Community involved fungal genome annotation at the JGI-LANL

Gary Xie (Corresponding author), Randy M. Berka, Bernard Henrissat, Markku Saloheimo, Jon Magnuson, Alfredo de Leon, Daniel Cullen, Beth Nelson, Mikko Arvas, Ann Westerholm-Parvinen, Sandy Merino, Scott E. Baker, Monika Schmoll, Paul Harris, Mick Ward, Luis F. Larrondo, Jian Yao, Merja Penttilä, Melissa Jackson, Monica Misra & 15 others David Goodstein, Nina Thayer, Astrid Terry, Wayne Huang, Sam Rash, Paramvir Dehal, Nick Putnam, Jarrod Chapman, Barbara Robbertse, Christian P. Kubicek, Dan Rokhsar, Paul Gilna, Tom Brettin, Susan Lucas, Diego A. Martinez

Research output: Chapter in Book/Report/Conference proceedingConference abstract in proceedingsScientific

Abstract

The role of the fungal genome annotation team at LANL is to provide high quality manually curated annotation of fungal genomic sequence. The JGI-LANL and fungal research community are teaming up to publish a full analysis and annotation of Trichoderma reesei and Aspergillus niger chromosomes. Work on the T. reesei genome was completed earlier this year and will appear in publication in the coming months. We begin our analysis by running each genome through an automated pipeline that combines evidence-based and abintio methods. All information is displayed before manual review in the JGI’s Genome Portal, available at http://genome.jgi.doe.gov/. Utilizing a combination of the Genome Portal, local tools and the Apollo editing system each predicted gene is then manually reviewed by comparing the predicted gene to EST and mRNA sequences from the T. reesei and A. niger genomes as well as closely related species, such as Neurospora crassa, Fusarium graminarium, Magnaporthe grisea and other Apergillus species. This suite of tools allows a distributed group of annotators from the fungal research community to correct errors as necessary and enrich the automated information with comments and human annotations. All manual annotations are immediately viewable and searchable in the Genome Portal.
Original languageEnglish
Title of host publication8th European Conference on Fungal Genetics
Subtitle of host publicationBook of Abstracts
EditorsIrina S. Druzhinina, Alexey G. Kopchinskiy, Christian P. Kubicek
PublisherVienna University of Technology
ChapterII Comparative Fungal Genomics
Pages21
Publication statusPublished - 2006
Event8th European Conference on Fungal Genetics - Vienna, Austria
Duration: 8 Apr 200611 Apr 2006

Conference

Conference8th European Conference on Fungal Genetics
CountryAustria
CityVienna
Period8/04/0611/04/06

Fingerprint

Fungal Genome
Genome
Aspergillus niger
Magnaporthe
Neurospora crassa
Trichoderma
Expressed Sequence Tags
Fusarium
Research
Running
Genes
Publications
Chromosomes
Messenger RNA

