Literature DB >> 19146970

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

Jennifer Russo Wortman1, 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, 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.   

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.

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Year:  2008        PMID: 19146970      PMCID: PMC2826280          DOI: 10.1016/j.fgb.2008.12.003

Source DB:  PubMed          Journal:  Fungal Genet Biol        ISSN: 1087-1845            Impact factor:   3.495


  69 in total

1.  The genetics of Aspergillus nidulans.

Authors:  G PONTECORVO; J A ROPER; L M HEMMONS; K D MACDONALD; A W J BUFTON
Journal:  Adv Genet       Date:  1953       Impact factor: 1.944

2.  Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence data.

Authors:  Austen R D Ganley; Takehiko Kobayashi
Journal:  Genome Res       Date:  2007-01-02       Impact factor: 9.043

3.  Two Aspergillus nidulans genes encoding methylenetetrahydrofolate reductases are up-regulated by homocysteine.

Authors:  Marzena Sieńko; Renata Natorff; Zbigniew Zieliński; Arkadiusz Hejduk; Andrzej Paszewski
Journal:  Fungal Genet Biol       Date:  2006-12-16       Impact factor: 3.495

4.  The tightly regulated promoter of the xanA gene of Aspergillus nidulans is included in a helitron.

Authors:  Antonietta Cultrone; Yazmid Reyes Domínguez; Christine Drevet; Claudio Scazzocchio; Rafael Fernández-Martín
Journal:  Mol Microbiol       Date:  2007-03       Impact factor: 3.501

5.  Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans.

Authors:  Sebastian Bergmann; Julia Schümann; Kirstin Scherlach; Corinna Lange; Axel A Brakhage; Christian Hertweck
Journal:  Nat Chem Biol       Date:  2007-03-18       Impact factor: 15.040

6.  Sequence, exon-intron organization, transcription and mutational analysis of prnA, the gene encoding the transcriptional activator of the prn gene cluster in Aspergillus nidulans.

Authors:  B Cazelle; A Pokorska; E Hull; P M Green; G Stanway; C Scazzocchio
Journal:  Mol Microbiol       Date:  1998-04       Impact factor: 3.501

7.  Genomic mining for Aspergillus natural products.

Authors:  Jin Woo Bok; Dirk Hoffmeister; Lori A Maggio-Hall; Renato Murillo; Jeremy D Glasner; Nancy P Keller
Journal:  Chem Biol       Date:  2006-01

8.  NudF, a nuclear migration gene in Aspergillus nidulans, is similar to the human LIS-1 gene required for neuronal migration.

Authors:  X Xiang; A H Osmani; S A Osmani; M Xin; N R Morris
Journal:  Mol Biol Cell       Date:  1995-03       Impact factor: 4.138

9.  Genetic manipulation of Aspergillus nidulans: heterokaryons and diploids for dominance, complementation and haploidization analyses.

Authors:  Richard B Todd; Meryl A Davis; Michael J Hynes
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

10.  Global discriminative learning for higher-accuracy computational gene prediction.

Authors:  Axel Bernal; Koby Crammer; Artemis Hatzigeorgiou; Fernando Pereira
Journal:  PLoS Comput Biol       Date:  2007-02-02       Impact factor: 4.475

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  48 in total

1.  Insights into dynamic mitotic chromatin organization through the NIMA kinase suppressor SonC, a chromatin-associated protein involved in the DNA damage response.

Authors:  Jennifer R Larson; Eric M Facemyer; Kuo-Fang Shen; Leena Ukil; Stephen A Osmani
Journal:  Genetics       Date:  2013-11-08       Impact factor: 4.562

2.  Characterization of an autoinducer of penicillin biosynthesis in Penicillium chrysogenum.

Authors:  Jorge Martín; Carlos García-Estrada; Angel Rumbero; Eliseo Recio; Silvia M Albillos; Ricardo V Ullán; Juan-Francisco Martín
Journal:  Appl Environ Microbiol       Date:  2011-07-01       Impact factor: 4.792

3.  Involvement of transposon-like elements in penicillin gene cluster regulation.

Authors:  Mona Shaaban; Jonathan M Palmer; Wael A El-Naggar; M A El-Sokkary; El-Sayed E Habib; Nancy P Keller
Journal:  Fungal Genet Biol       Date:  2010-02-26       Impact factor: 3.495

4.  Azonazine, a novel dipeptide from a Hawaiian marine sediment-derived fungus, Aspergillus insulicola.

Authors:  Quan-Xiang Wu; Mitchell S Crews; Marija Draskovic; Johann Sohn; Tyler A Johnson; Karen Tenney; Frederick A Valeriote; Xiao-Jun Yao; Leonard F Bjeldanes; Phillip Crews
Journal:  Org Lett       Date:  2010-10-15       Impact factor: 6.005

5.  Genome-based deletion analysis reveals the prenyl xanthone biosynthesis pathway in Aspergillus nidulans.

Authors:  James F Sanchez; Ruth Entwistle; Jui-Hsiang Hung; Junko Yaegashi; Sofina Jain; Yi-Ming Chiang; Clay C C Wang; Berl R Oakley
Journal:  J Am Chem Soc       Date:  2011-02-25       Impact factor: 15.419

6.  NO-inducible nitrosothionein mediates NO removal in tandem with thioredoxin.

Authors:  Shengmin Zhou; Toshiaki Narukami; Shunsuke Masuo; Motoyuki Shimizu; Tomoya Fujita; Yuki Doi; Yosuke Kamimura; Naoki Takaya
Journal:  Nat Chem Biol       Date:  2013-08-18       Impact factor: 15.040

7.  Genetic, molecular, and biochemical basis of fungal tropolone biosynthesis.

Authors:  Jack Davison; Ahmed al Fahad; Menghao Cai; Zhongshu Song; Samar Y Yehia; Colin M Lazarus; Andrew M Bailey; Thomas J Simpson; Russell J Cox
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-16       Impact factor: 11.205

Review 8.  Unlocking fungal cryptic natural products.

Authors:  Yi-Ming Chiang; Kuan-Han Lee; James F Sanchez; Nancy P Keller; Clay C C Wang
Journal:  Nat Prod Commun       Date:  2009-11       Impact factor: 0.986

9.  Re-annotation is an essential step in systems biology modeling of functional genomics data.

Authors:  Bart H J van den Berg; Fiona M McCarthy; Susan J Lamont; Shane C Burgess
Journal:  PLoS One       Date:  2010-05-14       Impact factor: 3.240

10.  The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community.

Authors:  Martha B Arnaud; Marcus C Chibucos; Maria C Costanzo; Jonathan Crabtree; Diane O Inglis; Adil Lotia; Joshua Orvis; Prachi Shah; Marek S Skrzypek; Gail Binkley; Stuart R Miyasato; Jennifer R Wortman; Gavin Sherlock
Journal:  Nucleic Acids Res       Date:  2009-09-22       Impact factor: 16.971

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