling and regulation in the lineages of white rotters. Furthermore, we identified conserved cupredoxins, thaumatin-like proteins and Lytic Polysaccharide Monooxygenases with a yet uncharacterized appended module as new candidate players in wood decomposition.Given the current need for enzymatic toolkits dedicated to the transformation of renewable carbon sources, the observed genomic diversity among Polyporales strengthens the relevance of mining Polyporales biodiversity to understand the molecular mechanisms of wood decay.

Published
2021

10. Patterns of pan‐genome occupancy and gene coexpression under water‐deficit in Brachypodium distachyon

Author

Rubén Sancho, Pilar Catalán, Bruno Contreras‐Moreira, Thomas E. Juenger, David L. Des Marais, Department of Agriculture (US), Ministerio de Ciencia e Innovación (España), Universidad de Zaragoza, Joint Genome Institute (US), Ministerio de Economía y Competitividad (España), Ibercaja, Instituto de Estudios Altoaragoneses, ARAID Foundation, and Contreras-Moreira, Bruno

Subjects
transcriptomics, Protect, restore and promote sustainable use of terrestrial ecosystems, sustainably manage forests, combat desertification, and halt and reverse land degradation and halt biodiversity loss, genomics/proteomics, molecular evolution, Genetics, Water, Genes, Plant, Transcriptome, phenotypic plasticity, Ecology, Evolution, Behavior and Systematics, Brachypodium, Droughts
Abstract

22 Pags.- 3 Figs.- 4 Tabls. © 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License., Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequencing complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome. These analyses demonstrate that many genes are absent from the first reference genomes, whose analysis dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analysed weighted gene coexpression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and the differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable “occupancy” in the pan-genome – genes which are either present in all studied genotypes or missing in some genotypes – show different distributions among coexpression modules. Coexpression analysis united genes expressed in drought-stressed plants into nine modules covering 72 hub genes (87 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 190 hub genes (251 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response., This work was supported by the USDA (NIFA-2011-67012-30663) to D.L.D., NSF (IOS-0922457) to T.E.J., the Spanish Ministry of Science and Innovation CGL2016-79790-P and PID2019-108195GB-I00, University of Zaragoza UZ2016_TEC02 grant projects to P.C., and the Joint Genome Institute FP00006675 contract to P.C. and FP00006746 to D.L.D. R.S. was funded by a Spanish Ministry of Economy and Competitiveness (Mineco) FPI PhD fellowship, Mineco and Ibercaja-CAI mobility grants and Instituto de Estudios Altoaragoneses grant. B.C.M. was funded by Fundación ARAID. P.C. and R.S. were partially funded by a European Social Fund/Spanish Aragón Government Bioflora grant.

Published
2022
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11. Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability

Author

Cassandra L. Ettinger, Morgan Saunders, Laura Selbmann, Manuel Delgado-Baquerizo, Claudio Donati, Davide Albanese, Simon Roux, Susannah Tringe, Christa Pennacchio, Tijana G. del Rio, Jason E. Stajich, Claudia Coleine, National Science Foundation (US), European Commission, Italian Antarctic National Museum, Università degli Studi della Tuscia, Ministerio de Ciencia e Innovación (España), Junta de Andalucía, University of California, Riverside, Joint Genome Institute (US), National Institutes of Health (US), Department of Energy (US), Canadian Institute for Advanced Research, Ettinger, Cassandra L., Delgado-Baquerizo, Manuel, Donati, Claudio, Albanese, Davide, Stajich, Jason E., and Coleine, Claudia