Cite this

Xie, G., Berka, R. M., Henrissat, B., Saloheimo, M., Magnuson, J., de Leon, A., ... Martinez, D. A. (2006). Community involved fungal genome annotation at the JGI-LANL. In I. S. Druzhinina, A. G. Kopchinskiy, & C. P. Kubicek (Eds.), 8th European Conference on Fungal Genetics: Book of Abstracts (pp. 21). [IIo-2] Vienna University of Technology.
Xie, Gary ; Berka, Randy M. ; Henrissat, Bernard ; Saloheimo, Markku ; Magnuson, Jon ; de Leon, Alfredo ; Cullen, Daniel ; Nelson, Beth ; Arvas, Mikko ; Westerholm-Parvinen, Ann ; Merino, Sandy ; Baker, Scott E. ; Schmoll, Monika ; Harris, Paul ; Ward, Mick ; Larrondo, Luis F. ; Yao, Jian ; Penttilä, Merja ; Jackson, Melissa ; Misra, Monica ; Goodstein, David ; Thayer, Nina ; Terry, Astrid ; Huang, Wayne ; Rash, Sam ; Dehal, Paramvir ; Putnam, Nick ; Chapman, Jarrod ; Robbertse, Barbara ; Kubicek, Christian P. ; Rokhsar, Dan ; Gilna, Paul ; Brettin, Tom ; Lucas, Susan ; Martinez, Diego A. / Community involved fungal genome annotation at the JGI-LANL. 8th European Conference on Fungal Genetics: Book of Abstracts. editor / Irina S. Druzhinina ; Alexey G. Kopchinskiy ; Christian P. Kubicek. Vienna University of Technology, 2006. pp. 21
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title = "Community involved fungal genome annotation at the JGI-LANL",
abstract = "The role of the fungal genome annotation team at LANL is to provide high quality manually curated annotation of fungal genomic sequence. The JGI-LANL and fungal research community are teaming up to publish a full analysis and annotation of Trichoderma reesei and Aspergillus niger chromosomes. Work on the T. reesei genome was completed earlier this year and will appear in publication in the coming months. We begin our analysis by running each genome through an automated pipeline that combines evidence-based and abintio methods. All information is displayed before manual review in the JGI’s Genome Portal, available at http://genome.jgi.doe.gov/. Utilizing a combination of the Genome Portal, local tools and the Apollo editing system each predicted gene is then manually reviewed by comparing the predicted gene to EST and mRNA sequences from the T. reesei and A. niger genomes as well as closely related species, such as Neurospora crassa, Fusarium graminarium, Magnaporthe grisea and other Apergillus species. This suite of tools allows a distributed group of annotators from the fungal research community to correct errors as necessary and enrich the automated information with comments and human annotations. All manual annotations are immediately viewable and searchable in the Genome Portal.",
author = "Gary Xie and Berka, {Randy M.} and Bernard Henrissat and Markku Saloheimo and Jon Magnuson and {de Leon}, Alfredo and Daniel Cullen and Beth Nelson and Mikko Arvas and Ann Westerholm-Parvinen and Sandy Merino and Baker, {Scott E.} and Monika Schmoll and Paul Harris and Mick Ward and Larrondo, {Luis F.} and Jian Yao and Merja Penttil{\"a} and Melissa Jackson and Monica Misra and David Goodstein and Nina Thayer and Astrid Terry and Wayne Huang and Sam Rash and Paramvir Dehal and Nick Putnam and Jarrod Chapman and Barbara Robbertse and Kubicek, {Christian P.} and Dan Rokhsar and Paul Gilna and Tom Brettin and Susan Lucas and Martinez, {Diego A.}",
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Xie, G, Berka, RM, Henrissat, B, Saloheimo, M, Magnuson, J, de Leon, A, Cullen, D, Nelson, B, Arvas, M, Westerholm-Parvinen, A, Merino, S, Baker, SE, Schmoll, M, Harris, P, Ward, M, Larrondo, LF, Yao, J, Penttilä, M, Jackson, M, Misra, M, Goodstein, D, Thayer, N, Terry, A, Huang, W, Rash, S, Dehal, P, Putnam, N, Chapman, J, Robbertse, B, Kubicek, CP, Rokhsar, D, Gilna, P, Brettin, T, Lucas, S & Martinez, DA 2006, Community involved fungal genome annotation at the JGI-LANL. in IS Druzhinina, AG Kopchinskiy & CP Kubicek (eds), 8th European Conference on Fungal Genetics: Book of Abstracts., IIo-2, Vienna University of Technology, pp. 21, 8th European Conference on Fungal Genetics, Vienna, Austria, 8/04/06.

Community involved fungal genome annotation at the JGI-LANL. / Xie, Gary (Corresponding author); Berka, Randy M.; Henrissat, Bernard; Saloheimo, Markku; Magnuson, Jon; de Leon, Alfredo; Cullen, Daniel; Nelson, Beth; Arvas, Mikko; Westerholm-Parvinen, Ann; Merino, Sandy; Baker, Scott E.; Schmoll, Monika; Harris, Paul; Ward, Mick; Larrondo, Luis F.; Yao, Jian; Penttilä, Merja; Jackson, Melissa; Misra, Monica; Goodstein, David; Thayer, Nina; Terry, Astrid; Huang, Wayne; Rash, Sam; Dehal, Paramvir; Putnam, Nick; Chapman, Jarrod; Robbertse, Barbara; Kubicek, Christian P.; Rokhsar, Dan; Gilna, Paul; Brettin, Tom; Lucas, Susan; Martinez, Diego A.

