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 R. Andersen; David Archer; Mojca Bencina; Gerhard Braus; Pedro Coutinho; Hans von Doehren; John Doonan; Arnold J. M. Driessen; Pawel Durek; Eduardo Espeso; Erzsebet 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 Karanyi; 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 Krasevec; Christian P. Kubicek; Bo Liu; Andrew MacCabe; Vera Meyer; Pete Mirabito; Marton Miskei; Magdalena Mos; Jonathan Mullins; David R. Nelson; Jens Nielsen; Berl R. Oakley; Stephen A. Osmani; Tiina Pakula; Andrzej Paszewski; Ian Paulsen; Sebastian Pilsyk; Istvan Pocsi; 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; 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; Nada Kraševec; Patricia A. van Kuyk; D.H. Döhren; B van Seilboth; R. de Vries

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 R. Andersen, David Archer, Mojca Bencina, Gerhard Braus, Pedro Coutinho, Hans von Doehren, John Doonan, Arnold J. M. Driessen, Pawel Durek, Eduardo Espeso, Erzsebet Fekete, Michel Flipphi, Carlos Garcia Estrada, Steven Geysens, Gustavo GoldmanPiet 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 Karanyi, 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 Krasevec, Christian P. Kubicek, Bo Liu, Andrew MacCabe, Vera Meyer, Pete Mirabito, Marton Miskei, Magdalena Mos, Jonathan Mullins, David R. Nelson, Jens Nielsen, Berl R. Oakley, Stephen A. Osmani, Tiina Pakula, Andrzej Paszewski, Ian Paulsen, Sebastian Pilsyk, Istvan Pocsi, 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, 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^*, Nada Kraševec, Patricia A. van Kuyk, D.H. Döhren, B van Seilboth, R. de Vries

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

73 Citations (Scopus)

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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. (C) 2009 Elsevier Inc. All rights reserved.

Original language	English
Pages (from-to)	S2-S13
Number of pages	12
Journal	Fungal Genetics and Biology
Volume	46
Issue number	1
DOIs	https://doi.org/10.1016/j.fgb.2008.12.003
Publication status	Published - Mar-2009

Keywords

Aspergillus nidulans
Aspergilli
Genome
Annotation
Fungal community
Assembly
Transcription factors
CADRE
GENE-CLUSTER
TRANSCRIPTIONAL ACTIVATOR
CELL-WALL
A-FUMIGATUS
PREDICTION
SEQUENCE
NIGER
DNA
IDENTIFICATION
BIOSYNTHESIS

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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 Doehren, H., Doonan, J., Driessen, A. J. M., Durek, P., Espeso, E., Fekete, E., Flipphi, M., Garcia Estrada, C., Geysens, S., ... de Vries, R. (2009). The 2008 update of the Aspergillus nidulans genome annotation: A community effort. Fungal Genetics and Biology, 46(1), S2-S13. https://doi.org/10.1016/j.fgb.2008.12.003

Wortman, Jennifer Russo ; Gilsenan, Jane Mabey ; Joardar, Vinita ; Deegan, Jennifer ; Clutterbuck, John ; Andersen, Mikael R. ; Archer, David ; Bencina, Mojca ; Braus, Gerhard ; Coutinho, Pedro ; von Doehren, Hans ; Doonan, John ; Driessen, Arnold J. M. ; Durek, Pawel ; Espeso, Eduardo ; Fekete, Erzsebet ; Flipphi, Michel ; Garcia Estrada, Carlos ; Geysens, Steven ; Goldman, Gustavo ; de Groot, Piet W. J. ; Hansen, Kim ; Harris, Steven D. ; Heinekamp, Thorsten ; Helmstaedt, Kerstin ; Henrissat, Bernard ; Hofmann, Gerald ; Homan, Tim ; Horio, Tetsuya ; Horiuchi, Hiroyuki ; James, Steve ; Jones, Meriel ; Karaffa, Levente ; Karanyi, Zsolt ; Kato, Masashi ; Keller, Nancy ; Kelly, Diane E. ; Kiel, Jan A. K. W. ; Kim, Jung-Mi ; van der Klei, Ida J. ; Klis, Frans M. ; Kovalchuk, Andriy ; Krasevec, Nada ; Kubicek, Christian P. ; Liu, Bo ; MacCabe, Andrew ; Meyer, Vera ; Mirabito, Pete ; Miskei, Marton ; Mos, Magdalena ; Mullins, Jonathan ; Nelson, David R. ; Nielsen, Jens ; Oakley, Berl R. ; Osmani, Stephen A. ; Pakula, Tiina ; Paszewski, Andrzej ; Paulsen, Ian ; Pilsyk, Sebastian ; Pocsi, Istvan ; Punt, Peter J. ; Ram, Arthur F. J. ; Ren, Qinghu ; Robellet, Xavier ; Robson, Geoff ; Seiboth, Bernhard ; van Solingen, Piet ; Specht, Thomas ; Sun, Jibin ; Taheri-Talesh, Naimeh ; Takeshita, Norio ; Ussery, Dave ; Vankuyk, Patricia A. ; Visser, Hans ; de Vondervoort, Peter J. I. van ; Walton, Jonathan ; Xiang, Xin ; Xiong, Yi ; Zeng, An Ping ; Brandt, Bernd W. ; Cornell, Michael J. ; van den Hondel, Cees A. M. J. J. ; Visser, Jacob ; Oliver, Stephen G. ; Turner, Geoffrey ; Kraševec, Nada ; Kuyk, Patricia A. van ; Döhren, D.H. ; van Seilboth, B ; de Vries, R. / The 2008 update of the Aspergillus nidulans genome annotation : A community effort. In: Fungal Genetics and Biology. 2009 ; Vol. 46, No. 1. pp. S2-S13.

