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5. Development of Immunoassay for Detection of Engineered Endolysin LysAm24-SMAP.

Author

Klimova, A. A., Grigoriev, I. V., Vasina, D. V., Anurova, M. N., Gushchin, V. A., and Antonova, N. P.

Subjects
*ENZYME-linked immunosorbent assay, *IMMUNOASSAY, *LYSINS, *MATRIX effect
Abstract

In recent years modified bacteriophage lysins have widely been investigated for the purposes of development of antibacterial therapy. Thus, effective and precise methods for the quantitative analysis of these enzymes are in high demand. The enzyme-linked immunosorbent assay (ELISA) method has been developed for the detection of recombinant modified endolysin LysAm24-SMAP in biological samples. The optimal parameters for protein detection were determined, in particular, the influence of salt and the composition of the buffer system for preparation of the samples was studied. The applicability of the immunodetection system of the genetically engineered endolysin LysAm24-SMAP in various biological samples with enzyme concentrations from 0.4 ng/mL was demonstrated. In addition, the influence of matrix effects in samples of animal organs and tissue homogenates and producer strain lysates and their individual components during the analysis was assessed and it was shown that 0.65 M NaCl addition in the ELISA buffer is crucial for achieving correct results and reduces nonspecific interactions in the case of LysAm24-SMAP. The effectiveness of the developed system in the immunochemical control of the bacteriolytic enzyme was confirmed. [ABSTRACT FROM AUTHOR]

Published
2024
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6. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Author

Riley, R., Salamov, A. A., Brown, D. W., Nagy, L. G., Floudas, D., Held, B. W., Levasseur, A., Lombard, V., Morin, E., Otillar, R., Lindquist, E. A., Sun, H., LaButti, K. M., Schmutz, J., Jabbour, D., Luo, H., Baker, S. E., Pisabarro, A. G., Walton, J. D., Blanchette, R. A., Henrissat, B., Martin, F., Cullen, D., Hibbett, D. S., and Grigoriev, I. V.

Published
2014

9. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

Author

Martin, F., Aerts, A., Ahren, D., Brun, A., Danchin, E. G. J., Duchaussoy, F., Gibon, J., Kohler, A., Lindquist, E., Peresa, V., Salamov, A., Shapiro, H. J., Wuyts, J., Blaudez, D., Buee, M., Brokstein, P., Canback, B., Cohen, D., Courty, P. E., Coutinho, P. M., Delaruelle, C., Detter, J. C., Deveau, A., DiFazio, S., Duplessis, S., Fraissinet-Tachet, L., Lucic, E., Frey-Klett, P., Fourrey, C., Feussner, I., Gay, G., Grimwood, J., Hoegger, P. J., Jain, P., Kilaru, S., Labbe, J., Lin, Y. C., Legue, V., Tacon, F. Le, Marmeisse, R., Melayah, D., Montanini, B., Muratet, M., Nehls, U., Niculita-Hirzel, H., Secq, M. P. Oudot-Le, Peter, M., Quesneville, H., Rajashekar, B., Reich, M., Rouhier, N., Schmutz, J., Yin, T., Chalot, M., Henrissat, B., Kues, U., Lucas, S., Peer, Y. Van de, Podila, G. K., Polle, A., Pukkila, P. J., Richardson, P. M., Rouze, P., Sanders, I. R., Stajich, J. E., Tunlid, A., Tuskan, G., and Grigoriev, I. V.

Abstract

Mycorrhizal symbioses the union of roots and soil fungi are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants 1, 2. Boreal, temperate and montane forests all depend on ectomycorrhizae1. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.

Published
2008

15. 101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens

Author

Haridas, S., Albert, R., Binder, M., Bloem, J., LaButti, K., Salamov, A., Andreopoulos, B., Baker, S. E., Barry, K., Bills, G., Bluhm, B. H., Cannon, C., Castanera, R., Culley, D. E., Daum, C., Ezra, D., González, J. B., Henrissat, B., Kuo, A., Liang, C., Lipzen, A., Lutzoni, F., Magnuson, J., Mondo, S. J., Nolan, M., Ohm, R. A., Pangilinan, J., Park, H. J., Ramírez, L., Alfaro, M., Sun, H., Tritt, A., Yoshinaga, Y., Zwiers, L. H., Turgeon, B. G., Goodwin, S. B., Spatafora, J. W., Crous, P. W., Grigoriev, I. V., Haridas, S., Albert, R., Binder, M., Bloem, J., LaButti, K., Salamov, A., Andreopoulos, B., Baker, S. E., Barry, K., Bills, G., Bluhm, B. H., Cannon, C., Castanera, R., Culley, D. E., Daum, C., Ezra, D., González, J. B., Henrissat, B., Kuo, A., Liang, C., Lipzen, A., Lutzoni, F., Magnuson, J., Mondo, S. J., Nolan, M., Ohm, R. A., Pangilinan, J., Park, H. J., Ramírez, L., Alfaro, M., Sun, H., Tritt, A., Yoshinaga, Y., Zwiers, L. H., Turgeon, B. G., Goodwin, S. B., Spatafora, J. W., Crous, P. W., and Grigoriev, I. V.

Abstract

Dothideomycetes is the largest class of kingdom Fungi and comprises an incredible diversity of lifestyles, many of which have evolved multiple times. Plant pathogens represent a major ecological niche of the class Dothideomycetes and they are known to infect most major food crops and feedstocks for biomass and biofuel production. Studying the ecology and evolution of Dothideomycetes has significant implications for our fundamental understanding of fungal evolution, their adaptation to stress and host specificity, and practical implications with regard to the effects of climate change and on the food, feed, and livestock elements of the agro-economy. In this study, we present the first large-scale, whole-genome comparison of 101 Dothideomycetes introducing 55 newly sequenced species. The availability of whole-genome data produced a high-confidence phylogeny leading to reclassification of 25 organisms, provided a clearer picture of the relationships among the various families, and indicated that pathogenicity evolved multiple times within this class. We also identified gene family expansions and contractions across the Dothideomycetes phylogeny linked to ecological niches providing insights into genome evolution and adaptation across this group. Using machine-learning methods we classified fungi into lifestyle classes with >95 % accuracy and identified a small number of gene families that positively correlated with these distinctions. This can become a valuable tool for genome-based prediction of species lifestyle, especially for rarely seen and poorly studied species.