8th European Conference on Fungal Genetics: Book of Abstracts. ed. / Irina S. Druzhinina; Alexey G. Kopchinskiy; Christian P. Kubicek. Vienna University of Technology, 2006. p. 21 IIo-2.

Research output: Chapter in Book/Report/Conference proceedingConference abstract in proceedingsScientific

TY - CHAP

T1 - Community involved fungal genome annotation at the JGI-LANL

AU - Xie, Gary

AU - Berka, Randy M.

AU - Henrissat, Bernard

AU - Saloheimo, Markku

AU - Magnuson, Jon

AU - de Leon, Alfredo

AU - Cullen, Daniel

AU - Nelson, Beth

AU - Arvas, Mikko

AU - Westerholm-Parvinen, Ann

AU - Merino, Sandy

AU - Baker, Scott E.

AU - Schmoll, Monika

AU - Harris, Paul

AU - Ward, Mick

AU - Larrondo, Luis F.

AU - Yao, Jian

AU - Penttilä, Merja

AU - Jackson, Melissa

AU - Misra, Monica

AU - Goodstein, David

AU - Thayer, Nina

AU - Terry, Astrid

AU - Huang, Wayne

AU - Rash, Sam

AU - Dehal, Paramvir

AU - Putnam, Nick

AU - Chapman, Jarrod

AU - Robbertse, Barbara

AU - Kubicek, Christian P.

AU - Rokhsar, Dan

AU - Gilna, Paul

AU - Brettin, Tom

AU - Lucas, Susan

AU - Martinez, Diego A.

N1 - CA2: TK402

PY - 2006

Y1 - 2006

N2 - The role of the fungal genome annotation team at LANL is to provide high quality manually curated annotation of fungal genomic sequence. The JGI-LANL and fungal research community are teaming up to publish a full analysis and annotation of Trichoderma reesei and Aspergillus niger chromosomes. Work on the T. reesei genome was completed earlier this year and will appear in publication in the coming months. We begin our analysis by running each genome through an automated pipeline that combines evidence-based and abintio methods. All information is displayed before manual review in the JGI’s Genome Portal, available at http://genome.jgi.doe.gov/. Utilizing a combination of the Genome Portal, local tools and the Apollo editing system each predicted gene is then manually reviewed by comparing the predicted gene to EST and mRNA sequences from the T. reesei and A. niger genomes as well as closely related species, such as Neurospora crassa, Fusarium graminarium, Magnaporthe grisea and other Apergillus species. This suite of tools allows a distributed group of annotators from the fungal research community to correct errors as necessary and enrich the automated information with comments and human annotations. All manual annotations are immediately viewable and searchable in the Genome Portal.

AB - The role of the fungal genome annotation team at LANL is to provide high quality manually curated annotation of fungal genomic sequence. The JGI-LANL and fungal research community are teaming up to publish a full analysis and annotation of Trichoderma reesei and Aspergillus niger chromosomes. Work on the T. reesei genome was completed earlier this year and will appear in publication in the coming months. We begin our analysis by running each genome through an automated pipeline that combines evidence-based and abintio methods. All information is displayed before manual review in the JGI’s Genome Portal, available at http://genome.jgi.doe.gov/. Utilizing a combination of the Genome Portal, local tools and the Apollo editing system each predicted gene is then manually reviewed by comparing the predicted gene to EST and mRNA sequences from the T. reesei and A. niger genomes as well as closely related species, such as Neurospora crassa, Fusarium graminarium, Magnaporthe grisea and other Apergillus species. This suite of tools allows a distributed group of annotators from the fungal research community to correct errors as necessary and enrich the automated information with comments and human annotations. All manual annotations are immediately viewable and searchable in the Genome Portal.

M3 - Conference abstract in proceedings

SP - 21

BT - 8th European Conference on Fungal Genetics

A2 - Druzhinina, Irina S.

A2 - Kopchinskiy, Alexey G.

A2 - Kubicek, Christian P.

PB - Vienna University of Technology

ER -

Xie G, Berka RM, Henrissat B, Saloheimo M, Magnuson J, de Leon A et al. Community involved fungal genome annotation at the JGI-LANL. In Druzhinina IS, Kopchinskiy AG, Kubicek CP, editors, 8th European Conference on Fungal Genetics: Book of Abstracts. Vienna University of Technology. 2006. p. 21. IIo-2