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United States Department of Agriculture

Agricultural Research Service

Title: Genomic and Est Sequencing of Mycosphaerella Species Will Permit Comparative Analyses with Related Fungi and Anamorphs

Authors
item Goodwin, Stephen
item Dunkle, Larry
item Churchill, Alice - CORNELL UNIV.
item Carlier, Jean - CIRAD, MONTPELLIER, FRANC
item James, Andy - CICY, MERIDA, MEXICO
item Souza, Manoel - EMBRAPA, BRASILIA, BRAZIL
item Crous, Pedro - FUNGAL BIODIV CENTRE, NET
item Roux, Nicolas - INIBAP, MONTPELLIER, FRAN
item Van Der Lee, Theo - WAGENINGEN, NETHERLANDS
item Waalwijk, Cees - WAGENINGEN, NETHERLANDS
item Lindquist, Erika - DOE-JOINT GENOME INST.
item Bristow, Jim - DOE-JOINT GENOME INST.
item Kema, Gert - WAGENINGEN, NETHERLANDS

Submitted to: Mycological International Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: June 6, 2006
Publication Date: August 27, 2006
Citation: Goodwin, S.B., Dunkle, L.D., Churchill, A.C.L., Carlier, J., James, A., Souze, M.T., Crous, P., Roux, N., van der Lee, T.A.J., Waalwijk, C., Lindquist, E., Bristow, J., and Kema, G.H.J. 2006. Genomic and EST sequencing of mycosphaerella species will permit comparative analyses with related fungi and anamorphs. 8th Mycological International Conference Proceedings. p. 57.

Technical Abstract: MYCOSPHAERELLA and its associated anamorphs form one of the largest phylogenetically distinct groups of plant pathogenic fungi. A few species in this group also cause disease in humans and other vertebrates. Understanding the ecology and pathology of members of the genus MYCOSPHAERELLA will be greatly facilitated by a comparative genomics approach. To further this goal, two species of MYCOSPHAERELLA, M. GRAMINICOLA and M. FIJIENSIS, were selected by the International Mycosphaerella Genomics Consortium for complete genome sequencing. These species were chosen because they are two of the most economically significant pathogens of wheat and banana/plantain, respectively, and affect the global economy by causing huge losses annually to growers of these crops worldwide. A joint project between the USDA-ARS/Purdue University and Plant Research International B.V. was initiated to sequence both genomes, along with 40,000 ESTs from both M. FIJIENSIS and the related maize pathogen CEROSPORA ZEAE-MAYDIS. The work was conducted through the Community Sequencing Program sponsored by the U.S. DOE-Joint Genome Institute. The initial goals of the project are to: assemble 8' genomic shotgun sequences of M. GRAMINICOLA strain IPO323 and M. FIJIENSIS strain CIRAD 86; perform automated annotations of these genomic sequences as well as directed annotations using the 80,000 ESTs from M. FIJIENSIS and C. ZEAE-MAYDIS plus 37,000 ESTs from M. GRAMINICOLA that will be made available by Syngenta; and make these sequences available publicly through a series of linked web sites for comparative analyses. Currently, the 8' M. GRAMINICOLA sequencing is complete and the raw data have been deposited in the trace archive at NCBI (SPECIES_CODE = 'MYCOSPHAERELLA GRAMINICOLA IPO323'). The 518,271 traces were assembled at JGI into 1008 contigs spanning 38.72 Mb, with an N50 contig number of 64 and an N50 contig size of 198 kb. These contigs were assembled into 129 scaffolds covering 41.86 Mb, so the genome size is slightly larger than estimated previously. The N50 scaffold number was 6 and the N50 scaffold size was 2.44 Mb, so at least half of the bases in the assembly are in a scaffold of that size or larger. A draft assembly of 43,962 bases appears to cover the complete mitochondrial genome. A community-wide effort for annotation culminating in an annotation jamboree will be open to all interested participants. This project will be coordinated with sequencing efforts being planned for other species of MYCOSPHAERELLA and its relatives to greatly increase the power of future comparative genomics analyses.

Last Modified: 7/30/2014
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