Published
2020

16. 101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens

Author

Sub Molecular Microbiology, Molecular Microbiology, Haridas, S., Albert, R., Binder, M., Bloem, J., LaButti, K., Salamov, A., Andreopoulos, B., Baker, S. E., Barry, K., Bills, G., Bluhm, B. H., Cannon, C., Castanera, R., Culley, D. E., Daum, C., Ezra, D., González, J. B., Henrissat, B., Kuo, A., Liang, C., Lipzen, A., Lutzoni, F., Magnuson, J., Mondo, S. J., Nolan, M., Ohm, R. A., Pangilinan, J., Park, H. J., Ramírez, L., Alfaro, M., Sun, H., Tritt, A., Yoshinaga, Y., Zwiers, L. H., Turgeon, B. G., Goodwin, S. B., Spatafora, J. W., Crous, P. W., Grigoriev, I. V., Sub Molecular Microbiology, Molecular Microbiology, Haridas, S., Albert, R., Binder, M., Bloem, J., LaButti, K., Salamov, A., Andreopoulos, B., Baker, S. E., Barry, K., Bills, G., Bluhm, B. H., Cannon, C., Castanera, R., Culley, D. E., Daum, C., Ezra, D., González, J. B., Henrissat, B., Kuo, A., Liang, C., Lipzen, A., Lutzoni, F., Magnuson, J., Mondo, S. J., Nolan, M., Ohm, R. A., Pangilinan, J., Park, H. J., Ramírez, L., Alfaro, M., Sun, H., Tritt, A., Yoshinaga, Y., Zwiers, L. H., Turgeon, B. G., Goodwin, S. B., Spatafora, J. W., Crous, P. W., and Grigoriev, I. V.

Published
2020

18. Erratum for Myers et al., “Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses”

Author

Myers, J. M., primary, Bonds, A. E., additional, Clemons, R. A., additional, Thapa, N. A., additional, Simmons, D. R., additional, Carter-House, D., additional, Ortanez, J., additional, Liu, P., additional, Miralles-Durán, A., additional, Desirò, A., additional, Longcore, J. E., additional, Bonito, G., additional, Stajich, J. E., additional, Spatafora, J. W., additional, Chang, Y., additional, Corrochano, L. M., additional, Gryganskyi, A., additional, Grigoriev, I. V., additional, and James, T. Y., additional

Published
2020
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20. Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses

Author

Myers, J. M., primary, Bonds, A. E., additional, Clemons, R. A., additional, Thapa, N. A., additional, Simmons, D. R., additional, Carter-House, D., additional, Ortanez, J., additional, Liu, P., additional, Miralles-Durán, A., additional, Desirò, A., additional, Longcore, J. E., additional, Bonito, G., additional, Stajich, J. E., additional, Spatafora, J. W., additional, Chang, Y., additional, Corrochano, L. M., additional, Gryganskyi, A., additional, Grigoriev, I. V., additional, and James, T. Y., additional

Published
2020
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23. Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli

Author

Mäkelä, M R, DiFalco, M, McDonnell, E, Nguyen, T T M, Wiebenga, A, Hildén, K, Peng, M, Grigoriev, I V, Tsang, A, de Vries, R P, Sub Software Technology begr. 1-1-13, Sub Molecular Microbiology, Sub Biomol.Mass Spectrometry & Proteom., Sub Cell Biology, Sub Molecular Plant Physiology, Celbiologie, Molecular Plant Physiology, Department of Microbiology, Fungal Genetics and Biotechnology, Helsinki Institute of Sustainability Science (HELSUS), Westerdijk Fungal Biodiversity Institute, Westerdijk Fungal Biodiversity Institute - Fungal Physiology, Sub Software Technology begr. 1-1-13, Sub Molecular Microbiology, Sub Biomol.Mass Spectrometry & Proteom., Sub Cell Biology, Sub Molecular Plant Physiology, Celbiologie, and Molecular Plant Physiology

Subjects
0301 basic medicine, EXPRESSION, CAZy, Sugar beet pulp, GENES, Mycology & Parasitology, Wheat bran, Polysaccharide, Genome, Microbiology, EXO-ARABINANASE, 03 medical and health sciences, chemistry.chemical_compound, Xylan, D-GALACTURONIC ACID, CARBOHYDRATE, Cellulose, Xyloglucan, lcsh:QH301-705.5, Gene, 1183 Plant biology, microbiology, virology, 2. Zero hunger, chemistry.chemical_classification, Aspergillus, biology, Phylogenetic tree, Plant biomass degradation, food and beverages, 15. Life on land, NIGER, biology.organism_classification, Agricultural and Biological Sciences (miscellaneous), Pectin, TRANSCRIPTIONAL ACTIVATOR, 030104 developmental biology, Enzyme, lcsh:Biology (General), chemistry, Biochemistry, XLNR, FUNGAL PATHOGEN, REGULATOR, Research Paper
Abstract

We classified the genes encoding carbohydrate-active enzymes (CAZymes) in 17 sequenced genomes representing 16 evolutionarily diverse Aspergillus species. We performed a phylogenetic analysis of the encoding enzymes, along with experimentally characterized CAZymes, to assign molecular function to the Aspergilli CAZyme families and subfamilies. Genome content analysis revealed that the numbers of CAZy genes per CAZy family related to plant biomass degradation follow closely the taxonomic distance between the species. On the other hand, growth analysis showed almost no correlation between the number of CAZyme genes and the efficiency in polysaccharide utilization. The exception is A. clavatus where a reduced number of pectinolytic enzymes can be correlated with poor growth on pectin. To gain detailed information on the enzymes used by Aspergilli to breakdown complex biomass, we conducted exoproteome analysis by mass spectrometry. These results showed that Aspergilli produce many different enzymes mixtures in the presence of sugar beet pulp and wheat bran. Despite the diverse enzyme mixtures produced, species of section Nigri, A. aculeatus, A. nidulans and A. terreus, produce mixtures of enzymes with activities that are capable of digesting all the major polysaccharides in the available substrates, suggesting that they are capable of degrading all the polysaccharides present simultaneously. For the other Aspergilli, typically the enzymes produced are targeted to a subset of polysaccharides present, suggesting that they can digest only a subset of polysaccharides at a given time. Key words: Aspergillus, Cellulose, Pectin, Plant biomass degradation, Sugar beet pulp, Wheat bran, Xylan, Xyloglucan

