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1. Developmental dynamics of sea urchin and sea star cis-regulation and the evolution of echinoderm genome organization

Author

Magri, Marta Silvia, Voronov, D., Foley, S., Franke, Martin, Cuomo, C., Gil-Galvez, Alejandro, Acemel, Rafael D., Paganos, P., Rancelovic, J., Firbas, Panos, Hinman, V. F., Arnone, M. I., Maeso, Ignacio, and Gómez-Skarmeta, José Luis

Abstract

Trabajo presentado en EMBO Workshop The evolution of animal genomes, celebrado en modalidad virtual del 13 al 17 de septiembre de 2021.

Published
2021

2. ATAC-Seq for Assaying Chromatin Accessibility Protocol Using Echinoderm Embryos

Author

Ministerio de Economía y Competitividad (España), European Commission, Stazione Zoologica Anton Dohrn, Magri, Marta Silvia, Voronov, D., Ranđelović, Jovana, Cuomo, C., Gómez-Skarmeta, José Luis, Arnone, M. I., Ministerio de Economía y Competitividad (España), European Commission, Stazione Zoologica Anton Dohrn, Magri, Marta Silvia, Voronov, D., Ranđelović, Jovana, Cuomo, C., Gómez-Skarmeta, José Luis, and Arnone, M. I.

Abstract

Cis-regulatory elements (CREs) and transcription factors (TFs) associated with them determine temporal and spatial domains of gene expression. Therefore, identification of these CREs and TFs is crucial to elucidating transcriptional programs across taxa. With chromatin accessibility facilitating transcription factor access to DNA, the identification of regions of open chromatin sheds light both on the function of the regulatory elements and their evolution, thus allowing the recognition of potential CREs. Buenrostro and colleagues have developed a novel method for exploring chromatin accessibility: assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), which can be used for the purpose of identifying putative CREs. This method was shown to have considerable advantages when compared to traditional methods such as sequence conservation analyses or functional assays. Here we present the adaptation of the ATAC-seq method to echinoderm species and discuss how it can be used for CRE discovery.

Published
2021

3. Phylogenomic analysis of a 55.1 kb 19-gene dataset resolves a monophyletic Fusarium that includes the Fusarium solani Species Complex

