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 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 Krasevec; Christian P. Kubicek; B. 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; Y. 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 R. 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 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 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 Krasevec, Christian P. Kubicek, B. 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, Y. 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

Biology

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

91 Scopus citations

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
Pages (from-to)	S2-13
Journal	Fungal Genetics and Biology
Volume	46 Suppl 1
DOIs	https://doi.org/10.1016/j.fgb.2008.12.003
State	Published - Mar 2009

Bibliographical note

Funding Information:
We acknowledge financial support by the European Commission under contract LSSG-CT-2005-018964. MC, and the use of the e-Fungi data warehouse, was supported by a grant to SGO and others as part of the BBSRC’s Bioinformatics and e-Science programme II. We wish to thank Dr Michael Anderson for his input on the assembly, whilst at The University of Manchester. We also acknowledge Todd Creasy for Manatee set-up and support, currently at IGS; Brian Haas for data management and computational support (annotation), currently at the Broad; Joshua Orvis for data management and computational support (annotation), currently at IGS; Jonathan Crabtree for data management and computational support (orthologues), currently at IGS. Sandra M.J. Langeveld is acknowledged for her assistance in preparing part of the manuscript.

ASJC Scopus subject areas

Microbiology
Genetics

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10.1016/j.fgb.2008.12.003

Cite this

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 Suppl 1, S2-13. https://doi.org/10.1016/j.fgb.2008.12.003

@article{fba451fb249b4c3fb692c7fe7c42a9e9,

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.",

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 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 Kim, {Jung Mi} and {van der Klei}, {Ida J.} and Klis, {Frans M.} and Andriy Kovalchuk and Nada Krasevec and Kubicek, {Christian P.} and B. 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 Y. 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",

note = "Funding Information: We acknowledge financial support by the European Commission under contract LSSG-CT-2005-018964. MC, and the use of the e-Fungi data warehouse, was supported by a grant to SGO and others as part of the BBSRC{\textquoteright}s Bioinformatics and e-Science programme II. We wish to thank Dr Michael Anderson for his input on the assembly, whilst at The University of Manchester. We also acknowledge Todd Creasy for Manatee set-up and support, currently at IGS; Brian Haas for data management and computational support (annotation), currently at the Broad; Joshua Orvis for data management and computational support (annotation), currently at IGS; Jonathan Crabtree for data management and computational support (orthologues), currently at IGS. Sandra M.J. Langeveld is acknowledged for her assistance in preparing part of the manuscript. ",

year = "2009",

month = mar,

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

language = "English",

volume = "46 Suppl 1",

pages = "S2--13",

}

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, JM, 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, 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, Zeng, AP, 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 Suppl 1, pp. S2-13. https://doi.org/10.1016/j.fgb.2008.12.003

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 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 - Krasevec, Nada

AU - Kubicek, Christian P.

AU - Liu, B.

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, Y.

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

N1 - Funding Information: We acknowledge financial support by the European Commission under contract LSSG-CT-2005-018964. MC, and the use of the e-Fungi data warehouse, was supported by a grant to SGO and others as part of the BBSRC’s Bioinformatics and e-Science programme II. We wish to thank Dr Michael Anderson for his input on the assembly, whilst at The University of Manchester. We also acknowledge Todd Creasy for Manatee set-up and support, currently at IGS; Brian Haas for data management and computational support (annotation), currently at the Broad; Joshua Orvis for data management and computational support (annotation), currently at IGS; Jonathan Crabtree for data management and computational support (orthologues), currently at IGS. Sandra M.J. Langeveld is acknowledged for her assistance in preparing part of the manuscript.

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.

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.

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UR - http://www.scopus.com/inward/citedby.url?scp=63849241807&partnerID=8YFLogxK

U2 - 10.1016/j.fgb.2008.12.003

DO - 10.1016/j.fgb.2008.12.003

M3 - Article

C2 - 19146970

AN - SCOPUS:63849241807

SN - 1087-1845

VL - 46 Suppl 1

SP - S2-13

JO - Fungal Genetics and Biology

JF - Fungal Genetics and Biology

ER -

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

Abstract

Bibliographical note

ASJC Scopus subject areas

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