The 2008 update of the Aspergillus nidulans genome annotation: A community effort

Jennifer Russo Wortman; Jane Mabey Gilsenan; Vinita Joardar; Jennifer Deegan; John Clutterbuck; Mikael Rørdam Andersen; David Archer; Mojca Bencina; Gerhard Braus; Pedro Coutinho; Hans von Döhren; John Doonan; Arnold J.M. Driessen; Pawel Durek; Eduardo Espeso; Erzsébet Fekete; Michel Flipphi; Carlos Garcia Estrada; Steven Geysens; Gustavo Goldman; Piet W.J. de Groot; Kim Hansen; Steven D. Harris; Thorsten Heinekamp; Kerstin Helmstaedt; Bernard Henrissat; Gerald Hofmann; Tim Homan; Tetsuya Horio; Hiroyuki Horiuchi; Steve James; Meriel Jones; Levente Karaffa; Zsolt Karányi; Masashi Kato; Nancy Keller; Diane E. Kelly; Jan A.K.W. Kiel; Jung-Mi Kim; Ida J. van der Klei; Frans M. Klis; Andriy Kovalchuk; Nada Kraševec; Christian P. Kubicek; Bo Liu; Andrew MacCabe; Vera Meyer; Pete Mirabito; Márton Miskei; Magdalena Mos; Jonathan Mullins; David R. Nelson; Jens Nielsen; Berl R. Oakley; Stephen A. Osmani; Tiina Pakula; Andrzej Paszewski; Ian Paulsen; Sebastian Pilsyk; István Pócsi; Peter J. Punt; Arthur F.J. Ram; Qinghu Ren; Xavier Robellet; Geoff Robson; Bernhard Seiboth; Piet van Solingen; Thomas Specht; Jibin Sun; Naimeh Taheri-Talesh; Norio Takeshita; Dave Ussery; Patricia A. vanKuyk; Hans Visser; Peter J.I. van de Vondervoort; Ronald P. de Vries; Jonathan Walton; Xin Xiang; Yi Xiong; An Ping Zeng; Bernd W. Brandt; Michael J. Cornell; Cees A.M.J.J. van den Hondel; Jacob Visser; Stephen G. Oliver; Geoffrey Turner

doi:10.1016/j.fgb.2008.12.003

The 2008 update of the Aspergillus nidulans genome annotation: A community effort

Jennifer Russo Wortman
, Jane Mabey Gilsenan
, Vinita Joardar
, Jennifer Deegan
, John Clutterbuck
, Mikael Rørdam Andersen
, David Archer
, Mojca Bencina
, Gerhard Braus
, Pedro Coutinho
, Hans von Döhren
, John Doonan
, Arnold J.M. Driessen
, Pawel Durek
, Eduardo Espeso
, Erzsébet Fekete
, Michel Flipphi
, Carlos Garcia Estrada
, Steven Geysens
, Gustavo Goldman

Piet W.J. de Groot, Kim Hansen, Steven D. Harris, Thorsten Heinekamp, Kerstin Helmstaedt, Bernard Henrissat, Gerald Hofmann, Tim Homan, Tetsuya Horio, Hiroyuki Horiuchi, Steve James, Meriel Jones, Levente Karaffa, Zsolt Karányi, Masashi Kato, Nancy Keller, Diane E. Kelly, Jan A.K.W. Kiel, Jung-Mi Kim, Ida J. van der Klei, Frans M. Klis, Andriy Kovalchuk, Nada Kraševec, Christian P. Kubicek, Bo Liu, Andrew MacCabe, Vera Meyer, Pete Mirabito, Márton Miskei, Magdalena Mos, Jonathan Mullins, David R. Nelson, Jens Nielsen, Berl R. Oakley, Stephen A. Osmani, Tiina Pakula, Andrzej Paszewski, Ian Paulsen, Sebastian Pilsyk, István Pócsi, Peter J. Punt, Arthur F.J. Ram, Qinghu Ren, Xavier Robellet, Geoff Robson, Bernhard Seiboth, Piet van Solingen, Thomas Specht, Jibin Sun, Naimeh Taheri-Talesh, Norio Takeshita, Dave Ussery, Patricia A. vanKuyk, Hans Visser, Peter J.I. van de Vondervoort, Ronald P. de Vries, Jonathan Walton, Xin Xiang, Yi Xiong, An Ping Zeng, Bernd W. Brandt, Michael J. Cornell, Cees A.M.J.J. van den Hondel, Jacob Visser, Stephen G. Oliver, Geoffrey Turner