Author

Geiser, D. M., Al-Hatmi, A., Aoki, T., Arie, T., Balmas, V., Barnes, I., Bergstrom, G. C, Bhattacharyya, M. K. K., Blomquist, C. L., Bowden, R., Brankovics, B., Guarro, J., Ward, T., Wickes, B., Everts, K. L., Wiederhold, N. P., Wingfield, M. J., Wood, A. K. M., Xu, J. R., Carrillo, J. D., Yang, X. B., Scauflaire, J., Yli-Matilla, T., Gugino, B., Yun, S. H., Zakaria, L., Zhang, H., Fernández-Pavía, S. P., Zhang, N., Zhang, S., Zhang, X., Chang, H. X., Kim, H., Chen, C. Y., Chen, W., Gutiérrez, S., Chilvers, M. I., Chulze, S. N., Coleman, J. J., Cuomo, C. A., da Silva, G. F., de Beer, Z. W., de Hoog, G. S., Kistler, H. C., Del Castillo-Múnera, J., Del Ponte, E., Dieguez-Uribeondo, Javier, Hammond-Kosack, K., Di Pietro, A., Edel-Hermann, V., Elmer, W. H., Foroud, N. A., Fourie, G., Frandsen, R. J. N., Nucci, M., Freeman, S., Munaut, F., Freitag, Michael, Frenkel, O., Harris, L. J., Fuller, K. K., Gagkaeva, T., Gardiner, D. M., Glenn, A. E., Gold, S., Kuldau, G. A., Gordon, T., Gregory, N. F., Gryzenhout, M., Homa, M., Hong, C. F., Hornok, L., Huang, J. W., Burgess, L. W., Ilkit, M., Nicholson, P., Kulik, T., Jacobs, A., Jacobs, K., Jiang, C., Jiménez-Gasco, M. Mar, Kang, S., Kasson, M. T., Kazan, K., Kennell, J. C., Kurzai, O., Laraba, I., Laurence, M. H., Lee, T. Y., Eskalen, A., Lee, Y. W., Schmale, D. III., Lee, Y. H., Leslie, J. F., Liew, E. C. Y., O'Donnell, K., Lofton, L. W., Logrieco, A., López-Berges, M. S., Luque, A. G., Tortorano, A. M., Lysøe, E., Ma, L. J., Short, D. P., Marra, R. E., Martin, Frank N., May, S. R., McCormick, S., Pasquali, M., McGee, C. T., Meis, J. F., Urban, M., Migheli, Q., Mohamed Nor, N. M. I., Monod, M., Šišic, A., Moretti, A., Mostert, D., Mulé, G., Pfenning, L. H., Prigitano, A., Proctor, R., Busman, M., Ranque, S., Brown, D. W., Rehner, S., Rep, M., Smith, J., Rodríguez-Alvarado, G., Rose, L. J., Roth, M. G., Ruiz-Roldán, C., Saleh, A. A., Vaillancourt, L. J., Salleh, B., Sang, H., Scandiani, M., Smyth, C. W., Son, H., Spahr, E., Stajich, Jason E., Epstein, L., Steenkamp, Emma, Bushley, K., Vallad, G. E., Steinberg, C., Subramaniam, R., Suga, H., Summerell, B. A., Susca, A., Swett, C. L., Toomajian, C., Torres-Cruz, T. J., van der Lee, T., Vanderpool, D., van Diepeningen, A. D., Vaughan, M., Munkvold, G. P., Venter, E., Esposto, M. C., Vermeulen, M., Verweij, P. E., Viljoen, A., Cano-Lira, J. F., Waalwijk, C., Wallace, E. C., Walther, G., Wang, J., Geiser, D. M., Al-Hatmi, A., Aoki, T., Arie, T., Balmas, V., Barnes, I., Bergstrom, G. C, Bhattacharyya, M. K. K., Blomquist, C. L., Bowden, R., Brankovics, B., Guarro, J., Ward, T., Wickes, B., Everts, K. L., Wiederhold, N. P., Wingfield, M. J., Wood, A. K. M., Xu, J. R., Carrillo, J. D., Yang, X. B., Scauflaire, J., Yli-Matilla, T., Gugino, B., Yun, S. H., Zakaria, L., Zhang, H., Fernández-Pavía, S. P., Zhang, N., Zhang, S., Zhang, X., Chang, H. X., Kim, H., Chen, C. Y., Chen, W., Gutiérrez, S., Chilvers, M. I., Chulze, S. N., Coleman, J. J., Cuomo, C. A., da Silva, G. F., de Beer, Z. W., de Hoog, G. S., Kistler, H. C., Del Castillo-Múnera, J., Del Ponte, E., Dieguez-Uribeondo, Javier, Hammond-Kosack, K., Di Pietro, A., Edel-Hermann, V., Elmer, W. H., Foroud, N. A., Fourie, G., Frandsen, R. J. N., Nucci, M., Freeman, S., Munaut, F., Freitag, Michael, Frenkel, O., Harris, L. J., Fuller, K. K., Gagkaeva, T., Gardiner, D. M., Glenn, A. E., Gold, S., Kuldau, G. A., Gordon, T., Gregory, N. F., Gryzenhout, M., Homa, M., Hong, C. F., Hornok, L., Huang, J. W., Burgess, L. W., Ilkit, M., Nicholson, P., Kulik, T., Jacobs, A., Jacobs, K., Jiang, C., Jiménez-Gasco, M. Mar, Kang, S., Kasson, M. T., Kazan, K., Kennell, J. C., Kurzai, O., Laraba, I., Laurence, M. H., Lee, T. Y., Eskalen, A., Lee, Y. W., Schmale, D. III., Lee, Y. H., Leslie, J. F., Liew, E. C. Y., O'Donnell, K., Lofton, L. W., Logrieco, A., López-Berges, M. S., Luque, A. G., Tortorano, A. M., Lysøe, E., Ma, L. J., Short, D. P., Marra, R. E., Martin, Frank N., May, S. R., McCormick, S., Pasquali, M., McGee, C. T., Meis, J. F., Urban, M., Migheli, Q., Mohamed Nor, N. M. I., Monod, M., Šišic, A., Moretti, A., Mostert, D., Mulé, G., Pfenning, L. H., Prigitano, A., Proctor, R., Busman, M., Ranque, S., Brown, D. W., Rehner, S., Rep, M., Smith, J., Rodríguez-Alvarado, G., Rose, L. J., Roth, M. G., Ruiz-Roldán, C., Saleh, A. A., Vaillancourt, L. J., Salleh, B., Sang, H., Scandiani, M., Smyth, C. W., Son, H., Spahr, E., Stajich, Jason E., Epstein, L., Steenkamp, Emma, Bushley, K., Vallad, G. E., Steinberg, C., Subramaniam, R., Suga, H., Summerell, B. A., Susca, A., Swett, C. L., Toomajian, C., Torres-Cruz, T. J., van der Lee, T., Vanderpool, D., van Diepeningen, A. D., Vaughan, M., Munkvold, G. P., Venter, E., Esposto, M. C., Vermeulen, M., Verweij, P. E., Viljoen, A., Cano-Lira, J. F., Waalwijk, C., Wallace, E. C., Walther, G., and Wang, J.