Published
2018

24. The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi

Author

Aguilar-Pontes, M V, Brandl, J, McDonnell, E, Strasser, K, Nguyen, T T M, Riley, R, Mondo, S, Salamov, A, Nybo, J L, Vesth, T C, Grigoriev, I V, Andersen, M R, Tsang, A, de Vries, R P, Sub Software Technology begr. 1-1-13, Sub Cell Biology, Sub Molecular Plant Physiology, Celbiologie, Molecular Plant Physiology, Westerdijk Fungal Biodiversity Institute, Westerdijk Fungal Biodiversity Institute - Fungal Physiology, Sub Software Technology begr. 1-1-13, Sub Cell Biology, Sub Molecular Plant Physiology, Celbiologie, and Molecular Plant Physiology

Subjects
0301 basic medicine, 030106 microbiology, Mycology & Parasitology, Computational biology, Microbiology, Genome, 03 medical and health sciences, Gold standard genome, Genetics, Sugar, lcsh:QH301-705.5, Sugar catabolism, Gene, Aspergillus, biology, Genomic diversity, Catabolism, Classical genetics, Human Genome, Aspergillus niger, biology.organism_classification, Agricultural and Biological Sciences (miscellaneous), 030104 developmental biology, lcsh:Biology (General), Adaptation
Abstract

The fungal kingdom is too large to be discovered exclusively by classical genetics. The access to omics data opens a new opportunity to study the diversity within the fungal kingdom and how adaptation to new environments shapes fungal metabolism. Genomes are the foundation of modern science but their quality is crucial when analysing omics data. In this study, we demonstrate how one gold-standard genome can improve functional prediction across closely related species to be able to identify key enzymes, reactions and pathways with the focus on primary carbon metabolism.Based on this approach we identified alternative genes encoding various steps of the different sugar catabolic pathways, and as such provided leads for functional studies into this topic. We also revealed significant diversity with respect to genome content, although this did not always correlate to the ability of the species to use the corresponding sugar as a carbon source. Key words: Aspergillus, Genomic diversity, Gold standard genome, Sugar catabolism

Published
2018

26. Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli

Author

Sub Software Technology begr. 1-1-13, Sub Molecular Microbiology, Sub Biomol.Mass Spectrometry & Proteom., Sub Cell Biology, Sub Molecular Plant Physiology, Celbiologie, Molecular Plant Physiology, Mäkelä, M R, DiFalco, M, McDonnell, E, Nguyen, T T M, Wiebenga, A, Hildén, K, Peng, M, Grigoriev, I V, Tsang, A, de Vries, R P, Sub Software Technology begr. 1-1-13, Sub Molecular Microbiology, Sub Biomol.Mass Spectrometry & Proteom., Sub Cell Biology, Sub Molecular Plant Physiology, Celbiologie, Molecular Plant Physiology, Mäkelä, M R, DiFalco, M, McDonnell, E, Nguyen, T T M, Wiebenga, A, Hildén, K, Peng, M, Grigoriev, I V, Tsang, A, and de Vries, R P

Published
2018

27. The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi

Author

Sub Software Technology begr. 1-1-13, Sub Cell Biology, Sub Molecular Plant Physiology, Celbiologie, Molecular Plant Physiology, Aguilar-Pontes, M V, Brandl, J, McDonnell, E, Strasser, K, Nguyen, T T M, Riley, R, Mondo, S, Salamov, A, Nybo, J L, Vesth, T C, Grigoriev, I V, Andersen, M R, Tsang, A, de Vries, R P, Sub Software Technology begr. 1-1-13, Sub Cell Biology, Sub Molecular Plant Physiology, Celbiologie, Molecular Plant Physiology, Aguilar-Pontes, M V, Brandl, J, McDonnell, E, Strasser, K, Nguyen, T T M, Riley, R, Mondo, S, Salamov, A, Nybo, J L, Vesth, T C, Grigoriev, I V, Andersen, M R, Tsang, A, and de Vries, R P

Published
2018

28. Evolutionary genomics of the cold-Adapted diatom Fragilariopsis cylindrus

Author

Mock, T., Otillar, R. P., Strauss, Jan, McMullan, M., Paajanen, P., Schmutz, J., Salamov, A., Sanges, R., Toseland, A., Ward, B. J., Allen, A. E., Dupont, C. L., Frickenhaus, S., Maumus, F., Veluchamy, A., Wu, T., Barry, K. W., Falciatore, A., Ferrante, M. I., Fortunato, A. E., Glöckner, G., Gruber, A., Hipkin, R., Janech, M. G., Kroth, P. G., Leese, F., Lindquist, E. A., Lyon, B. R., Martin, J., Mayer, C., Parker, M., Quesneville, H., Raymond, J. A., Uhlig, C., Valas, R. E., Valentin, K. U., Worden, Alexandra Z., Armbrust, E. V., Clark, M. D., Bowler, C., Green, B. R., Moulton, V., Van Oosterhout, C., Grigoriev, I. V., Mock, T., Otillar, R. P., Strauss, Jan, McMullan, M., Paajanen, P., Schmutz, J., Salamov, A., Sanges, R., Toseland, A., Ward, B. J., Allen, A. E., Dupont, C. L., Frickenhaus, S., Maumus, F., Veluchamy, A., Wu, T., Barry, K. W., Falciatore, A., Ferrante, M. I., Fortunato, A. E., Glöckner, G., Gruber, A., Hipkin, R., Janech, M. G., Kroth, P. G., Leese, F., Lindquist, E. A., Lyon, B. R., Martin, J., Mayer, C., Parker, M., Quesneville, H., Raymond, J. A., Uhlig, C., Valas, R. E., Valentin, K. U., Worden, Alexandra Z., Armbrust, E. V., Clark, M. D., Bowler, C., Green, B. R., Moulton, V., Van Oosterhout, C., and Grigoriev, I. V.

Abstract

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-Adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2 . Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

Published
2017
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29. What drives speciation? Examination into the evolutionary events of more than 100 Aspergillus species

Author

Rasmussen, Jane Lind Nybo, Vesth, Tammi Camilla, Theobald, Sebastian, Kjærbølling, Inge, Frisvad, Jens Christian, Larsen, Thomas Ostenfeld, Riley, Robert, Salamov, A., Grigoriev, I. V., Baker, S. E., Andersen, Mikael Rørdam, Rasmussen, Jane Lind Nybo, Vesth, Tammi Camilla, Theobald, Sebastian, Kjærbølling, Inge, Frisvad, Jens Christian, Larsen, Thomas Ostenfeld, Riley, Robert, Salamov, A., Grigoriev, I. V., Baker, S. E., and Andersen, Mikael Rørdam

