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 MisraDavid 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

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  • Cite this

    Xie, G., Berka, R. M., Henrissat, B., Saloheimo, M., Magnuson, J., de Leon, A., Cullen, D., Nelson, B., Arvas, M., Westerholm-Parvinen, A., Merino, S., Baker, S. E., Schmoll, M., Harris, P., Ward, M., Larrondo, L. F., Yao, J., Penttilä, M., Jackson, M., ... 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. http://www.fgsc.net/ecfg8/symposiumIIoral.pdf