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283 results on '"Schoch, Conrad L."'

1. Fungal taxonomy and sequence-based nomenclature

Author

Lücking, Robert, Aime, M. Catherine, Robbertse, Barbara, Miller, Andrew N., Aoki, Takayuki, Ariyawansa, Hiran A., Cardinali, Gianluigi, Crous, Pedro W., Druzhinina, Irina S., Geiser, David M., Hawksworth, David L., Hyde, Kevin D., Irinyi, Laszlo, Jeewon, Rajesh, Johnston, Peter R., Kirk, Paul M., Malosso, Elaine, May, Tom W., Meyer, Wieland, Nilsson, Henrik R., Öpik, Maarja, Robert, Vincent, Stadler, Marc, Thines, Marco, Vu, Duong, Yurkov, Andrey M., Zhang, Ning, and Schoch, Conrad L.

Published
2021
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2. Database resources of the National Center for Biotechnology Information

Author

Sayers, Eric W, primary, Beck, Jeff, additional, Bolton, Evan E, additional, Brister, J Rodney, additional, Chan, Jessica, additional, Comeau, Donald C, additional, Connor, Ryan, additional, DiCuccio, Michael, additional, Farrell, Catherine M, additional, Feldgarden, Michael, additional, Fine, Anna M, additional, Funk, Kathryn, additional, Hatcher, Eneida, additional, Hoeppner, Marilu, additional, Kane, Megan, additional, Kannan, Sivakumar, additional, Katz, Kenneth S, additional, Kelly, Christopher, additional, Klimke, William, additional, Kim, Sunghwan, additional, Kimchi, Avi, additional, Landrum, Melissa, additional, Lathrop, Stacy, additional, Lu, Zhiyong, additional, Malheiro, Adriana, additional, Marchler-Bauer, Aron, additional, Murphy, Terence D, additional, Phan, Lon, additional, Prasad, Arjun B, additional, Pujar, Shashikant, additional, Sawyer, Amanda, additional, Schmieder, Erin, additional, Schneider, Valerie A, additional, Schoch, Conrad L, additional, Sharma, Shobha, additional, Thibaud-Nissen, Françoise, additional, Trawick, Barton W, additional, Venkatapathi, Thilakam, additional, Wang, Jiyao, additional, Pruitt, Kim D, additional, and Sherry, Stephen T, additional

Published
2023
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4. How to publish a new fungal species, or name, version 3.0

Author

Aime, M. Catherine, Miller, Andrew N., Aoki, Takayuki, Bensch, Konstanze, Cai, Lei, Crous, Pedro W., Hawksworth, David L., Hyde, Kevin D., Kirk, Paul M., Lücking, Robert, May, Tom W., Malosso, Elaine, Redhead, Scott A., Rossman, Amy Y., Stadler, Marc, Thines, Marco, Yurkov, Andrey M., Zhang, Ning, and Schoch, Conrad L.

Published
2021
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6. Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains.

Author

Renner, Susanne S, Scherz, Mark D, Schoch, Conrad L, Gottschling, Marc, and Vences, Miguel

Subjects
NUCLEOTIDE sequence, DNA data banks, DNA sequencing, IDENTIFICATION of fungi, DATABASES, IDENTIFICATION, EUKARYOTES
Abstract

Scientific names permit humans and search engines to access knowledge about the biodiversity that surrounds us, and names linked to DNA sequences are playing an ever-greater role in search-and-match identification procedures. Here, we analyze how users and curators of the National Center for Biotechnology Information (NCBI) are flagging and curating sequences derived from nomenclatural type material, which is the only way to improve the quality of DNA-based identification in the long run. For prokaryotes, 18,281 genome assemblies from type strains have been curated by NCBI staff and improve the quality of prokaryote naming. For Fungi, type-derived sequences representing over 21,000 species are now essential for fungus naming and identification. For the remaining eukaryotes, however, the numbers of sequences identifiable as type-derived are minuscule, representing only 739 species of arthropods, 1542 vertebrates, and 125 embryophytes. An increase in the production and curation of such sequences will come from (i) sequencing of types or topotypic specimens in museum collections, (ii) the March 2023 rule changes at the International Nucleotide Sequence Database Collaboration requiring more metadata for specimens, and (iii) efforts by data submitters to facilitate curation, including informing NCBI curators about a specimen's type status. We illustrate different type-data submission journeys and provide best-practice examples from a range of organisms. Expanding the number of type-derived sequences in DNA databases, especially of eukaryotes, is crucial for capturing, documenting, and protecting biodiversity. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes

Author

Ohm, Robin A., Feau, Nicolas, Henrissat, Bernard, Schoch, Conrad L., Horwitz, Benjamin A., Barry, Kerrie W., Condon, Bradford J., Copeland, Alex C., Dhillon, Braham, Glaser, Fabian, Hesse, Cedar N., Kosti, Idit, LaButti, Kurt, Lindquist, Erika A., Lucas, Susan, Salamov, Asaf A., Bradshaw, Rosie E., Ciuffetti, Lynda, Hamelin, Richard C., Kema, Gert H. J., Lawrence, Christopher, Scott, James A., Spatafora, Joseph W., Turgeon, B. Gillian, Wit, Pierre J. G. M. de, Zhong, Shaobin, Goodwin, Stephen B., and Grigoriev, Igor V.

Abstract

The class of Dothideomycetes is one of the largest and most diverse groups of fungi. Many are plant pathogens and pose a serious threat to agricultural crops that are grown for biofuel, food or feed. Most Dothideomycetes have only a single host plant, and related species can have very diverse hosts. Eighteen genomes of Dothideomycetes have currently been sequenced by the Joint Genome Institute and other sequencing centers. Here we describe the results of comparative analyses of the fungi in this group.

Published
2013

8. Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

Author

Ohm, Robin A., Feau, Nicolas, Henrissat, Bernard, Schoch, Conrad L., Horwitz, Benjamin A., Barry, Kerrie W., Condon, Bradford J., Copeland, Alex C., Dhillon, Braham, Glaser, Fabian, Hesse, Cedar N., Kosti, Idit, LaButti, Kurt, Lindquist, Erika A., Lucas, Susan, Salamov, Asaf A., Bradshaw, Rosie E., Ciuffetti, Lynda, Hamelin, Richard C., Kema, Gert H. J., Lawrence, Christopher, Scott, James A., Spatafora, Joseph W., Turgeon, B. Gillian, Wit, Pierre J. G. M. de, Zhong, Shaobin, Goodwin, Stephen B., and Grigoriev, Igor V.

Abstract

The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, includingoxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.

Published
2012

9. Diverse Life Styles Encoded in the Genomes of Eighteen Dothideomycetes

Author

Ohm, Robin A., Bradshaw, Rosie E., Condon, Bradford J., Feau, Nicolas, Henrissat, Bernard, Horwitz, Benjamin A., Schoch, Conrad L., Turgeon, B. Gillian, Aerts, Andrea, Barry, Kerrie, Copeland, Alex, Dhillon, Braham, Glaser, Fabian, Grimwood, Jane, Hesse, Cedar, Kosti, Idit, LaButti, Kurt, Lindquist, Erika, Lowry, Steve, Lucas, Susan, Otillar, Robert, Salamov, Asaf A., Schmutz, Jeremy, Sun, Hui, Ciuffetti, Lynda, Hamelin, Richard C., Kema, Gert, Lawrence, Christopher, Spatafora, Joey, Wit, Pierre J. G. M. de, Zhong, Shaobin, Goodwin, Stephen B., and Grigoriev, Igor V.

Published
2012

10. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

Author

Lücking, Robert, Aime, M. Catherine, Robbertse, Barbara, Miller, Andrew N., Ariyawansa, Hiran A., Aoki, Takayuki, Cardinali, Gianluigi, Crous, Pedro W., Druzhinina, Irina S., Geiser, David M., Hawksworth, David L., Hyde, Kevin D., Irinyi, Laszlo, Jeewon, Rajesh, Johnston, Peter R., Kirk, Paul M., Malosso, Elaine, May, Tom W., Meyer, Wieland, Öpik, Maarja, Robert, Vincent, Stadler, Marc, Thines, Marco, Vu, Duong, Yurkov, Andrey M., Zhang, Ning, and Schoch, Conrad L.

Published
2020
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12. Author Correction: Fungal taxonomy and sequence-based nomenclature

Author

Lücking, Robert, Aime, M. Catherine, Robbertse, Barbara, Miller, Andrew N., Aoki, Takayuki, Ariyawansa, Hiran A., Cardinali, Gianluigi, Crous, Pedro W., Druzhinina, Irina S., Geiser, David M., Hawksworth, David L., Hyde, Kevin D., Irinyi, Laszlo, Jeewon, Rajesh, Johnston, Peter R., Kirk, Paul M., Malosso, Elaine, May, Tom W., Meyer, Wieland, Nilsson, Henrik R., Öpik, Maarja, Robert, Vincent, Stadler, Marc, Thines, Marco, Vu, Duong, Yurkov, Andrey M., Zhang, Ning, and Schoch, Conrad L.