University of Maryland School of Medicine
University of Manchester
J. Craig Venter Institute
European Bioinformatics Institute
University of Glasgow
University of Nottingham
National Institute of Chemistry Ljubljana
Georg-August-Universität Göttingen
Université de Provence
Technical University of Berlin
John Innes Centre
University of Amsterdam
CSIC
University of Debrecen
Instituto de Biotecnología de León
Flanders Institute for Biotechnology
Novozymes A/S
University of Nebraska
Leibniz-Institute for Natural Product Research and Infection Biology
Leiden University
University of Kansas
The University of Tokyo
Gettysburg College
University of Liverpool
Graduate School of Bioagricultural Sciences
University of Wisconsin-Madison
University of California at San Diego
TU Wien
University of Tennessee
Ohio State University
VTT Technical Research Centre of Finland Ltd.
Institute of Biochemistry and Biophysics
Netherlands Organisation for Applied Scientific Research
Université Paris-Sud
DuPont Danisco Cellulosic Ethanol LLC
Sandoz GmbH
Helmholtz Centre for Infection Research
Karlsruhe Institute of Technology
Dyadic Nederland BV
DSM Food Specialties
Michigan State University
Uniformed Services University of the Health Sciences
Hamburg University of Technology
University of Cambridge
Macquarie University
Swansea University
University of Groningen
University of Kentucky
Universidade de São Paulo
University of Sheffield
Utrecht University

Research output: Contribution to journal › Journal article › Research › peer-review

Abstract

The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology.

Original language	English
Journal	Fungal Genetics and Biology
Volume	46
Issue number	1
Pages (from-to)	2-13
ISSN	1087-1845
DOIs	https://doi.org/10.1016/j.fgb.2008.12.003
Publication status	Published - 2009

Keywords

Aspergillus nidulans
Fungal community
Transcription factors
CADRE
Annotation
Assembly
Aspergilli
Genome

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10.1016/j.fgb.2008.12.003

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Wortman, J. R., Gilsenan, J. M., Joardar, V., Deegan, J., Clutterbuck, J., Andersen, M. R., Archer, D., Bencina, M., Braus, G., Coutinho, P., von Döhren, H., Doonan, J., Driessen, A. J. M., Durek, P., Espeso, E., Fekete, E., Flipphi, M., Estrada, C. G., Geysens, S., ... Turner, G. (2009). The 2008 update of the Aspergillus nidulans genome annotation: A community effort. Fungal Genetics and Biology, 46(1), 2-13. https://doi.org/10.1016/j.fgb.2008.12.003

@article{6a02e79ece6a44f7a699073fbeb48d9c,

title = "The 2008 update of the Aspergillus nidulans genome annotation: A community effort",

abstract = "The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology.",

keywords = "Aspergillus nidulans, Fungal community, Transcription factors, CADRE, Annotation, Assembly, Aspergilli, Genome",