Published
2017

30. The ecoresponsive genome of Daphnia pulex

Author

Colbourne, J. K., Pfrender, M. E., Gilbert, D., Thomas, W. K., Tucker, A., Oakley, T. H., Tokishita, S., Aerts, A., Arnold, G. J., Basu, M. K., Bauer, D. J., C當eres, C. E., Carmel, L., Casola, C., Choi, J. H., Detter, J. C., Dong, Q., Dusheyko, S., Eads, B. D., Frlich, T., Geiler-Samerotte, K. A., Gerlach, D., Hatcher, P., Jogdeo, S., Krijgsveld, J., Kriventseva, E. V., K�ltz, D., Laforsch, C., Lindquist, E., Lopez, J., Manak, J. R., Muller, J., Pangilinan, J., Patwardhan, R. P., Pitluck, S., Pritham, E. J., Rechtsteiner, A., Rho, M., Rogozin, I. B., Sakarya, O., Salamov, A., Schaack, S., Shapiro, H., Shiga, Y., Skalitzky, C., Smith, Z., Souvorov, A., Sung, W., Tang, Z., Tsuchiya, D., Tu, H., Vos, H., Wang, M., Wolf, Y. I., Yamagata, H., Yamada, Takuji, Ye, Y., Shaw, J. R., Andrews, J., Crease, T. J., Tang, H., Lucas, S. M., Robertson, H. M., Bork, P., Koonin, E. V., Zdobnov, E. M., Grigoriev, I. V., Lynch, M., Boore, J. L., Gerlach, Daniel, Kriventseva, Evgenia, and Zdobnov, Evgeny

Subjects
0106 biological sciences, Molecular Sequence Data, Gene Conversion, Gene Expression, Biology, Environment, 010603 evolutionary biology, 01 natural sciences, Genome, Daphnia pulex, Evolution, Molecular, 03 medical and health sciences, Genes, Duplicate, Gene Duplication, Gene duplication, Gene family, Animals, ddc:576.5, Gene conversion, Amino Acid Sequence, Gene, Ecosystem, Phylogeny, 030304 developmental biology, Regulation of gene expression, Genetics, 0303 health sciences, Multidisciplinary, Base Sequence, Daphnia/genetics/physiology, Metabolic Networks and Pathways/genetics, Gene Expression Profiling, fungi, Chromosome Mapping, Molecular Sequence Annotation, Sequence Analysis, DNA, biology.organism_classification, Adaptation, Physiological, Gene expression profiling, Daphnia, Gene Expression Regulation, Genes, Multigene Family, Metabolic Networks and Pathways
Abstract

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.

Published
2011
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32. Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants

Author

van Baren, M. J., Bachy, C., Reistetter, E. N., Purvine, S. O., Grimwood, J., Sudek, S., Yu, H., Poirier, C., Deerinck, T. J., Kuo, A., Grigoriev, I. V., Wong, C.-H., Smith, R. D., Callister, S. J., Wei, C.-L., Schmutz, J., Worden, Alexandra Z., van Baren, M. J., Bachy, C., Reistetter, E. N., Purvine, S. O., Grimwood, J., Sudek, S., Yu, H., Poirier, C., Deerinck, T. J., Kuo, A., Grigoriev, I. V., Wong, C.-H., Smith, R. D., Callister, S. J., Wei, C.-L., Schmutz, J., and Worden, Alexandra Z.

Abstract

Background: Prasinophytes are widespread marine green algae that are related to plants. Cellular abundance of the prasinophyte Micromonas has reportedly increased in the Arctic due to climate-induced changes. Thus, studies of these unicellular eukaryotes are important for marine ecology and for understanding Viridiplantae evolution and diversification. Results: We generated evidence-based Micromonas gene models using proteomics and RNA-Seq to improve prasinophyte genomic resources. First, sequences of four chromosomes in the 22 Mb Micromonas pusilla (CCMP1545) genome were finished. Comparison with the finished 21 Mb genome of Micromonas commoda (RCC299; named herein) shows they share ≤8,141 of ~10,000 protein-encoding genes, depending on the analysis method. Unlike RCC299 and other sequenced eukaryotes, CCMP1545 has two abundant repetitive intron types and a high percent (26 ) GC splice donors. Micromonas has more genus-specific protein families (19 ) than other genome sequenced prasinophytes (11 ). Comparative analyses using predicted proteomes from other prasinophytes reveal proteins likely related to scale formation and ancestral photosynthesis. Our studies also indicate that peptidoglycan (PG) biosynthesis enzymes have been lost in multiple independent events in select prasinophytes and plants. However, CCMP1545, polar Micromonas CCMP2099 and prasinophytes from other classes retain the entire PG pathway, like moss and glaucophyte algae. Surprisingly, multiple vascular plants also have the PG pathway, except the Penicillin-Binding Protein, and share a unique bi-domain protein potentially associated with the pathway. Alongside Micromonas experiments using antibiotics that halt bacterial PG biosynthesis, the findings highlight unrecognized phylogenetic complexity in PG-pathway retention and implicate a role in chloroplast structure or division in several extant Viridiplantae lineages. Conclusions: Extensive differences in gene loss and architecture between related

Published
2016
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34. The Heterobasidion irregulare genome project

Author

Olson, Å., Aerts, A., Asiegbu, F., Belbahri, L., Bouzid, O., Broberg, A., Canbäck, B., Coutinho, P. M., Cullen, D., Dalman, K., Deflorio, G., VAN DIEPEN, L. T. A., Dunand, C., Duplessis, S., Durling, M., Gonthier, Paolo, Grimwood, J., Fossdal, C. G., Hansson, D., Henrissat, B., Hietala, A., Himmelstrand, K., Hoffmeister, D., Högberg, N., James, T. Y., Karlsson, M., Lind, M., Kohler, A., Kües, U., Lee, Y. H., Lin, Y. C., Lindquist, E., Lombard, V., Lucas, S., Lundén, K., Morin, E., Murat, C., Park, J., Raffaello, T., Rouzé, P., Salamov, A., Schmutz, J., Solheim, H., Ståhlberg, J., Vélëz, H., DE VRIES, R. P., Wiebenga, A., Woodward, S., Yakovlev, I., Garbelotto, M., Martin, F., Grigoriev, I. V., and Stenlid, J.

