Data > Genomes > Puccinia graminis > Project Info > FAQ

Sequencing

• How big is the Puccinia graminis genome?
• What strain was sequenced?
• What is the current state of the assembly?
• How has the sequence been generated for the Puccinia graminis project?
• Will the genome be finished?
• How will we know the assembly is correct?
• What data are available?
• This sequence release looks different from previous releases, like Neurospora crassa. What's different?

Misc

• How do I cite the sequence for publication?
• Who do I contact with questions about the sequencing?
• Where can I get the Fosmids from this sequencing project?
• What are the descriptions of the photos in this website?

Sequencing

1. How big is the Puccinia graminis genome?
   

   Our current total unique contig length is 81,521,292 base pairs. The estimated genome size of Puccinia graminis is 81.5 Mb.

2. What strain was sequenced?
   

   Puccinia graminis f. sp. tritici CRL 75-36-700-3

3. What is the current state of the assembly?
   

   The current assembly contains 4557 contigs in 392 scaffolds (supercontigs). There are no current plans for additional sequencing or finishing. See Assembly for detail.

4. How has the sequence been generated for the Puccinia graminis project?
   

   Our data consist of over 280,000 individual sequencing reads obtained by sequencing each end of plasmids and Fosmids from libraries containing randomly sheared fragments of 4 kb, 10 kb, and 40 kb average size respectively. See Assembly for details.

5. Will the genome be finished?
   

   There are no plans to finish this genome at this time.

6. How will we know if the assembly is correct?
   

   The quality of the assembly will be assessed in several ways. In addition to requiring that the paired plasmid and fosmid ends occur in a logical manner, our assembly of the Puccinia graminis genome will be verified through comparison with available genomic sequences.

7. What data are available?
   

   In this version of our data release, all sequence contigs and supercontigs are available. Sequence data can be accessed in several ways: either through a search with BLASTN or TBLASTN, retrieving of a specific region of the assembly, or by downloading the entire genome. Supercontig and contig sequences are subject to change throughout this project, so each data release version number will be appended to the contig number as a prefix (e.g. 1.1 denotes assembly version 1, supercontig #1).

   A fasta file of raw reads excluded from the assembly is also available for BLAST and download. Also available for download are an AGP file describing the supercontigs and contigs in this assembly and a file listing coordinates of paired endreads.

8. This sequence release looks different from previous releases, like Neurospora crassa. What's different?
   

   Important information about this release can be found here.

Misc

1. How do I cite the sequence for publication?
   

   Publications should include the following citation:
   Puccinia graminis Sequencing Project. Broad Institute of Harvard and MIT (http://www.broad.mit.edu)

2. Who do I contact with questions about the sequencing?
   

   Our email address is annotation-webmaster(at)broad.mit.edu.

3. Where can I get the Fosmids from this sequencing project?
   

   They are available from the FGSC (Fungal Genetics Stock Center).

4. What are the descriptions of the photos in this website?
   

   Captions for the photos in the Home page (from top to bottom):

   1. Infected wheat stem with the uredinial stage of P. graminis. Courtesy of Charlie W. Barnes, University of Minnesota.
   2. P. graminis urediniospores, spore in bottom right corner stained to show germ pores. Courtesy of Yehoshua Anikster and Tamar Eliam, Tel Aviv University.
   3. P. graminis teliospores. Courtesy of Yehoshua Anikster and Tamar Eliam, Tel Aviv University.