Abstract

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user¿s needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available

Published
2021

7. Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris

Author

Rhodes, J, Abdolrasouli, A, Farrer, R, Cuomo, C, Aanensen, D, Armstrong-James, D, Fisher, M, Schelenz, S, Medical Research Council (MRC), and Wellcome Trust

Subjects
Science & Technology, SEQUENCING DATA, DATABASE, REAL-TIME, Immunology, MENINGITIS, NOSOCOMIAL FUNGEMIA, RNA GENES, Microbiology, POPULATION GENOMICS, MECHANISMS, PROTEIN FAMILIES, FLUCYTOSINE RESISTANCE, Life Sciences & Biomedicine
Abstract

Candida auris was first described in 2009, and it has since caused nosocomial outbreaks, invasive infections, and fungaemia across at least 19 countries on five continents. An outbreak of C. auris occurred in a specialized cardiothoracic London hospital between April 2015 and November 2016, which to date has been the largest outbreak in the UK, involving a total of 72 patients. To understand the genetic epidemiology of C. auris infection both within this hospital and within a global context, we sequenced the outbreak isolate genomes using Oxford Nanopore Technologies and Illumina platforms to detect antifungal resistance alleles and reannotate the C. auris genome. Phylogenomic analysis placed the UK outbreak in the India/Pakistan clade, demonstrating an Asian origin; the outbreak showed similar genetic diversity to that of the entire clade, and limited local spatiotemporal clustering was observed. One isolate displayed resistance to both echinocandins and 5-flucytosine; the former was associated with a serine to tyrosine amino acid substitution in the gene FKS1, and the latter was associated with a phenylalanine to isoleucine substitution in the gene FUR1. These mutations add to a growing body of research on multiple antifungal drug targets in this organism. Multiple differential episodic selection of antifungal resistant genotypes has occurred within a genetically heterogenous population across this outbreak, creating a resilient pathogen and making it difficult to define local-scale patterns of transmission and implement outbreak control measures.

Published
2019
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10. Whole genome analysis illustrates global clonal population structure of the ubiquitous dermatophyte pathogenTrichophyton rubrum

Author

Persinoti, G, Martinez, D, Li, W, Döğen, A, Billmyre, B, Averette, A, Goldberg, J, Shea, T, Young, S, Zeng, Q, Oliver, B, Barton, R, Metin, B, Hilmioğlu-Polat, S, Ilkit, M, Gräser, Y, Martinez-Rossi, N, White, T, Heitman, J, Cuomo, C, Persinoti, G, Martinez, D, Li, W, Döğen, A, Billmyre, B, Averette, A, Goldberg, J, Shea, T, Young, S, Zeng, Q, Oliver, B, Barton, R, Metin, B, Hilmioğlu-Polat, S, Ilkit, M, Gräser, Y, Martinez-Rossi, N, White, T, Heitman, J, and Cuomo, C