Published
2021
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17. Reports

Author

Miller, Andrew, Cai, Lei, Crous, Pedro W., Beer, Z. Wilhelm De, Hawksworth, David L., Hyde, Kevin D., Kirk, Paul M., Lücking, Robert, Lumbsch, H. Thorsten, May, Tom W., Rossman, Amy Y., Seifert, Keith A., Schardl, Chris I., Pfister, Donald H., Rodréguez, Sharon A. Cantrell, Schoch, Conrad L., Miller, Andrew N., and Li, Chang-tian

Published
2017
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22. Reports

Author

Luangsa-ard, Janet Jennifer Divinagracia, Taylor, John W., Schoch, Conrad L., Vasco-Palacios, Aída, Franco-Molano, Ana Esperanza, Dearnaley, John, Wilson, Calum, Tegg, Robert, and Robert, Vincent

Published
2014
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24. The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits

Author

Schoch, Conrad L., Sung, Gi-Ho, López-Giráldez, Francesc, Townsend, Jeffrey P., Miadlikowska, Jolanta, Hofstetter, Valérie, Robbertse, Barbara, Matheny, P. Brandon, Kauff, Frank, Wang, Zheng, Gueidan, Cécile, Andrie, Rachael M., Trippe, Kristin, Ciufetti, Linda M., Wynns, Anja, Fraker, Emily, Hodkinson, Brendan P., Bonito, Gregory, Groenewald, Johannes Z., Arzanlou, Mahdi, de Hoog, G. Sybren, Crous, Pedro W., Hewitt, David, Pfister, Donald H., Peterson, Kristin, Gryzenhout, Marieka, Wingfield, Michael J., Aptroot, André, Suh, Sung-Oui, Blackwell, Meredith, Hillis, David M., Griffith, Gareth W., Castlebury, Lisa A., Rossman, Amy Y., Lumbsch, H. Thorsten, Lücking, Robert, Büdel, Burkhard, Rauhut, Alexandra, Diederich, Paul, Ertz, Damien, Geiser, David M., Hosaka, Kentaro, Inderbitzin, Patrik, Kohlmeyer, Jan, Volkmann-Kohlmeyer, Brigitte, Mostert, Lizel, O'Donnell, Kerry, Sipman, Harrie, Rogers, Jack D., Shoemaker, Robert A., Sugiyama, Junta, Summerbell, Richard C., Untereiner, Wendy, Johnston, Peter R., Stenroos, Soili, Zuccaro, Alga, Dyer, Paul S., Crittenden, Peter D., Cole, Mariette S., Hansen, Karen, Trappe, James M., Yahr, Rebecca, Lutzoni, François, and Spatafora, Joseph W.

Published
2009

26. Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae

Author

Geiser, David M., Gueidan, Cécile, Miadlikowska, Jolanta, Lutzoni, François, Kauff, Frank, Hofstetter, Valérie, Fraker, Emily, Schoch, Conrad L., Tibell, Leif, Untereiner, Wendy A., and Aptroot, André

Published
2006

27. New Insights into Classification and Evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from Phylogenetic Analyses of Three Ribosomal RNA- and Two Protein-Coding Genes

Author

Miadlikowska, Jolanta, Kauff, Frank, Hofstetter, Valérie, Fraker, Emily, Grube, Martin, Hafellner, Josef, Reeb, Valérie, Hodkinson, Brendan P., Kukwa, Martin, Lücking, Robert, Hestmark, Geir, Otalora, Monica Garcia, Rauhut, Alexandra, Büdel, Burkhard, Scheidegger, Christoph, Timdal, Einar, Stenroos, Soili, Brodo, Irwin, Perlmutter, Gary B., Ertz, Damien, Diederich, Paul, Lendemer, James C., May, Philip, Schoch, Conrad L., Arnold, A. Elizabeth, Gueidan, Cécile, Tripp, Erin, Yahr, Rebecca, Robertson, Connie, and Lutzoni, François