Subjects
Microbiology (medical), Microbiology
Abstract

8 páginas.- 2 figuras.- 64 referencias.- The online version contains supplementary material available at https:// doi.org/10.1186/s40168‑023‑01554‑6.- Video sobre el artículo en YouTube https://youtu.be/ykjpjJgcVx4, Background: Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have been largely unexplored despite important roles related to host metabolism and nutrient cycling. To begin to address this, we present a large-scale viral catalog from Antarctic rock microbial communities. Results: We performed metagenomic analyses on rocks from across Antarctica representing a broad range of environmental and spatial conditions, and which resulted in a predicted viral catalog comprising > 75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities which had predicted auxiliary metabolic genes (AMGs) with functions indicating that they may be potentially influencing bacterial adaptation and biogeochemistry. Conclusion: This catalog lays the foundation for expanding knowledge of virosphere diversity, function, spatial ecology, and dynamics in extreme environments. This work serves as a step towards exploring adaptability of microbial communities in the face of a changing climate. [MediaObject not available: see fulltext.] © 2023, The Author(s), C.L.E. is supported by the National Science Foundation (NSF) under a NSF Ocean Sciences Postdoctoral Fellowship (Award No. 2205744). M.S. was supported by the NSF REU The National Summer Undergraduate Research Project, Award No. 2149582. C.C. is supported by the European Commission under the Marie Sklodowska-Curie Grant Agreement No. 702057 (DRYLIFE). C.C. and L.S. wish to thank the Italian National Antarctic Research Program for funding sampling campaigns and research activities in Italy in the frame of PNRA projects. The Italian Antarctic National Museum (MNA) is kindly acknowledged for financial support to the Mycological Section of the MNA and for providing rock samples used in this study stored in the Culture Collection of Antarctic fungi (MNA-CCFEE), University of Tuscia, Italy. M.D-B. is supported by a project from the Spanish Ministry of Science and Innovation (PID2020-115813RA-I00), and a project of the Fondo Europeo de Desarrollo Regional (FEDER) and the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía (FEDER Andalucía 2014–2020 Objetivo temático '01–Refuerzo de la investigación, el desarrollo tecnológico y la innovación') associated with the research project P20_00879 (ANDABIOMA). J.E.S. is a CIFAR fellow in the Fungal Kingdom: Threats and Opportunities program. Data analyses performed at the High-Performance Computing Cluster at the University of California Riverside in the Institute of Integrative Genome Biology were supported by NSF grant DBI-1429826 and NIH grant S10-OD016290. Part of this work (proposals https://doi.org/10.46936/10.25585/60000791 and https://doi.org/10.46936/fics.proj.2020.51548/60000213 ) was conducted by the U.S. Department of Energy Joint Genome Institute ( https://ror.org/04xm1d337 ), a DOE Office of Science User Facility, supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication

Published
2023
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12. Brachypodium: 20 years as a grass biology model system; the way forward?

Author

Robert Hasterok, Pilar Catalan, Samuel P. Hazen, Anne C. Roulin, John P. Vogel, Kai Wang, Luis A.J. Mur, National Science Centre (Poland), University of Silesia in Katowice, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Gobierno de Aragón, European Commission, Joint Genome Institute (US), National Science Foundation (US), University of Zurich, Swiss National Science Foundation, Department of Energy (US), National Natural Science Foundation of China, National Key Research and Development Program (China), Biotechnology and Biological Sciences Research Council (UK), and Hasterok, Robert

Subjects
polyploid speciation, model grass genus, food and beverages, Genomics, Plant Science, 580 Plants (Botany), genome and karyotype structure and evolution, Chromosomes, Plant, UFSP13-7 Evolution in Action: From Genomes to Ecosystems, 10126 Department of Plant and Microbial Biology, Biofuels, 1110 Plant Science, cell wall, 10211 Zurich-Basel Plant Science Center, environmental adaptation, Genome, Plant, Brachypodium
Abstract

It has been 20 years since Brachypodium distachyon was suggested as a model grass species, but ongoing research now encompasses the entire genus. Extensive Brachypodium genome sequencing programmes have provided resources to explore the determinants and drivers of population diversity. This has been accompanied by cytomolecular studies to make Brachypodium a platform to investigate speciation, polyploidisation, perenniality, and various aspects of chromosome and interphase nucleus organisation. The value of Brachypodium as a functional genomic platform has been underscored by the identification of key genes for development, biotic and abiotic stress, and cell wall structure and function. While Brachypodium is relevant to the biofuel industry, its impact goes far beyond that as an intriguing model to study climate change and combinatorial stress., R.H. is grateful to the National Science Centre Poland (2018/31/B/NZ3/01761 and 2015/18/M/NZ2/00394) and acknowledges the support under the Research Excellence Initiative of the University of Silesia in Katowice. P.C. thanks the Spanish Ministry of Science and Innovation (PID2019-108195GB-I00), the Spanish Aragon Government and European Social Fund (Bioflora grant A01-20R), and the JGI Community Science Program (503504). S.H. acknowledges the National Science Foundation Division of Integrative Organismal Systems (NSF IOS-2049966). A.C.R. thanks the University of Zurich Research Priority Programs (URPP) Evolution in Action and the Swiss National Science Foundation (SNSF 31003A_182785). The work conducted by J.P.V. at the US DOE Joint Genome Institute is supported by the Office of Science of the US Department of Energy (DE-AC02-05CH1123). K.W. acknowledges the support from the National Natural Science Foundation of China (32070544) and National Key R&D Program of China (2019YFD1000500). LA.J.M. recognises the support of the UK Biotechnology and Biological Sciences Research Council (BB/M027945/1).