author = "Wortman, \{Jennifer Russo\} and Gilsenan, \{Jane Mabey\} and Vinita Joardar and Jennifer Deegan and John Clutterbuck and Andersen, \{Mikael R{\o}rdam\} and David Archer and Mojca Bencina and Gerhard Braus and Pedro Coutinho and \{von D{\"o}hren\}, Hans and John Doonan and Driessen, \{Arnold J.M.\} and Pawel Durek and Eduardo Espeso and Erzs{\'e}bet Fekete and Michel Flipphi and Estrada, \{Carlos Garcia\} and Steven Geysens and Gustavo Goldman and \{de Groot\}, \{Piet W.J.\} and Kim Hansen and Harris, \{Steven D.\} and Thorsten Heinekamp and Kerstin Helmstaedt and Bernard Henrissat and Gerald Hofmann and Tim Homan and Tetsuya Horio and Hiroyuki Horiuchi and Steve James and Meriel Jones and Levente Karaffa and Zsolt Kar{\'a}nyi and Masashi Kato and Nancy Keller and Kelly, \{Diane E.\} and Kiel, \{Jan A.K.W.\} and Jung-Mi Kim and \{van der Klei\}, \{Ida J.\} and Klis, \{Frans M.\} and Andriy Kovalchuk and Nada Kra{\v s}evec and Kubicek, \{Christian P.\} and Bo Liu and Andrew MacCabe and Vera Meyer and Pete Mirabito and M{\'a}rton Miskei and Magdalena Mos and Jonathan Mullins and Nelson, \{David R.\} and Jens Nielsen and Oakley, \{Berl R.\} and Osmani, \{Stephen A.\} and Tiina Pakula and Andrzej Paszewski and Ian Paulsen and Sebastian Pilsyk and Istv{\'a}n P{\'o}csi and Punt, \{Peter J.\} and Ram, \{Arthur F.J.\} and Qinghu Ren and Xavier Robellet and Geoff Robson and Bernhard Seiboth and \{van Solingen\}, Piet and Thomas Specht and Jibin Sun and Naimeh Taheri-Talesh and Norio Takeshita and Dave Ussery and vanKuyk, \{Patricia A.\} and Hans Visser and \{van de Vondervoort\}, \{Peter J.I.\} and \{de Vries\}, \{Ronald P.\} and Jonathan Walton and Xin Xiang and Yi Xiong and \{Ping Zeng\}, An and Brandt, \{Bernd W.\} and Cornell, \{Michael J.\} and \{van den Hondel\}, \{Cees A.M.J.J.\} and Jacob Visser and Oliver, \{Stephen G.\} and Geoffrey Turner",

year = "2009",

doi = "10.1016/j.fgb.2008.12.003",

language = "English",

volume = "46",

pages = "2--13",

journal = "Fungal Genetics and Biology",

issn = "1087-1845",

publisher = "Academic Press",

number = "1",

}

Wortman, JR, Gilsenan, JM, Joardar, V, Deegan, J, Clutterbuck, J, Andersen, MR, Archer, D, Bencina, M, Braus, G, Coutinho, P, von Döhren, H, Doonan, J, Driessen, AJM, Durek, P, Espeso, E, Fekete, E, Flipphi, M, Estrada, CG, Geysens, S, Goldman, G, de Groot, PWJ, Hansen, K, Harris, SD, Heinekamp, T, Helmstaedt, K, Henrissat, B, Hofmann, G, Homan, T, Horio, T, Horiuchi, H, James, S, Jones, M, Karaffa, L, Karányi, Z, Kato, M, Keller, N, Kelly, DE, Kiel, JAKW, Kim, J-M, van der Klei, IJ, Klis, FM, Kovalchuk, A, Kraševec, N, Kubicek, CP, Liu, B, MacCabe, A, Meyer, V, Mirabito, P, Miskei, M, Mos, M, Mullins, J, Nelson, DR, Nielsen, J, Oakley, BR, Osmani, SA, Pakula, T, Paszewski, A, Paulsen, I, Pilsyk, S, Pócsi, I, Punt, PJ, Ram, AFJ, Ren, Q, Robellet, X, Robson, G, Seiboth, B, van Solingen, P, Specht, T, Sun, J, Taheri-Talesh, N, Takeshita, N, Ussery, D, vanKuyk, PA, Visser, H, van de Vondervoort, PJI, de Vries, RP, Walton, J, Xiang, X, Xiong, Y, Ping Zeng, A, Brandt, BW, Cornell, MJ, van den Hondel, CAMJJ, Visser, J, Oliver, SG & Turner, G 2009, 'The 2008 update of the Aspergillus nidulans genome annotation: A community effort', Fungal Genetics and Biology, vol. 46, no. 1, pp. 2-13. https://doi.org/10.1016/j.fgb.2008.12.003