Published
2018

11. Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes

Author

Burguera, D, Marquez, Y, Racioppi, C, Permanyer, J, Torres-Mendez, A, Esposito, R, Albuixech-Crespo, B, Fanlo, L, D'Agostino, Y, Gohr, A, Navas-Perez, E, Riesgo, A, Cuomo, C, Benvenuto, G, Christiaen, LA, Marti, E, D'Aniello, S, Spagnuolo, A, Ristoratore, F, Arnone, MI, Garcia-Fernandez, J, Irimia, M, Burguera, D, Marquez, Y, Racioppi, C, Permanyer, J, Torres-Mendez, A, Esposito, R, Albuixech-Crespo, B, Fanlo, L, D'Agostino, Y, Gohr, A, Navas-Perez, E, Riesgo, A, Cuomo, C, Benvenuto, G, Christiaen, LA, Marti, E, D'Aniello, S, Spagnuolo, A, Ristoratore, F, Arnone, MI, Garcia-Fernandez, J, and Irimia, M

Abstract

Epithelial-mesenchymal interactions are crucial for the development of numerous animal structures. Thus, unraveling how molecular tools are recruited in different lineages to control interplays between these tissues is key to understanding morphogenetic evolution. Here, we study Esrp genes, which regulate extensive splicing programs and are essential for mammalian organogenesis. We find that Esrp homologs have been independently recruited for the development of multiple structures across deuterostomes. Although Esrp is involved in a wide variety of ontogenetic processes, our results suggest ancient roles in non-neural ectoderm and regulating specific mesenchymal-to-epithelial transitions in deuterostome ancestors. However, consistent with the extensive rewiring of Esrp-dependent splicing programs between phyla, most developmental defects observed in vertebrate mutants are related to other types of morphogenetic processes. This is likely connected to the origin of an event in Fgfr, which was recruited as an Esrp target in stem chordates and subsequently co-opted into the development of many novel traits in vertebrates.

Published
2017

12. Biclonal gammopathies: review of 19 cases

Author

GUASTAFIERRO, Salvatore, Falcone U, Ferrara MG, Parascandola RR, Fiorillo P, Cuomo C, Santangelo S, Sica A., Guastafierro, Salvatore, Falcone, U, Ferrara, Mg, Parascandola, Rr, Fiorillo, P, Cuomo, C, Santangelo, S, and Sica, A.

Published
2010

13. Weak ABO variants: two cases of Ael

Author

GUASTAFIERRO, Salvatore, Falcone U, Cuomo C, Sessa F., Guastafierro, Salvatore, Falcone, U, Cuomo, C, and Sessa, F.

Published
2010

14. Blood donation and plasmatic fibrinogen levels

Author

GUASTAFIERRO, Salvatore, Sessa F, Falcone U, Ferrara MG, Sica A, Cuomo C, Mastrolorenzo L, Coppola L., Guastafierro, Salvatore, Sessa, F, Falcone, U, Ferrara, Mg, Sica, A, Cuomo, C, Mastrolorenzo, L, and Coppola, L.

Published
2010

16. Validation of vacuum-based refrigerated system for biobanking tissue preservation: analysis of cellular morphology, protein stability, and RNA quality

Author

Cuomo C, Fiorella D'Auria, Pellegrino Musto, Giacomo Lettini, Condelli, Giulia Vita, Matteo Landriscina, D'Amico M, and Giuseppe Patitucci

Subjects
Pathology, medicine.medical_specialty, Tissue Preservation, Vacuum, Molecular pathology, Protein Stability, Histological Techniques, Medicine (miscellaneous), RNA, Proteins, Cell Biology, General Medicine, Biology, Biobank, General Biochemistry, Genetics and Molecular Biology, Cell biology, Protein stability, Gene expression, medicine, Humans, Cellular Morphology, Gene, Biological Specimen Banks
Abstract