Published
2022

13. Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives

Author

Christopher Daum, Aditi Sharma, Mana Iwata, Daniel Cullen, Gisela Marques, Grzegorz Sabat, Anna Lipzen, Igor V. Grigoriev, Chiaki Hori, Jennifer M. Bhatnagar, Catherine Adam, Ana Gutiérrez, Yuko Yoshinaga, Vivian Ng, Philip J. Kersten, Jagjit S. Yadav, Joint Genome Institute (US), National Science Foundation (US), Department of Energy (US), Japan Society for the Promotion of Science, Consejo Superior de Investigaciones Científicas (España), Hokkaido University, Gutiérrez Suárez, Ana [0000-0002-8823-9029], Marques, Gisela [0000-0002-6431-8267], Bhatnagar, Jennifer M. [0000-0001-6424-4133], Gutiérrez Suárez, Ana, Marques, Gisela, and Bhatnagar, Jennifer M.

Subjects
0301 basic medicine, Softwood, Science, 030106 microbiology, Biomass, Microbiology, Article, 03 medical and health sciences, chemistry.chemical_compound, Botany, Metabolome, Hemicellulose, Lipase, Cellulose, Multidisciplinary, biology, Fungi, Gigantea, biology.organism_classification, Microcrystalline cellulose, 030104 developmental biology, chemistry, biology.protein, Medicine
Abstract

14 páginas.- 6 figuras. 1 tabla.- 50 referencias.- Supplementary Information Te online version contains supplementary material available at https://doi.org/10.1038/s41598-021-91756-5, Wood extractives, solvent-soluble fractions of woody biomass, are considered to be a factor impeding or excluding fungal colonization on the freshly harvested conifers. Among wood decay fungi, the basidiomycete Phlebiopsis gigantea has evolved a unique enzyme system to efficiently transform or degrade conifer extractives but little is known about the mechanism(s). In this study, to clarify the mechanism(s) of softwood degradation, we examined the transcriptome, proteome, and metabolome of P. gigantea when grown on defined media containing microcrystalline cellulose and pine sapwood extractives. Beyond the conventional enzymes often associated with cellulose, hemicellulose and lignin degradation, an array of enzymes implicated in the metabolism of softwood lipophilic extractives such as fatty and resin acids, steroids and glycerides was significantly up-regulated. Among these, a highly expressed and inducible lipase is likely responsible for lipophilic extractive degradation, based on its extracellular location and our characterization of the recombinant enzyme. Our results provide insight into physiological roles of extractives in the interaction between wood and fungi. © 2021, The Author(s)., The work partly conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Research was also supported by NSF Grants 1457695 and 1457721 to J.M.B. and D.C., respectively, by CSIC project 201740E071 to A.G. and by JSPS Grant-in-Aid for Scientific Research 19K15881, JST-ACTX PJ2519A059 and 2017 Feasibility Study Program of the Frontier Chemistry Center, Faculty of Engineering, Hokkaido University to C.H.

Published
2021
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14. Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay

Author

Hayat, Hage, Shingo, Miyauchi, Máté, Virágh, Elodie, Drula, Byoungnam, Min, Delphine, Chaduli, David, Navarro, Anne, Favel, Manon, Norest, Laurence, Lesage-Meessen, Balázs, Bálint, Zsolt, Merényi, Laura, de Eugenio, Emmanuelle, Morin, Angel T, Martínez, Petr, Baldrian, Martina, Štursová, María Jesús, Martínez, Cenek, Novotny, Jon K, Magnuson, Joey W, Spatafora, Sundy, Maurice, Jasmyn, Pangilinan, Willian, Andreopoulos, Kurt, LaButti, Hope, Hundley, Hyunsoo, Na, Alan, Kuo, Kerrie, Barry, Anna, Lipzen, Bernard, Henrissat, Robert, Riley, Steven, Ahrendt, László G, Nagy, Igor V, Grigoriev, Francis, Martin, Marie-Noëlle, Rosso, Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Max Planck Institute for Plant Breeding Research (MPIPZ), Biological Research Centre [Szeged] (BRC), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), US Department of Energy Joint Genome Institute, University of California, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Centro de Investigaciones Biológicas Margarita Salas, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Microbiology of the ASCR, v. v. i. [Prague, Czech Republic], Technical University of Ostrava [Ostrava] (VSB), Pacific Northwest National Laboratory (PNNL), Department of Botany and Plant Pathology, Oregon State University (OSU), University of Oslo (UiO), King Abdulaziz University, Institute of Biology [Budapest], Faculty of Sciences [Budapest], Eötvös Loránd University (ELTE)-Eötvös Loránd University (ELTE), United States Department of Energy (DOE) DE-AC02-05CH11231DE-SC0019427Institut Carnot 3BCARRegion Provence-Alpes-Cote d'AzurGroupement de Recherche Genomique EnvironnementaleRegion Grand-EstEuropean CommissionHungarian Academy of Sciences' Momentum Program LP2019-13/2019Spanish Ministry of Economy, Industry and Competitiveness BIO2017-86559-RConsejo Superior de Investigaciones Cientificas PIE-201620E081Agencia Estatal de InvestigacionMinistry of Science, Innovation and Universities RTI2018-093683-B-I00Grant Agency of the Czech Republic 17-20110SFrench National Research Institute for Agriculture, Food and Environment, ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011), University of California (UC), Joint Genome Institute (US), Institut Carnot Pasteur MS, l’Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (France), Conseil Régional Provence-Alpes-Côte d'Azur, Centre National de la Recherche Scientifique (France), Labex ARBRE, Conseil Régional de Lorraine, European Commission, Hungarian Academy of Sciences, Ministerio de Economía, Industria y Competitividad (España), Consejo Superior de Investigaciones Científicas (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Czech Science Foundation, Hage, Hayat, Miyauchi, Shingo, Virágh, Máté, Drula, Elodie, Min, Byoungnam, Favel, Anne, Lesage-Meessen, Laurence, Merényi, Z., Eugenio, Laura I. de, Morin, Emmanuelle, Martínez, Ángel T., Baldrian, Petr, Stursová, Martina, Martínez, María Jesús, Novotny, Cenek, Maurice, Sundy, Andreopoulos, William, LaButti, Kurt M., Na, Hyunsoo, Barry, Kerrie, Lipzen, Anna, Henrissat, Bernard, Ahrendt, Steven, Grigoriev, Igor V., Rosso, Marie-Noëlle, Hage, Hayat [0000-0003-4118-1816], Miyauchi, Shingo [0000-0002-0620-5547], Virágh, Máté [0000-0002-2278-1288], Drula, Elodie [0000-0002-9168-5214], Min, Byoungnam [0000-0002-7469-088X], Favel, Anne [0000-0003-2255-3637], Lesage-Meessen, Laurence [0000-0003-2275-2978], Merényi, Z. [0000-0003-1114-3739], Eugenio, Laura I. de [0000-0002-0496-8663], Morin, Emmanuelle [0000-0002-7268-972X], Martínez, Ángel T. [0000-0002-1584-2863], Baldrian, Petr [0000-0002-8983-2721], Stursová, Martina [0000-0003-1387-6426], Martínez, María Jesús [0000-0003-2166-1097], Novotny, Cenek [0000-0003-3274-471X], Maurice, Sundy [0000-0002-5376-0981], Andreopoulos, William [0000-0001-9097-1123], LaButti, Kurt M. [0000-0002-5838-1972], Na, Hyunsoo [0000-0002-4386-017X], Barry, Kerrie [0000-0002-8999-6785], Lipzen, Anna [0000-0003-2293-9329], Henrissat, Bernard [0000-0002-3434-8588], Ahrendt, Steven [0000-0002-3029-2126], Grigoriev, Igor V. [0000-0002-3136-8903], and Rosso, Marie-Noëlle [0000-0001-8317-7220]