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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. (C) 2009 Elsevier Inc. All rights reserved.",

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author = "Wortman, {Jennifer Russo} and Gilsenan, {Jane Mabey} and Vinita Joardar and Jennifer Deegan and John Clutterbuck and Andersen, {Mikael R.} and David Archer and Mojca Bencina and Gerhard Braus and Pedro Coutinho and {von Doehren}, Hans and John Doonan and Driessen, {Arnold J. M.} and Pawel Durek and Eduardo Espeso and Erzsebet Fekete and Michel Flipphi and {Garcia Estrada}, Carlos 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 Karanyi 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 Krasevec and Kubicek, {Christian P.} and Bo Liu and Andrew MacCabe and Vera Meyer and Pete Mirabito and Marton 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 Istvan Pocsi 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 {de Vondervoort}, {Peter J. I. van} and Jonathan Walton and Xin Xiang and Yi Xiong and Zeng, {An Ping} 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 and Nada Kra{\v s}evec and Kuyk, {Patricia A. van} and D.H. D{\"o}hren and {van Seilboth}, B and {de Vries}, R.",

year = "2009",

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

language = "English",

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journal = "Fungal Genetics and Biology",

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publisher = "ACADEMIC PRESS INC ELSEVIER SCIENCE",

number = "1",

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Wortman, JR, Gilsenan, JM, Joardar, V, Deegan, J, Clutterbuck, J, Andersen, MR, Archer, D, Bencina, M, Braus, G, Coutinho, P, von Doehren, H, Doonan, J, Driessen, AJM, Durek, P, Espeso, E, Fekete, E, Flipphi, M, Garcia Estrada, C, 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, Karanyi, Z, Kato, M, Keller, N, Kelly, DE, Kiel, JAKW, Kim, J-M, van der Klei, IJ, Klis, FM, Kovalchuk, A, Krasevec, 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, Pocsi, 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, de Vondervoort, PJIV, Walton, J, Xiang, X, Xiong, Y, Zeng, AP, Brandt, BW, Cornell, MJ, van den Hondel, CAMJJ, Visser, J, Oliver, SG, Turner, G, Kraševec, N, Kuyk, PAV, Döhren, DH, van Seilboth, B & de Vries, R 2009, 'The 2008 update of the Aspergillus nidulans genome annotation: A community effort', Fungal Genetics and Biology, vol. 46, no. 1, pp. S2-S13. https://doi.org/10.1016/j.fgb.2008.12.003