TY - JOUR

T1 - The 2008 update of the Aspergillus nidulans genome annotation: A community effort

AU - Wortman, Jennifer Russo

AU - Gilsenan, Jane Mabey

AU - Joardar, Vinita

AU - Deegan, Jennifer

AU - Clutterbuck, John

AU - Andersen, Mikael Rørdam

AU - Archer, David

AU - Bencina, Mojca

AU - Braus, Gerhard

AU - Coutinho, Pedro

AU - von Döhren, Hans

AU - Doonan, John

AU - Driessen, Arnold J.M.

AU - Durek, Pawel

AU - Espeso, Eduardo

AU - Fekete, Erzsébet

AU - Flipphi, Michel

AU - Estrada, Carlos Garcia

AU - Geysens, Steven

AU - Goldman, Gustavo

AU - de Groot, Piet W.J.

AU - Hansen, Kim

AU - Harris, Steven D.

AU - Heinekamp, Thorsten

AU - Helmstaedt, Kerstin

AU - Henrissat, Bernard

AU - Hofmann, Gerald

AU - Homan, Tim

AU - Horio, Tetsuya

AU - Horiuchi, Hiroyuki

AU - James, Steve

AU - Jones, Meriel

AU - Karaffa, Levente

AU - Karányi, Zsolt

AU - Kato, Masashi

AU - Keller, Nancy

AU - Kelly, Diane E.

AU - Kiel, Jan A.K.W.

AU - Kim, Jung-Mi

AU - van der Klei, Ida J.

AU - Klis, Frans M.

AU - Kovalchuk, Andriy

AU - Kraševec, Nada

AU - Kubicek, Christian P.

AU - Liu, Bo

AU - MacCabe, Andrew

AU - Meyer, Vera

AU - Mirabito, Pete

AU - Miskei, Márton

AU - Mos, Magdalena

AU - Mullins, Jonathan

AU - Nelson, David R.

AU - Nielsen, Jens

AU - Oakley, Berl R.

AU - Osmani, Stephen A.

AU - Pakula, Tiina

AU - Paszewski, Andrzej

AU - Paulsen, Ian

AU - Pilsyk, Sebastian

AU - Pócsi, István

AU - Punt, Peter J.

AU - Ram, Arthur F.J.

AU - Ren, Qinghu

AU - Robellet, Xavier

AU - Robson, Geoff

AU - Seiboth, Bernhard

AU - van Solingen, Piet

AU - Specht, Thomas

AU - Sun, Jibin

AU - Taheri-Talesh, Naimeh

AU - Takeshita, Norio

AU - Ussery, Dave

AU - vanKuyk, Patricia A.

AU - Visser, Hans

AU - van de Vondervoort, Peter J.I.

AU - de Vries, Ronald P.

AU - Walton, Jonathan

AU - Xiang, Xin

AU - Xiong, Yi

AU - Ping Zeng, An

AU - Brandt, Bernd W.

AU - Cornell, Michael J.

AU - van den Hondel, Cees A.M.J.J.

AU - Visser, Jacob

AU - Oliver, Stephen G.

AU - Turner, Geoffrey

PY - 2009

Y1 - 2009

N2 - The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology.

AB - The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology.

KW - Aspergillus nidulans

KW - Fungal community

KW - Transcription factors

KW - CADRE

KW - Annotation

KW - Assembly

KW - Aspergilli

KW - Genome

U2 - 10.1016/j.fgb.2008.12.003

DO - 10.1016/j.fgb.2008.12.003

M3 - Journal article

C2 - 19146970

SN - 1087-1845

VL - 46

SP - 2

EP - 13

JO - Fungal Genetics and Biology

JF - Fungal Genetics and Biology

IS - 1

ER -

The 2008 update of the Aspergillus nidulans genome annotation: A community effort

Abstract

Keywords

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