Subjects
Special Issue Articles, [SDV]Life Sciences [q-bio], Wood decay, Microbiology, Fungal Proteins, Genetics, Plant cell wall, Fungal ecology, Phylogeny, Evolutionary Biology, Genome, Basidiomycota, Human Genome, Special Issue Article, Phylogenomics, Biodiversity, Wood, Climate Action, Fungal, Genome, Fungal, Polyporales, Transcriptome, Lignocellulose, CAZymes, Biotechnology
Abstract

17 p.-7 fig., Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. Despite continuous discoveries on the enzymatic machinery involved in wood decomposition, the vision on their evolutionary adaptation to wood decay and genome diversity remains incomplete., We combined the genome sequence information from 50 Polyporales species, including 26 newly sequenced genomes and sought for genomic and functional adaptations to wood decay through the analysis of genome composition and transcriptome responses to different carbon sources.The genomes of Polyporales from different phylogenetic clades showed poor conservation in macrosynteny, indicative of genome rearrangements. We observed different gene family expansion/contraction histories for plant cell wall degrading enzymes in core polyporoids and phlebioids and captured expansions for genes involved in signaling and regulation in the lineages of white rotters. Furthermore, we identified conserved cupredoxins, thaumatin-like proteins and Lytic Polysaccharide Monooxygenases with a yet uncharacterized appended module as new candidate players in wood decomposition.Given the current need for enzymatic toolkits dedicated to the transformation of renewable carbon sources, the observed genomic diversity among Polyporales strengthens the relevance of mining Polyporales biodiversity to understand the molecular mechanisms of wood decay., This work was supported by the U.S. Department of Energy Joint Genome Institute, a Department of Energy Office of Science User Facility (grant # DE-AC02-05CH11231, DESC0019427 to I.V.G. and B.M.); Institut Carnot 3BCAR, the French National Research Institute for Agriculture, Food and Environment, The Region Provence Alpes Côte d’Azur and the Groupement de Recherche Génomique Environnementale to H.H.; the Laboratory of Excellence ARBRE (grant # ANR-11-LABX-0002-01 to F.M.); the Region Lorraine and the European Regional Development Fund to F.M.; the Hungarian Academy of Sciences’ Momentum Program (grant # LP2019-13/2019 to L.G.N.); the Spanish Ministry of Economy, Industry and Competitiveness (grant # BIO2017-86559-R to A.T.M.); the Consejo Superior de Investigaciones Científicas (grant # PIE-201620E081 to A.T.M.); the Agencia Estatal de Investigación, the European Regional Development Fund and the Ministry of Science, Innovation and Universities (grant # RTI2018-093683-B-I00 to L.D.E. and M.J.M.) and the Czech Science Foundation (grant# 17-20110S to P.B. and M.Š.).

Published
2021
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15. Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes.

Author

Andreopoulos WB, Geller AM, Lucke M, Balewski J, Clum A, Ivanova NN, and Levy A

Subjects
Animals, Chromosomes, Bacterial genetics, Reproducibility of Results, Sequence Analysis, DNA, Deep Learning, Genome, Bacterial, Plasmids genetics
Abstract

Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many microbial genomes have been sequenced by short read sequencers and have resulted in a mix of contigs that derive from plasmids or chromosomes. New tools that accurately identify plasmids are needed to elucidate new plasmid-borne genes of high biological importance. We have developed Deeplasmid, a deep learning tool for distinguishing plasmids from bacterial chromosomes based on the DNA sequence and its encoded biological data. It requires as input only assembled sequences generated by any sequencing platform and assembly algorithm and its runtime scales linearly with the number of assembled sequences. Deeplasmid achieves an AUC-ROC of over 89%, and it was more accurate than five other plasmid classification methods. Finally, as a proof of concept, we used Deeplasmid to predict new plasmids in the fish pathogen Yersinia ruckeri ATCC 29473 that has no annotated plasmids. Deeplasmid predicted with high reliability that a long assembled contig is part of a plasmid. Using long read sequencing we indeed validated the existence of a 102 kb long plasmid, demonstrating Deeplasmid's ability to detect novel plasmids., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2022
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16. Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi.