Biobanks of fresh, unfixed human normal and malignant tissues represent a valuable source for gene expression analysis in translational cancer research and molecular pathology. However, the success of molecular and cellular analysis in both clinical and translational research is strongly dependent on the collection, handling, storage, and quality control of fresh human tissue samples. The aim of this study was to evaluate an innovative vacuum-based refrigerated system, as a logistically feasible technology to increase the collection of tissue specimens, preserving the integrity of cellular and molecular components. We tested randomly-selected tissues stored under vacuum at 4°C by using endpoints important for research and diagnosis, including tissue morphology, epitope stability, and RNA integrity. Gene expression was evaluated by qualitative and quantitative RT analysis of selected housekeeping and tissue-specific genes. Tissue morphology and overall protein stability were generally well preserved, being compromised only in gallbladder tissue. By contrast, phosphoprotein and RNA analysis demonstrated a time-dependent degree of degradation, with progressive loss of stability from 24 to 72 hours. However, this reduction in RNA quality did not represent a limitation for successful expression analysis of selected genes. Indeed, a comparative qualitative and quantitative RT-PCR analysis showed that RNA extracted from tissues stored under vacuum is suitable for gene expression profiling, but requires highly sensitive technologies, such as quantitative RT-PCR. These data suggest that the refrigerated vacuum-based system represents a suitable and feasible technology for routine transport of fresh specimens from surgery to biobanks, thus increasing the opportunity to collect biospecimens.

Published
2014

18. Object-based neglect for the near peripersonal space in drawing space in drawing tasks

Author

GROSSI, Dario, TROJANO, Luigi, ESPOSITO D, CUOMO C, CONCHIGLIA G, Grossi, Dario, Esposito, D, Cuomo, C, Conchiglia, G, and Trojano, Luigi

Abstract

We report a patient with a right cortical and subcortical temporo-occipital lesion who showed spatial neglect mainly involving the left and the near peripersonal space. In drawing tasks the patient omitted the elements closer to him within each figure. A copying task with pairs of radially aligned line drawings demonstrated that the patient's radial neglect was based on within-object coordinates. This novel observation extends the egocentric-allocentric distinction to the radial dimension.

Published
2007

23. A 5’ regulatory sequence containing two Ets motifs controls the expression of the Wiskott Aldrich syndrome protein (WASP) gene in human haematopoietic cells

Author

PETRELLA A, DOTI I, AGOSTI V, CARANDENTE GIARRUSSO P, VITALE D, BOND H. M, CUOMO C, BARBIERI V, FRANCO, BRUNELLA, VENUTA S, MORRONE G., BALLABIO, ANDREA, Petrella, A, Doti, I, Agosti, V, CARANDENTE GIARRUSSO, P, Vitale, D, Bond, H. M., Cuomo, C, Barbieri, V, Franco, Brunella, Ballabio, Andrea, Venuta, S, and Morrone, G.

Published
1998

28. Whole genome sequencing projects of the plant pathogenic fungi Botrytis Cinerea and Sclerotinia Sclerotiorum

Author

Fillinger, Sabine, Helma, Amselem, Joelle, Artiguenave, Francois, Billault, Arnaud, Choquer, Mathias, Couloux, A., Cuomo, C., Dickman, M., Fournier, Elisabeth, Gioti, Anastasia, Giraud-Delville, Corinne, Kodira, C., Kohn, L., Legeai, Fabrice, Levis, Caroline, Mauceli, E., Pommier, Cyril, Pradier, Jean Marc, Quevillon, Emmanuel, Rollins, J., Ségurens, B., Simon, Adeline, Viaud, Muriel, Weissenbach, Jean, Wincker, Patrick, Lebrun, Marc-Henri, BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Bayer Cropscience, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Institute for Plant Genomics and Biotechnology, University of Toronto, Physiologie des plantes et des champignons lors de l'infection, Bayer Cropscience-Centre National de la Recherche Scientifique (CNRS), Department of Plant Pathology, University of Kentucky, Philippe Jeandet (Editeur), Christophe Clément (Editeur), and Alexandra Conreux (Editeur)

Subjects
POLYPHAGEOUS PATHOGEN, BOTRYTIS CINEREA, SCLEROTIONIA SCLEROTIORUM, SYNTENY, WHITE ROT, [SDV]Life Sciences [q-bio], GENOME SEQUENCE, NECROTROPHE, HOMPLOGY, GREY MOULD, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2007

