November 13, 2006 Publication of genomic analysis paper in Nature
The collaboration among the Ustilago researcher scientists, the Broad Institute, the BayerCropScience AG, and Exelexis resulted in the publication of:Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis.
April 12, 2004 "Short" genes available for download
By request, "short" genes previously excluded by size (<100 aa) and lack of homology, are now available for download.
April 1, 2004 Release 2
We are pleased to announce the release of our putative gene set for Ustilago maydis. This release includes:
- Putative gene set (6522 genes) of the 521 assembly
- Genome assembly of strain FB1, available for Blast and download.
- Mitochondrial genome assembly, available for Blast and download.
- Single nucleotide polymorphisms (SNPs) identified between strains 521 and FB1.
- Alignment of assemblies of strains 521 & FB1
- Blast databases are available
- Improved graphical visualization tools, available from Search and View Regions
- Search feature annotations
- Genome statistics
The 5X whole-genome shotgun sequences of strain FB1 were generated at Exelixis and assembled at the Center for Genome Research.
Two of the contigs in the previous release (contigs 1.246 & 1.251) have been identified as mitochondrial contigs. The contig names were changed as follows:
Ustilago maydis mitochondria contig 1.1
Ustilago maydis contig 1.246
Ustilago maydis mitochondria contig 1.2
Ustilago maydis contig 1.251
June 20, 2003
The Ustilago maydis genome project is part of the Fungal Genome Initiative and represents a collaboration between Bayer CropScience, Exelixis Inc. and the Broad Institute of MIT and Harvard. Broad generated a 10X assembly using whole-genome shotgun sequences. Bayer CropScience contributed their genome sequence of U. maydis strain 521 generated from a minimal tiling path of overlapping BAC clones to be used as physical map to validate the 10X assembly generated at Broad and to anchor the scaffolds to the chromosomes. Exelixis provided their 5X whole-genome shotgun sequences of U. maydis strain FB1 to be aligned against our assembly to identify polymorphism between these two strains.
The initial release of our 10X sequence assembly of the Ustilago maydis assembly. The sequence traces from the Broad Institute sequencing can be downloaded from the NCBI trace repository. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the project accession AACP00000000. The version described in this release is the first version, AACP01000000.
This initial release allows:
- BLAST searches against our 10X genome assembly
- BLAST searches against Bayer's assembly
- Downloads of the consensus sequence of our 10X coverage assembly
- Downloads of Bayer's assembly
- Search and download a particular region of the 10X genome assembly
- View the alignment of our assembly to Bayer's physical map
- Download reads from large insert clones (Fosmids) in the 10X genome assembly
May 28, 2003 Assembly 1
- Greater than 10X sequencing coverage of the genome
- 276 contigs longer than 2 kb
- 48 supercontigs
- 72 kb average contig length (range 2-511 kb)
- 411 kb average supercontig length (range 3-2465 kb)
- 19 Mb total length of combined contigs (19,742,445 bp)
- Average base lies in a contig of length 127 kb
- Average base lies within a supercontig of length 818 kb