Author

Krizsán K, Almási É, Merényi Z, Sahu N, Virágh M, Kószó T, Mondo S, Kiss B, Bálint B, Kües U, Barry K, Cseklye J, Hegedüs B, Henrissat B, Johnson J, Lipzen A, Ohm RA, Nagy I, Pangilinan J, Yan J, Xiong Y, Grigoriev IV, Hibbett DS, and Nagy LG

Subjects
Gene Expression Regulation, Fungal physiology, Agaricales genetics, Agaricales growth & development, Databases, Nucleic Acid, Fruiting Bodies, Fungal genetics, Fruiting Bodies, Fungal growth & development, Fungal Proteins biosynthesis, Fungal Proteins genetics, Genes, Fungal, Transcriptome physiology
Abstract

The evolution of complex multicellularity has been one of the major transitions in the history of life. In contrast to simple multicellular aggregates of cells, it has evolved only in a handful of lineages, including animals, embryophytes, red and brown algae, and fungi. Despite being a key step toward the evolution of complex organisms, the evolutionary origins and the genetic underpinnings of complex multicellularity are incompletely known. The development of fungal fruiting bodies from a hyphal thallus represents a transition from simple to complex multicellularity that is inducible under laboratory conditions. We constructed a reference atlas of mushroom formation based on developmental transcriptome data of six species and comparisons of >200 whole genomes, to elucidate the core genetic program of complex multicellularity and fruiting body development in mushroom-forming fungi (Agaricomycetes). Nearly 300 conserved gene families and >70 functional groups contained developmentally regulated genes from five to six species, covering functions related to fungal cell wall remodeling, targeted protein degradation, signal transduction, adhesion, and small secreted proteins (including effector-like orphan genes). Several of these families, including F-box proteins, expansin-like proteins, protein kinases, and transcription factors, showed expansions in Agaricomycetes, many of which convergently expanded in multicellular plants and/or animals too, reflecting convergent solutions to genetic hurdles imposed by complex multicellularity among independently evolved lineages. This study provides an entry point to studying mushroom development and complex multicellularity in one of the largest clades of complex eukaryotic organisms., Competing Interests: The authors declare no conflict of interest.

Published
2019
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17. Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant-pathogen interactions in a tree.

Author

Muchero W, Sondreli KL, Chen JG, Urbanowicz BR, Zhang J, Singan V, Yang Y, Brueggeman RS, Franco-Coronado J, Abraham N, Yang JY, Moremen KW, Weisberg AJ, Chang JH, Lindquist E, Barry K, Ranjan P, Jawdy S, Schmutz J, Tuskan GA, and LeBoldus JM

Subjects
Alleles, Chromosome Mapping, Chromosomes, Plant chemistry, Disease Resistance genetics, Gene Expression Profiling, Genetic Loci, Host-Pathogen Interactions immunology, Mannose-Binding Lectin genetics, Mannose-Binding Lectin immunology, Plant Diseases immunology, Plant Diseases microbiology, Plant Immunity genetics, Plant Proteins immunology, Populus immunology, Populus microbiology, Protein Kinases genetics, Protein Kinases immunology, Receptors, Cell Surface genetics, Receptors, Cell Surface immunology, Saccharomycetales physiology, Gene Expression Regulation, Plant, Host-Pathogen Interactions genetics, Plant Diseases genetics, Plant Proteins genetics, Populus genetics, Saccharomycetales pathogenicity, Transcriptome
Abstract

Invasive microbes causing diseases such as sudden oak death negatively affect ecosystems and economies around the world. The deployment of resistant genotypes for combating introduced diseases typically relies on breeding programs that can take decades to complete. To demonstrate how this process can be accelerated, we employed a genome-wide association mapping of ca 1,000 resequenced Populus trichocarpa trees individually challenged with Sphaerulina musiva , an invasive fungal pathogen. Among significant associations, three loci associated with resistance were identified and predicted to encode one putative membrane-bound L-type receptor-like kinase and two receptor-like proteins. A susceptibility-associated locus was predicted to encode a putative G-type D-mannose-binding receptor-like kinase. Multiple lines of evidence, including allele analysis, transcriptomics, binding assays, and overexpression, support the hypothesized function of these candidate genes in the P. trichocarpa response to S. musiva ., Competing Interests: The authors declare no conflict of interest., (Copyright © 2018 the Author(s). Published by PNAS.)

Published
2018
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18. Author Correction: Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria.