Published
2006

30. A Five-Gene Phylogeny of Pezizomycotina

Author

Spatafora, Joseph W., Sung, Gi-Ho, Johnson, Desiree, Hesse, Cedar, O'Rourke, Benjamin, Serdani, Maryna, Spotts, Robert, Lutzoni, François, Hofstetter, Valérie, Miadlikowska, Jolanta, Reeb, Valérie, Gueidan, Cécile, Fraker, Emily, Lumbsch, Thorsten, Lücking, Robert, Schmitt, Imke, Hosaka, Kentaro, Aptroot, André, Roux, Claude, Miller, Andrew N., Geiser, David M., Hafellner, Josef, Hestmark, Geir, Arnold, A. Elizabeth, Büdel, Burkhard, Rauhut, Alexandra, Hewitt, David, Untereiner, Wendy A., Cole, Mariette S., Scheidegger, Christoph, Schultz, Matthias, Sipman, Harrie, and Schoch, Conrad L.

Published
2006

31. GenBank

Author

Sayers, Eric W, primary, Cavanaugh, Mark, additional, Clark, Karen, additional, Pruitt, Kim D, additional, Schoch, Conrad L, additional, Sherry, Stephen T, additional, and Karsch-Mizrachi, Ilene, additional

Published
2021
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36. Capnodiaceae

Author

Chomnunti, Putarak, Schoch, Conrad L., Aguirre-Hudson, Begoña, Ko-Ko, Thida W., Hongsanan, Sinang, Jones, E. B. Gareth, Kodsueb, Rampai, Phookamsak, Rungtiwa, Chukeatirote, Ekachai, Bahkali, Ali H., and Hyde, Kevin D.

Published
2011
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39. Reconstructing the early evolution of Fungi using a six-gene phylogeny

Author

James, Timothy Y., Kauff, Frank, Schoch, Conrad L., Matheny, P. Brandon, Hofstetter, Valerie, Cox, Cymon J., Celio, Gail, Gueidan, Cecile, Fraker, Emily, Miadlikowska, Jolanta, Lumbsch, H. Thorsten, Rauhut, Alexandra, Reeb, Valerie, Arnold, A. Elizabeth, Amtoft, Anja, Stajich, Jason E., Hosaka, Kentaro, Sung, Gi-Ho, Johnson, Desiree, O'Rourke, Ben, Crockett, Michael, Binder, Manfred, Curtis, Judd M., Slot, Jason C., Wang, Zheng, Wilson, Andrew W., Schußler, Arthur, Longcore, Joyce E., O'Donnell, Kerry, Mozley-Standridge, Sharon, Porter, David, Letcher, Peter M., Powell, Martha J., Taylor, John W., White, Merlin M., Griffith, Gareth W., Davies, David R., Humber, Richard A., Morton, Joseph B., Sugiyama, Junta, Rossman, Amy Y., Rogers, Jack D., Pfister, Don H., Hewitt, David, Hansen, Karen, Hambleton, Sarah, Shoemaker, Robert A., Kohlmeyer, Jan, Volkmann-Kohlmeyer, Brigitte, Spotts, Robert A., Serdani, Maryna, Crous, Pedro W., Hughes, Karen W., Matsuura, Kenji, Langer, Ewald, Langer, Gitta, Untereiner, Wendy A., Lucking, Robert, Budel, Burkhard, Geiser, David M., Aptroot, Andre, Diederich, Paul, Schmitt, Imke, Schultz, Matthias, Yahr, Rebecca, Hibbett, David S., Lutzoni, Francois, McLaughlin, David J., Spatafora, Joseph W., and Vilgalys, Rytas

Abstract

Author(s): Timothy Y. James (corresponding author) [1]; Frank Kauff [1]; Conrad L. Schoch [2, 36]; P. Brandon Matheny [3, 36]; Valérie Hofstetter [1, 36]; Cymon J. Cox [1, 37]; Gail [...]