Published
2013

35. Insight intotrade-off between wood decay and parasitism: Insights from the genome of a fungal forest pathogen

Author

Olson, Å., Aerts, A., Asiegbu, F., Belbahri, L., Bouzid, O., Broberg, A., Canbäck, B., Coutinho, P. M., Cullen, D., Dalman, K., Deflorio, G., VAN DIEPEN, L. T. A., Dunand, C., Duplessis, S., Durling, M., Gonthier, Paolo, Grimwood, J., Fossdal, C. G., Hansson, D., Henrissat, B., Hietala, A., Himmelstrand, K., Hoffmeister, D., Högberg, N., James, T. Y., Karlsson, M., Lind, M., Kohler, A., Kües, U., Lee, Y. H., Lin, Y. C., Lindquist, E., Lombard, V., Lucas, S., Lundén, K., Morin, E., Murat, C., Park, J., Raffaello, T., Rouzé, P., Salamov, A., Schmutz, J., Solheim, H., Ståhlberg, J., Vélëz, H., DE VRIES, R. P., Wiebenga, A., Woodward, S., Yakovlev, I., Garbelotto, M., Martin, F., Grigoriev, I. V., and Stenlid, J.

Subjects
parasitism, wood decay, pathology, genome, Heterobasidion, saprotrophy, trade-off
Published
2012

36. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Bowler, C., Allan, A. E., Badger, J. H., Grimwood, J., Jabbari, K., Kuo, A., Maheshwari, U., Martens, C., Maumus, F., Otillar, R. P., Rayko, E., Salamov, A., Vandepoele, K., Beszeri, B., Gruber, A., Heijde, M., Katinka, M., Mock, Thomas, Valentin, Klaus-Ulrich, Verret, F., Berges, J. A., Brownlee, C., Chiovitti, A., Jae Choi, C., Coesel, S., De Martino, A., Detter, J. C., Durkin, C., Falciatore, A., Fournet, J., Haruta, M., Huysman, M. J. J., Jenkins, B. D., Jiroutova, K., Jorgensen, R. E., Joubert, Y., Kaplan, A., Kröger, N., Kroth, P. G., La Roche, J., Lindquiste, E., Lommer, M., Martin-Jézéquel, V., Lopez, P. J., Lucas, S., Mangogna, M., McGinnis, K., Medlin, Linda, Monsant, A., Oudot-Le Secq, M.-P., Napoli, C., Obornik, M., Petit, J.-L., Porcel, B. M., Poulsen, N., Robison, M., Rychlewski, L., Rynearson, T. A., Schmutz, J., Schnitzler Parker, M., Shapiro, H., Siaur, M., Stanley, M., Sussman, M. J., Taylor, A. R., Vardi, A., von Dassow, P., Vyverman, W., Willis, A., Wyrwicz, L. S., Rokhsar, D. S., Weissenbach, J., Armbrust, E. V., Green, B. R., Van de Peer, Y., Grigoriev, I. V., and Cadoret, J.-P.

Published
2008

40. Pan genome of the phytoplankton Emiliania underpins its global distribution

Author

Read, B. A., Kegel, J., Klute, M. J., Kuo, A., Lefebvre, S. C., Maumus, F., Mayer, C., Miller, J., Monier, A., Salamov, A., Young, J., Aguilar, M., Claverie, J.-M., Frickenhaus, S., Gonzalez, K., Herman, E. K., Lin, Y.-C., Napier, J., Ogata, H., Sarno, A. F., Shmutz, J., Schroeder, D., De Vargas, C., Verret, F., Von Dassow, P., Valentin, K., Van De Peer, Y., Wheeler, G., Dacks, J. B., Delwiche, C. F., Dyhrman, S. T., Glöckner, G., John, U., Richards, T., Worden, Alexandra Z., Zhang, X., Grigoriev, I. V., Allen, A. E., Bidle, K., Borodovsky, M., Bowler, C., Brownlee, C., Mark Cock, J., Elias, M., Gladyshev, V. N., Groth, M., Guda, C., Hadaegh, A., Iglesias-Rodriguez, M. D., Jenkins, J., Jones, B. M., Lawson, T., Leese, F., Lindquist, E., Lobanov, A., Lomsadze, A., Malik, S.-B., Marsh, M. E., MacKinder, L., Mock, T., Mueller-Roeber, B., Pagarete, A., Parker, M., Probert, I., Quesneville, H., Raines, C., Rensing, S. A., Riaño-Pachón, D. M., Richier, S., Rokitta, S., Shiraiwa, Y., Soanes, D. M., Van Der Giezen, M., Wahlund, T. M., Williams, B., Wilson, W., Wolfe, G., Wurch, L. L., Read, B. A., Kegel, J., Klute, M. J., Kuo, A., Lefebvre, S. C., Maumus, F., Mayer, C., Miller, J., Monier, A., Salamov, A., Young, J., Aguilar, M., Claverie, J.-M., Frickenhaus, S., Gonzalez, K., Herman, E. K., Lin, Y.-C., Napier, J., Ogata, H., Sarno, A. F., Shmutz, J., Schroeder, D., De Vargas, C., Verret, F., Von Dassow, P., Valentin, K., Van De Peer, Y., Wheeler, G., Dacks, J. B., Delwiche, C. F., Dyhrman, S. T., Glöckner, G., John, U., Richards, T., Worden, Alexandra Z., Zhang, X., Grigoriev, I. V., Allen, A. E., Bidle, K., Borodovsky, M., Bowler, C., Brownlee, C., Mark Cock, J., Elias, M., Gladyshev, V. N., Groth, M., Guda, C., Hadaegh, A., Iglesias-Rodriguez, M. D., Jenkins, J., Jones, B. M., Lawson, T., Leese, F., Lindquist, E., Lobanov, A., Lomsadze, A., Malik, S.-B., Marsh, M. E., MacKinder, L., Mock, T., Mueller-Roeber, B., Pagarete, A., Parker, M., Probert, I., Quesneville, H., Raines, C., Rensing, S. A., Riaño-Pachón, D. M., Richier, S., Rokitta, S., Shiraiwa, Y., Soanes, D. M., Van Der Giezen, M., Wahlund, T. M., Williams, B., Wilson, W., Wolfe, G., and Wurch, L. L.

Abstract

Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO 2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO 2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions. © 2013 Macmillan Publishers Limited. All rights reserved.