36. Serum cholesterol in anorexia nervosa

Author

Carli, V, Barbarino, E, Camardese, G, Cuomo, C, Darista, P, and Sarchiapone, Marco

Subjects
Serum cholesterol, anorexia nervosa
Published
2003

39. Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection

Author

Martinez, D, Oliver, B, Graser, Y, Goldberg, J, Li, W, Martinez-Rossi, N, Monod, M, Shelest, E, Barton, R, Birch, E, Brakhage, A, Chen, Z, Gurr, S, Heiman, D, Heitman, J, Kosti, I, Rossi, A, Saif, S, Samalova, M, Saunders, C, Shea, T, Summerbell, R, Xu, J, Young, S, Zeng, Q, Birren, B, Cuomo, C, White, T, Martinez, D, Oliver, B, Graser, Y, Goldberg, J, Li, W, Martinez-Rossi, N, Monod, M, Shelest, E, Barton, R, Birch, E, Brakhage, A, Chen, Z, Gurr, S, Heiman, D, Heitman, J, Kosti, I, Rossi, A, Saif, S, Samalova, M, Saunders, C, Shea, T, Summerbell, R, Xu, J, Young, S, Zeng, Q, Birren, B, Cuomo, C, and White, T

Abstract

The major cause of athlete's foot is Trichophyton rubrum, a dermatophyte or fungal pathogen of human skin. To facilitate molecular analyses of the dermatophytes, we sequenced T. rubrum and four related species, Trichophyton tonsurans, Trichophyton equinum, Microsporum canis, and Microsporum gypseum. These species differ in host range, mating, and disease progression. The dermatophyte genomes are highly colinear yet contain gene family expansions not found in other human-associated fungi. Dermatophyte genomes are enriched for gene families containing the LysM domain, which binds chitin and potentially related carbohydrates. These LysM domains differ in sequence from those in other species in regions of the peptide that could affect substrate binding. The dermatophytes also encode novel sets of fungus-specific kinases with unknown specificity, including nonfunctional pseudokinases, which may inhibit phosphorylation by competing for kinase sites within substrates, acting as allosteric effectors, or acting as scaffolds for signaling. The dermatophytes are also enriched for a large number of enzymes that synthesize secondary metabolites, including dermatophyte-specific genes that could synthesize novel compounds. Finally, dermatophytes are enriched in several classes of proteases that are necessary for fungal growth and nutrient acquisition on keratinized tissues. Despite differences in mating ability, genes involved in mating and meiosis are conserved across species, suggesting the possibility of cryptic mating in species where it has not been previously detected. These genome analyses identify gene families that are important to our understanding of how dermatophytes cause chronic infections, how they interact with epithelial cells, and how they respond to the host immune response

Published
2012

40. Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens

Author

Klosterman, S.J., Subbarao, K.V., Kang, S., Veronese, P., Gold, S.E., Thomma, B.P.H.J., Chen, Z.J., Henrissat, B., Lee, Y.H., Park, J., Garcia-Pedrajas, M.D., Barbara, D.J., Anchieta, A., de Jonge, R., Santhanam, P., Maruthachalam, K., Atallah, Z., Amyotte, S.G., Paz, Z., Inderbitzin, P., Hayes, R.J., Heiman, D.I., Young, S., Zeng, Q., Engels, R., Galagan, J., Cuomo, C., Dobinson, K.F., Ma, L.J., Klosterman, S.J., Subbarao, K.V., Kang, S., Veronese, P., Gold, S.E., Thomma, B.P.H.J., Chen, Z.J., Henrissat, B., Lee, Y.H., Park, J., Garcia-Pedrajas, M.D., Barbara, D.J., Anchieta, A., de Jonge, R., Santhanam, P., Maruthachalam, K., Atallah, Z., Amyotte, S.G., Paz, Z., Inderbitzin, P., Hayes, R.J., Heiman, D.I., Young, S., Zeng, Q., Engels, R., Galagan, J., Cuomo, C., Dobinson, K.F., and Ma, L.J.