The 2008 update of the Aspergillus nidulans genome annotation : A community effort. / Wortman, Jennifer Russo; Gilsenan, Jane Mabey; Joardar, Vinita; Deegan, Jennifer; Clutterbuck, John; Andersen, Mikael R.; Archer, David; Bencina, Mojca; Braus, Gerhard; Coutinho, Pedro; von Doehren, Hans; Doonan, John; Driessen, Arnold J. M.; Durek, Pawel; Espeso, Eduardo; Fekete, Erzsebet; Flipphi, Michel; Garcia Estrada, Carlos; Geysens, Steven; Goldman, Gustavo; de Groot, Piet W. J.; Hansen, Kim; Harris, Steven D.; Heinekamp, Thorsten; Helmstaedt, Kerstin; Henrissat, Bernard; Hofmann, Gerald; Homan, Tim; Horio, Tetsuya; Horiuchi, Hiroyuki; James, Steve; Jones, Meriel; Karaffa, Levente; Karanyi, Zsolt; Kato, Masashi; Keller, Nancy; Kelly, Diane E.; Kiel, Jan A. K. W.; Kim, Jung-Mi; van der Klei, Ida J.; Klis, Frans M.; Kovalchuk, Andriy; Krasevec, Nada; Kubicek, Christian P.; Liu, Bo; MacCabe, Andrew; Meyer, Vera; Mirabito, Pete; Miskei, Marton; Mos, Magdalena; Mullins, Jonathan; Nelson, David R.; Nielsen, Jens; Oakley, Berl R.; Osmani, Stephen A.; Pakula, Tiina; Paszewski, Andrzej; Paulsen, Ian; Pilsyk, Sebastian; Pocsi, Istvan; Punt, Peter J.; Ram, Arthur F. J.; Ren, Qinghu; Robellet, Xavier; Robson, Geoff; Seiboth, Bernhard; van Solingen, Piet; Specht, Thomas; Sun, Jibin; Taheri-Talesh, Naimeh; Takeshita, Norio; Ussery, Dave; Vankuyk, Patricia A.; Visser, Hans; de Vondervoort, Peter J. I. van; Walton, Jonathan; Xiang, Xin; Xiong, Yi; Zeng, An Ping; Brandt, Bernd W.; Cornell, Michael J.; van den Hondel, Cees A. M. J. J.; Visser, Jacob; Oliver, Stephen G.; Turner, Geoffrey; Kraševec, Nada; Kuyk, Patricia A. van; Döhren, D.H.; van Seilboth, B; de Vries, R.

In: Fungal Genetics and Biology, Vol. 46, No. 1, 03.2009, p. S2-S13.

Research output: Contribution to journal › Article › Academic › peer-review

TY - JOUR

T1 - The 2008 update of the Aspergillus nidulans genome annotation

T2 - A community effort

AU - Wortman, Jennifer Russo

AU - Gilsenan, Jane Mabey

AU - Joardar, Vinita

AU - Deegan, Jennifer

AU - Clutterbuck, John

AU - Andersen, Mikael R.

AU - Archer, David

AU - Bencina, Mojca

AU - Braus, Gerhard

AU - Coutinho, Pedro

AU - von Doehren, Hans

AU - Doonan, John

AU - Driessen, Arnold J. M.

AU - Durek, Pawel

AU - Espeso, Eduardo

AU - Fekete, Erzsebet

AU - Flipphi, Michel

AU - Garcia Estrada, Carlos

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 - Karanyi, 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 - Krasevec, Nada

AU - Kubicek, Christian P.

AU - Liu, Bo

AU - MacCabe, Andrew

AU - Meyer, Vera

AU - Mirabito, Pete

AU - Miskei, Marton

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 - Pocsi, Istvan

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 - de Vondervoort, Peter J. I. van

AU - Walton, Jonathan

AU - Xiang, Xin

AU - Xiong, Yi

AU - Zeng, An Ping

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

AU - Kraševec, Nada

AU - Kuyk, Patricia A. van

AU - Döhren, D.H.

AU - van Seilboth, B

AU - de Vries, R.

PY - 2009/3

Y1 - 2009/3

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. (C) 2009 Elsevier Inc. All rights reserved.

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. (C) 2009 Elsevier Inc. All rights reserved.

KW - Aspergillus nidulans

KW - Aspergilli

KW - Genome

KW - Annotation

KW - Fungal community

KW - Assembly

KW - Transcription factors

KW - CADRE

KW - GENE-CLUSTER

KW - TRANSCRIPTIONAL ACTIVATOR

KW - CELL-WALL

KW - A-FUMIGATUS

KW - PREDICTION

KW - SEQUENCE

KW - NIGER

KW - DNA

KW - IDENTIFICATION

KW - BIOSYNTHESIS

U2 - 10.1016/j.fgb.2008.12.003

DO - 10.1016/j.fgb.2008.12.003

M3 - Article

VL - 46

SP - S2-S13

JO - Fungal Genetics and Biology

JF - Fungal Genetics and Biology

SN - 1087-1845

IS - 1

ER -