Published
2013
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41. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

Author

Curtis, B. A., Tanifuji, G., Maruyama, S., Gile, G. H., Hopkins, J. F., Eveleigh, R. J. M., Nakayama, T., Malik, S.-B., Onodera, N. T., Slamovits, C. H., Spencer, D. F., Lane, C. E., Gray, M. W., Archibald, J. M., Burki, F., Hirakawa, Y., Reyes-Prieto, A., Keeling, P. J., Fast, N. M., Green, B. R., Grisdale, C. J., Gruber, A., Kroth, P. G., Irimia, M., Arias, M. C., Ball, S. G., Kuo, A., Schmutz, J., Grimwood, J., Lindquist, E., Lucas, S., Salamov, A., Grigoriev, I. V., Rensing, S. A., Symeonidi, A., Elias, M., Herman, E. K., Klute, M. J., Dacks, J. B., Oborník, M., Kořený, L., Durnford, D. G., Neilson, J. A. D., Armbrust, E. V., Rocap, G., Aves, S. J., Liu, Y., Beiko, R. G., Coutinho, P., Henrissat, B., Hempel, F., Maier, U.G., Zauner, S., Häppner, M. P., Ishida, K.-I., Shirato, S., Suzuki, S., Kim, E., Richards, T. A., Mc Rose, D., Worden, Alexandra Z., Mock, T., Poole, A. M., Pritham, E. J., Roy, S. W., Schaack, S., Bell, C., Bharti, A. K., Crow, J. A., Kramer, R., Mc Fadden, G. I., Curtis, B. A., Tanifuji, G., Maruyama, S., Gile, G. H., Hopkins, J. F., Eveleigh, R. J. M., Nakayama, T., Malik, S.-B., Onodera, N. T., Slamovits, C. H., Spencer, D. F., Lane, C. E., Gray, M. W., Archibald, J. M., Burki, F., Hirakawa, Y., Reyes-Prieto, A., Keeling, P. J., Fast, N. M., Green, B. R., Grisdale, C. J., Gruber, A., Kroth, P. G., Irimia, M., Arias, M. C., Ball, S. G., Kuo, A., Schmutz, J., Grimwood, J., Lindquist, E., Lucas, S., Salamov, A., Grigoriev, I. V., Rensing, S. A., Symeonidi, A., Elias, M., Herman, E. K., Klute, M. J., Dacks, J. B., Oborník, M., Kořený, L., Durnford, D. G., Neilson, J. A. D., Armbrust, E. V., Rocap, G., Aves, S. J., Liu, Y., Beiko, R. G., Coutinho, P., Henrissat, B., Hempel, F., Maier, U.G., Zauner, S., Häppner, M. P., Ishida, K.-I., Shirato, S., Suzuki, S., Kim, E., Richards, T. A., Mc Rose, D., Worden, Alexandra Z., Mock, T., Poole, A. M., Pritham, E. J., Roy, S. W., Schaack, S., Bell, C., Bharti, A. K., Crow, J. A., Kramer, R., and Mc Fadden, G. I.

Abstract

Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote–eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have <21, 000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph. © 2012 Macmillan Publishers Limited. All rights reserved.

Published
2012
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42. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.

Author

Worden, A. Z., Lee, J.-H., Mock, Thomas, Rouzé, P., Simmson, M. P., Aerts, A. L., Allen, A. E., Cuvelier, M. L., Derelle, E., Everett, M. V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S. M., Parker, M. S., Rombauts, S., Salamov, A., Badger, J. H., Coutinho, P. M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J. E., John, Uwe, Lanier, W., Lindquist, E. A., Lucas, S., Mayer, K. F. X., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, E. V., Bhattacharya, D., Goodenough, U. W., Van de Peer, Y., Grigoriev, I. V., Worden, A. Z., Lee, J.-H., Mock, Thomas, Rouzé, P., Simmson, M. P., Aerts, A. L., Allen, A. E., Cuvelier, M. L., Derelle, E., Everett, M. V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S. M., Parker, M. S., Rombauts, S., Salamov, A., Badger, J. H., Coutinho, P. M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J. E., John, Uwe, Lanier, W., Lindquist, E. A., Lucas, S., Mayer, K. F. X., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, E. V., Bhattacharya, D., Goodenough, U. W., Van de Peer, Y., and Grigoriev, I. V.

Published
2009

43. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Cadoret, J.-P., Bowler, C., Allan, A. E., Badger, J. H., Grimwood, J., Jabbari, K., Kuo, A., Maheshwari, U., Martens, C., Maumus, F., Otillar, R. P., Rayko, E., Salamov, A., Vandepoele, K., Beszeri, B., Gruber, A., Heijde, M., Katinka, M., Mock, Thomas, Valentin, Klaus-Ulrich, Verret, F., Berges, J. A., Brownlee, C., Chiovitti, A., Jae Choi, C., Coesel, S., De Martino, A., Detter, J. C., Durkin, C., Falciatore, A., Fournet, J., Haruta, M., Huysman, M. J. J., Jenkins, B. D., Jiroutova, K., Jorgensen, R. E., Joubert, Y., Kaplan, A., Kröger, N., Kroth, P. G., La Roche, J., Lindquiste, E., Lommer, M., Martin-Jézéquel, V., Lopez, P. J., Lucas, S., Mangogna, M., McGinnis, K., Medlin, Linda, Monsant, A., Oudot-Le Secq, M.-P., Napoli, C., Obornik, M., Petit, J.-L., Porcel, B. M., Poulsen, N., Robison, M., Rychlewski, L., Rynearson, T. A., Schmutz, J., Schnitzler Parker, M., Shapiro, H., Siaur, M., Stanley, M., Sussman, M. J., Taylor, A. R., Vardi, A., von Dassow, P., Vyverman, W., Willis, A., Wyrwicz, L. S., Rokhsar, D. S., Weissenbach, J., Armbrust, E. V., Green, B. R., Van de Peer, Y., Grigoriev, I. V., Cadoret, J.-P., Bowler, C., Allan, A. E., Badger, J. H., Grimwood, J., Jabbari, K., Kuo, A., Maheshwari, U., Martens, C., Maumus, F., Otillar, R. P., Rayko, E., Salamov, A., Vandepoele, K., Beszeri, B., Gruber, A., Heijde, M., Katinka, M., Mock, Thomas, Valentin, Klaus-Ulrich, Verret, F., Berges, J. A., Brownlee, C., Chiovitti, A., Jae Choi, C., Coesel, S., De Martino, A., Detter, J. C., Durkin, C., Falciatore, A., Fournet, J., Haruta, M., Huysman, M. J. J., Jenkins, B. D., Jiroutova, K., Jorgensen, R. E., Joubert, Y., Kaplan, A., Kröger, N., Kroth, P. G., La Roche, J., Lindquiste, E., Lommer, M., Martin-Jézéquel, V., Lopez, P. J., Lucas, S., Mangogna, M., McGinnis, K., Medlin, Linda, Monsant, A., Oudot-Le Secq, M.-P., Napoli, C., Obornik, M., Petit, J.-L., Porcel, B. M., Poulsen, N., Robison, M., Rychlewski, L., Rynearson, T. A., Schmutz, J., Schnitzler Parker, M., Shapiro, H., Siaur, M., Stanley, M., Sussman, M. J., Taylor, A. R., Vardi, A., von Dassow, P., Vyverman, W., Willis, A., Wyrwicz, L. S., Rokhsar, D. S., Weissenbach, J., Armbrust, E. V., Green, B. R., Van de Peer, Y., and Grigoriev, I. V.