Published
2006
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40. Database resources of the National Center for Biotechnology Information

Author

Agarwala, Richa, Barrett, Tanya, Beck, Jeff, Benson, Dennis A, Bollin, Colleen, Bolton, Evan, Bourexis, Devon, Brister, J Rodney, Bryant, Stephen H, Canese, Kathi, Cavanaugh, Mark, Charowhas, Chad, Clark, Karen, Dondoshansky, Ilya, Feolo, Michael, Fitzpatrick, Lawrence, Funk, Kathryn, Geer, Lewis Y, Gorelenkov, Viatcheslav, Graeff, Alan, Hlavina, Wratko, Holmes, Brad, Johnson, Mark, Kattman, Brandi, Khotomlianski, Viatcheslav, Kimchi, Avi, Kimelman, Michael, Kimura, Masato, Kitts, Paul, Klimke, William, Kotliarov, Alex, Krasnov, Sergey, Kuznetsov, Anatoliy, Landrum, Melissa J, Landsman, David, Lathrop, Stacy, Lee, Jennifer M, Leubsdorf, Carl, Lu, Zhiyong, Madden, Thomas L, Marchler-Bauer, Aron, Malheiro, Adriana, Meric, Peter, Karsch-Mizrachi, Ilene, Mnev, Anatoly, Murphy, Terence, Orris, Rebecca, Ostell, James, O'Sullivan, Christopher, Palanigobu, Vasuki, Panchenko, Anna R, Phan, Lon, Pierov, Borys, Pruitt, Kim D, Rodarmer, Kurt, Sayers, Eric W, Schneider, Valerie, Schoch, Conrad L, Schuler, Gregory D, Sherry, Stephen T, Siyan, Karanjit, Soboleva, Alexandra, Soussov, Vladimir, Starchenko, Grigory, Tatusova, Tatiana A, Thibaud-Nissen, Francoise, Todorov, Kamen, Trawick, Bart W, Vakatov, Denis, Ward, Minghong, Yaschenko, Eugene, Zasypkin, Aleksandr, and Zbicz, Kerry

Subjects
0301 basic medicine, Internet, PubMed, National Library of Medicine (U.S.), 010402 general chemistry, Databases, Bibliographic, 01 natural sciences, United States, 0104 chemical sciences, 03 medical and health sciences, ComputingMethodologies_PATTERNRECOGNITION, 030104 developmental biology, Databases, Genetic, Genetics, Database Issue, Database Management Systems, Humans, Databases, Nucleic Acid, Databases, Chemical, Biotechnology
Abstract

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 39 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include PubMed Data Management, RefSeq Functional Elements, genome data download, variation services API, Magic-BLAST, QuickBLASTp, and Identical Protein Groups. Resources that were updated in the past year include the genome data viewer, a human genome resources page, Gene, virus variation, OSIRIS, and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Published
2017

41. GenBank

Author

Sayers, Eric W, primary, Cavanaugh, Mark, additional, Clark, Karen, additional, Pruitt, Kim D, additional, Schoch, Conrad L, additional, Sherry, Stephen T, additional, and Karsch-Mizrachi, Ilene, additional

Published
2020
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43. GenBank.

Author

Sayers, Eric W, Cavanaugh, Mark, Clark, Karen, Pruitt, Kim D, Schoch, Conrad L, Sherry, Stephen T, and Karsch-Mizrachi, Ilene

Published
2022
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46. NCBI Taxonomy: a comprehensive update on curation, resources and tools

Author

Schoch, Conrad L, primary, Ciufo, Stacy, additional, Domrachev, Mikhail, additional, Hotton, Carol L, additional, Kannan, Sivakumar, additional, Khovanskaya, Rogneda, additional, Leipe, Detlef, additional, Mcveigh, Richard, additional, O’Neill, Kathleen, additional, Robbertse, Barbara, additional, Sharma, Shobha, additional, Soussov, Vladimir, additional, Sullivan, John P, additional, Sun, Lu, additional, Turner, Seán, additional, and Karsch-Mizrachi, Ilene, additional

Published
2020
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48. Journal of Eukaryotic Microbiology / Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

Author

Adl, Sina M., Bass, David, Lane, Christopher E., Lukeš, Julius, Schoch, Conrad L., Smirnov, Alexey, Agatha, Sabine, Berney, Cedric, Brown, Matthew W., Burki, Fabien, Cárdenas, Paco, Čepička, Ivan, Chistyakova, Lyudmila, del Campo, Javier, Dunthorn, Micah, Edvardsen, Bente, Eglit Aaron A. Heiss Mon, Yana, Guillou, Laure, Hampl, Vladimír, Heiss, Aaron A., Hoppenrath, Mona, James, Timothy Y., Karnkowska, Anna, Karpov, Sergey, and Kudryavtsev

Subjects
amoebae, protozoa, taxonomy, Algae, fungus, microbiology, parasite, plankton, ecology, ciliate, systematics, flagellate, biodiversity
Abstract

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users. (VLID)3393271

Published
2019

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