Abstract

The vascular wilt fungi Verticillium dahliae and V. albo-atrum infect over 200 plant species, causing billions of dollars in annual crop losses. The characteristic wilt symptoms are a result of colonization and proliferation of the pathogens in the xylem vessels, which undergo fluctuations in osmolarity. To gain insights into the mechanisms that confer the organisms' pathogenicity and enable them to proliferate in the unique ecological niche of the plant vascular system, we sequenced the genomes of V. dahliae and V. albo-atrum and compared them to each other, and to the genome of Fusarium oxysporum, another fungal wilt pathogen. Our analyses identified a set of proteins that are shared among all three wilt pathogens, and present in few other fungal species. One of these is a homolog of a bacterial glucosyltransferase that synthesizes virulence-related osmoregulated periplasmic glucans in bacteria. Pathogenicity tests of the corresponding V. dahliae glucosyltransferase gene deletion mutants indicate that the gene is required for full virulence in the Australian tobacco species Nicotiana benthamiana. Compared to other fungi, the two sequenced Verticillium genomes encode more pectin-degrading enzymes and other carbohydrate-active enzymes, suggesting an extraordinary capacity to degrade plant pectin barricades. The high level of synteny between the two Verticillium assemblies highlighted four flexible genomic islands in V. dahliae that are enriched for transposable elements, and contain duplicated genes and genes that are important in signaling/transcriptional regulation and iron/lipid metabolism. Coupled with an enhanced capacity to degrade plant materials, these genomic islands may contribute to the expanded genetic diversity and virulence of V. dahliae, the primary causal agent of Verticillium wilts. Significantly, our study reveals insights into the genetic mechanisms of niche adaptation of fungal wilt pathogens, advances our understanding of the evolution and devel

Published
2011

41. Genome Variation in Cryptococcus gattii, an Emerging Pathogen of Immunocompetent Hosts

Author

D’Souza, C. A., primary, Kronstad, J. W., additional, Taylor, G., additional, Warren, R., additional, Yuen, M., additional, Hu, G., additional, Jung, W. H., additional, Sham, A., additional, Kidd, S. E., additional, Tangen, K., additional, Lee, N., additional, Zeilmaker, T., additional, Sawkins, J., additional, McVicker, G., additional, Shah, S., additional, Gnerre, S., additional, Griggs, A., additional, Zeng, Q., additional, Bartlett, K., additional, Li, W., additional, Wang, X., additional, Heitman, J., additional, Stajich, J. E., additional, Fraser, J. A., additional, Meyer, W., additional, Carter, D., additional, Schein, J., additional, Krzywinski, M., additional, Kwon-Chung, K. J., additional, Varma, A., additional, Wang, J., additional, Brunham, R., additional, Fyfe, M., additional, Ouellette, B. F. F., additional, Siddiqui, A., additional, Marra, M., additional, Jones, S., additional, Holt, R., additional, Birren, B. W., additional, Galagan, J. E., additional, and Cuomo, C. A., additional

Published
2011
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46. A 5′ Regulatory Sequence Containing Two Ets Motifs Controls the Expression of the Wiskott-Aldrich Syndrome Protein (WASP) Gene in Human Hematopoietic Cells

Author

Petrella, A., primary, Doti, I., additional, Agosti, V., additional, Giarrusso, P. Carandente, additional, Vitale, D., additional, Bond, H.M., additional, Cuomo, C., additional, Tassone, P., additional, Franco, B., additional, Ballabio, A., additional, Venuta, S., additional, and Morrone, G., additional

Published
1998
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47. Identification by Differential Display of Transcripts Regulated during Hematopoietic Differentiation

Author

Bond, H. M., primary, Bonelli, P., additional, Mesuraca, M., additional, Agosti, V., additional, Masone, C., additional, Cuomo, C., additional, Nisticò, A., additional, Tassone, P., additional, Tuccillo, F., additional, Cecco, L., additional, Iacopino, L., additional, Barbieri, V., additional, Cerra, M., additional, Costanzo, F. S., additional, Morrone, G., additional, and Venuta, S., additional

Published
1998
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