Published
2008

44. The Genome Portal of the Department of Energy Joint Genome Institute

Author

Grigoriev, I. V., primary, Nordberg, H., additional, Shabalov, I., additional, Aerts, A., additional, Cantor, M., additional, Goodstein, D., additional, Kuo, A., additional, Minovitsky, S., additional, Nikitin, R., additional, Ohm, R. A., additional, Otillar, R., additional, Poliakov, A., additional, Ratnere, I., additional, Riley, R., additional, Smirnova, T., additional, Rokhsar, D., additional, and Dubchak, I., additional

Published
2011
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45. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

Author

Martin, F., primary, Aerts, A., additional, Ahrén, D., additional, Brun, A., additional, Danchin, E. G. J., additional, Duchaussoy, F., additional, Gibon, J., additional, Kohler, A., additional, Lindquist, E., additional, Pereda, V., additional, Salamov, A., additional, Shapiro, H. J., additional, Wuyts, J., additional, Blaudez, D., additional, Buée, M., additional, Brokstein, P., additional, Canbäck, B., additional, Cohen, D., additional, Courty, P. E., additional, Coutinho, P. M., additional, Delaruelle, C., additional, Detter, J. C., additional, Deveau, A., additional, DiFazio, S., additional, Duplessis, S., additional, Fraissinet-Tachet, L., additional, Lucic, E., additional, Frey-Klett, P., additional, Fourrey, C., additional, Feussner, I., additional, Gay, G., additional, Grimwood, J., additional, Hoegger, P. J., additional, Jain, P., additional, Kilaru, S., additional, Labbé, J., additional, Lin, Y. C., additional, Legué, V., additional, Le Tacon, F., additional, Marmeisse, R., additional, Melayah, D., additional, Montanini, B., additional, Muratet, M., additional, Nehls, U., additional, Niculita-Hirzel, H., additional, Secq, M. P. Oudot-Le, additional, Peter, M., additional, Quesneville, H., additional, Rajashekar, B., additional, Reich, M., additional, Rouhier, N., additional, Schmutz, J., additional, Yin, T., additional, Chalot, M., additional, Henrissat, B., additional, Kües, U., additional, Lucas, S., additional, Van de Peer, Y., additional, Podila, G. K., additional, Polle, A., additional, Pukkila, P. J., additional, Richardson, P. M., additional, Rouzé, P., additional, Sanders, I. R., additional, Stajich, J. E., additional, Tunlid, A., additional, Tuskan, G., additional, and Grigoriev, I. V., additional

Published
2008
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47. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, R. P. De, Riley, R., Wiebenga, A., Aguilar-Osorio, G., Amillis, S., Uchima, C. A., Anderluh, G., Asadollahi, M., Askin, M., Barry, K., Battaglia, E., Bayram, O., Benocci, T., Braus-Stromeyer, S. A., Caldana, C., Cánovas, D., Cerqueira, G. C., Chen, F., Chen, W., Choi, C., Clum, A., Santos, R. A. C. Dos, Lima Damásio, A. R. De, Diallinas, G., Emri, T., Fekete, E., Flipphi, M., Freyberg, S., Gallo, A., Gournas, C., Habgood, R., Hainaut, M., Harispe, M. L., Henrissat, B., Hildén, K. S., Hope, R., Hossain, A., Karabika, E., Karaffa, L., Karányi, Z., KrašEvec, N., Kuo, A., Kusch, H., LaButti, K., Lagendijk, E. L., Lapidus, A., Levasseur, A., Lindquist, E., Lipzen, A., Logrieco, A. F., MacCabe, A., Mäkelä, M. R., Malavazi, I., Melin, P., Meyer, V., Mielnichuk, N., Miskei, M., Molnár, A. P., Mulé, G., Ngan, C. Y., Orejas, M., Orosz, E., Ouedraogo, J. P., Overkamp, K. M., Park, H.-S., Perrone, G., Piumi, F., Punt, P. J., Ram, A. F. J., Ramón, A., Rauscher, S., Record, E., Riaño-Pachón, D. M., Robert, V., Röhrig, J., Ruller, R., Salamov, A., Salih, N. S., Samson, R. A., Sándor, E., Sanguinetti, M., Schütze, T., Sep?I?, K., Shelest, E., Sherlock, G., Sophianopoulou, V., Squina, F. M., Sun, H., Susca, A., Todd, R. B., Tsang, A., Unkles, S. E., Wiele, N. Van De, Rossen-Uffink, D. Van, Castro Oliveira, J. V. De, Vesth, T. C., Visser, J., Yu, J.-H., Zhou, M., Andersen, M. R., Archer, D. B., Baker, S. E., Benoit, I., Brakhage, A. A., Braus, G. H., Fischer, R., Frisvad, J. C., Goldman, G. H., Houbraken, J., Oakley, B., Pócsi, I., Scazzocchio, C., Seiboth, B., VanKuyk, P. A., Wortman, J., Dyer, P. S., and Grigoriev, I. V.

Subjects
Fungal biology, Aspergillus, Comparative genomics, 15. Life on land, Genome sequencing, 3. Good health
Abstract

Background The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. Results We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. Conclusions Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.