Author

Sipos G, Prasanna AN, Walter MC, O'Connor E, Bálint B, Krizsán K, Kiss B, Hess J, Varga T, Slot J, Riley R, Bóka B, Rigling D, Barry K, Lee J, Mihaltcheva S, LaButti K, Lipzen A, Waldron R, Moloney NM, Sperisen C, Kredics L, Vágvölgyi C, Patrignani A, Fitzpatrick D, Nagy I, Doyle S, Anderson JB, Grigoriev IV, Güldener U, Münsterkötter M, and Nagy LG

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

Author

Sipos G, Prasanna AN, Walter MC, O'Connor E, Bálint B, Krizsán K, Kiss B, Hess J, Varga T, Slot J, Riley R, Bóka B, Rigling D, Barry K, Lee J, Mihaltcheva S, LaButti K, Lipzen A, Waldron R, Moloney NM, Sperisen C, Kredics L, Vágvölgyi C, Patrignani A, Fitzpatrick D, Nagy I, Doyle S, Anderson JB, Grigoriev IV, Güldener U, Münsterkötter M, and Nagy LG

Subjects
Proteomics, Sequence Analysis, RNA, Species Specificity, Transcriptome, Armillaria genetics, Fungal Proteins genetics, Genome, Fungal
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
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20. Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms.

Author

Hausmann B, Knorr KH, Schreck K, Tringe SG, Glavina Del Rio T, Loy A, and Pester M

Subjects
Bacteria classification, Bacteria genetics, Bacteria isolation & purification, Ecosystem, Fermentation, Methane metabolism, Oxidation-Reduction, Sulfur metabolism, Bacteria metabolism, Microbial Consortia, Soil Microbiology, Sulfates metabolism
Abstract

Dissimilatory sulfate reduction in peatlands is sustained by a cryptic sulfur cycle and effectively competes with methanogenic degradation pathways. In a series of peat soil microcosms incubated over 50 days, we identified bacterial consortia that responded to small, periodic additions of individual fermentation products (formate, acetate, propionate, lactate or butyrate) in the presence or absence of sulfate. Under sulfate supplementation, net sulfate turnover (ST) steadily increased to 16-174 nmol cm(-3) per day and almost completely blocked methanogenesis. 16S rRNA gene and cDNA amplicon sequencing identified microorganisms whose increases in ribosome numbers strongly correlated to ST. Natively abundant (⩾0.1% estimated genome abundance) species-level operational taxonomic units (OTUs) showed no significant response to sulfate. In contrast, low-abundance OTUs responded significantly to sulfate in incubations with propionate, lactate and butyrate. These OTUs included members of recognized sulfate-reducing taxa (Desulfosporosinus, Desulfopila, Desulfomonile, Desulfovibrio) and also members of taxa that are either yet unknown sulfate reducers or metabolic interaction partners thereof. Most responsive OTUs markedly increased their ribosome content but only weakly increased in abundance. Responsive Desulfosporosinus OTUs even maintained a constantly low population size throughout 50 days, which suggests a novel strategy of rare biosphere members to display activity. Interestingly, two OTUs of the non-sulfate-reducing genus Telmatospirillum (Alphaproteobacteria) showed strongly contrasting preferences towards sulfate in butyrate-amended microcosms, corroborating that closely related microorganisms are not necessarily ecologically coherent. We show that diverse consortia of low-abundance microorganisms can perform peat soil sulfate reduction, a process that exerts control on methane production in these climate-relevant ecosystems.

Published
2016
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21. Magnetic bead purification of labeled DNA fragments for high-throughput capillary electrophoresis sequencing.

Author

Elkin C, Kapur H, Smith T, Humphries D, Pollard M, Hammon N, and Hawkins T

Subjects
Ethanol metabolism, Glycols metabolism, Magnetics, Microspheres, Water metabolism, DNA isolation & purification, Electrophoresis, Capillary methods
Abstract

We have developed an automated purification method for dye-terminator-based DNA sequencing products using a magnetic bead approach. This 384-well protocol generates sequence fragments that are essentially free of template DNA, salt, and excess dye-terminator products. In comparison with traditional ethanol precipitation protocols, this method uses no centrifugation, is rapid, completely automated, and increases the phred-20 read length by an average of 40 bases. To date, we have processed over 4 million samples with 94% averaging 641 phred-20 bases on the MegaBACE 1000 and 4000 and the ABI PRISM 3700 capillary instruments.

Published
2002
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