48. Evolution and comparative genomics of the most common Trichoderma species

Author

Sabrina Sarrocco, Eva M. Kubicek, Andrei Stecca Steindorff, Igor V. Grigoriev, Bernard Henrissat, Qirong Shen, Alan Kuo, Alexey G. Kopchinskiy, Feng Cai, Giovanni Vannacci, Eliane Ferreira Noronha, Gelsomina Manganiello, Christian P. Kubicek, Jian Zhang, Komal Chenthamara, Irina S. Druzhinina, Riccardo Baroncelli, Vienna University of Technology, United States Department of Energy, Universidade de Brasília (UnB), Seconda Università degli Studi di Napoli = Second University of Naples, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Department of Biological Sciences, King Abdulaziz University, Nanjing Agricultural University (NAU), Universidad de Salamanca, Department of Agriculture, Food and Environment, University of California [Berkeley] (UC Berkeley), University of California (UC), 2017YFD 0200806, Austrian Science Foundation (FWF) 25613-B20 I-1249, CAPES foundation 99999.001745/2014-00, CNPq 482697/2011-3, 141180/2012-9, Office of Science of the U.S. Department of Energy DE-AC02-05CH11231, Seconda Università degli studi di Napoli, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Nanjing Agricultural University, University of California [Berkeley], University of California, Kubicek, C. P., Steindorff, A. S., Chenthamara, K., Manganiello, G., Henrissat, B., Zhang, J., Cai, F., Kopchinskiy, A. G., Kubicek, E. M., Kuo, A., Baroncelli, R., Sarrocco, S., Noronha, E. F., Vannacci, G., Shen, Q., Grigoriev, I. V., Druzhinina, I. S., Kubicek C.P., Steindorff A.S., Chenthamara K., Manganiello G., Henrissat B., Zhang J., Cai F., Kopchinskiy A.G., Kubicek E.M., Kuo A., Baroncelli R., Sarrocco S., Noronha E.F., Vannacci G., Shen Q., Grigoriev I.V., and Druzhinina I.S.

Subjects
hypocréales, 0106 biological sciences, enzyme cellulolytique, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Gene loss, Medical and Health Sciences, 01 natural sciences, Genome, Orphan, Biopolymers, Clade, Gene gain, Environmental opportunism, 2. Zero hunger, Trichoderma, 0303 health sciences, biology, Ascomycota, Orphans, Hydrolysis, Reproduction, Gene lo, food and beverages, Genomics, Biological Sciences, Ankyrin domains, CAZymes, Core genome, SSCPs, Fungal, CAZyme, Biotechnology, Research Article, Genome evolution, lcsh:QH426-470, Evolution, Bioinformatics, lcsh:Biotechnology, Hypocreales, Genes, Fungal, Biotechnologies, Evolution, Molecular, Fungal Proteins, 03 medical and health sciences, lcsh:TP248.13-248.65, Information and Computing Sciences, Genetics, analyse génomique, Gene, 030304 developmental biology, Comparative genomics, Human Genome, Molecular, diversité fongique, biology.organism_classification, Carbon, lcsh:Genetics, Genes, Evolutionary biology, Ankyrin domain, Extracellular Space, 010606 plant biology & botany
Abstract

Background The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma. However, the evolution of these traits is not yet understood. Results We selected 12 most commonly occurring Trichoderma species and studied the evolution of their genome sequences. Trichoderma evolved in the time of the Cretaceous-Palaeogene extinction event 66 (±15) mya, but the formation of extant sections (Longibrachiatum, Trichoderma) or clades (Harzianum/Virens) happened in Oligocene. The evolution of the Harzianum clade and section Trichoderma was accompanied by significant gene gain, but the ancestor of section Longibrachiatum experienced rapid gene loss. The highest number of genes gained encoded ankyrins, HET domain proteins and transcription factors. We also identified the Trichoderma core genome, completely curated its annotation, investigated several gene families in detail and compared the results to those of other fungi. Eighty percent of those genes for which a function could be predicted were also found in other fungi, but only 67% of those without a predictable function. Conclusions Our study presents a time scaled pattern of genome evolution in 12 Trichoderma species from three phylogenetically distant clades/sections and a comprehensive analysis of their genes. The data offer insights in the evolution of a mycoparasite towards a generalist. Electronic supplementary material The online version of this article (10.1186/s12864-019-5680-7) contains supplementary material, which is available to authorized users.

Published
2019

49. 101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens.

Author

Haridas S, Albert R, Binder M, Bloem J, LaButti K, Salamov A, Andreopoulos B, Baker SE, Barry K, Bills G, Bluhm BH, Cannon C, Castanera R, Culley DE, Daum C, Ezra D, González JB, Henrissat B, Kuo A, Liang C, Lipzen A, Lutzoni F, Magnuson J, Mondo SJ, Nolan M, Ohm RA, Pangilinan J, Park HJ, Ramírez L, Alfaro M, Sun H, Tritt A, Yoshinaga Y, Zwiers LH, Turgeon BG, Goodwin SB, Spatafora JW, Crous PW, and Grigoriev IV

Abstract

Dothideomycetes is the largest class of kingdom Fungi and comprises an incredible diversity of lifestyles, many of which have evolved multiple times. Plant pathogens represent a major ecological niche of the class Dothideomycetes and they are known to infect most major food crops and feedstocks for biomass and biofuel production. Studying the ecology and evolution of Dothideomycetes has significant implications for our fundamental understanding of fungal evolution, their adaptation to stress and host specificity, and practical implications with regard to the effects of climate change and on the food, feed, and livestock elements of the agro-economy. In this study, we present the first large-scale, whole-genome comparison of 101 Dothideomycetes introducing 55 newly sequenced species. The availability of whole-genome data produced a high-confidence phylogeny leading to reclassification of 25 organisms, provided a clearer picture of the relationships among the various families, and indicated that pathogenicity evolved multiple times within this class. We also identified gene family expansions and contractions across the Dothideomycetes phylogeny linked to ecological niches providing insights into genome evolution and adaptation across this group. Using machine-learning methods we classified fungi into lifestyle classes with >95 % accuracy and identified a small number of gene families that positively correlated with these distinctions. This can become a valuable tool for genome-based prediction of species lifestyle, especially for rarely seen and poorly studied species., (© 2020 Westerdijk Fungal Biodiversity Institute. Production and hosting by ELSEVIER B.V.)

Published
2020
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50. [Resection of a giant fusiform aneurysm of the pericallosal artery with «hemi-bonnet bypass» procedure (case report and literature review)].

Author

Lukyanchikov VA, Senko IV, Polunina NA, Staroverov MS, Grigoriev IV, Sinkin MV, Tikhomirov IV, and Guseynova GK

Subjects
Adult, Anastomosis, Surgical, Anterior Cerebral Artery surgery, Female, Humans, Radial Artery diagnostic imaging, Radial Artery surgery, Cerebral Revascularization, Intracranial Aneurysm surgery
Abstract

A 30-year-old woman with giant fusiform aneurysm of the azygos anterior cerebral artery is reported. Clipping of the aneurysm followed by modeling of pericallosal artery was performed in 2017. However, further enlargement of the aneurysm has been observed for subsequent 2 years. The patient underwent redo surgery with excision of the aneurysm followed by «hemi-bonnet bypass» procedure (anastomosis between superficial temporal artery and anterior cerebral artery with radial artery as an interposition graft). Literature data on reconstructive surgery in the treatment of complex pericallosal artery aneurysms are reviewed.

Published
2020
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