P. omnivora and E. festucae Genomic and EST Sequencing
Phymatotrichum omnivorum, the causative fungal agent of cotton root rot,
is one of the most destructive of plant diseases, with a significant
economic impact on numerous crops, including alfalfa, peanuts, pecans,
fruit trees, grapes, and vegetables.
Epichloe festucae, a mutualistic symbiont (endophyte) of temperate grasses,
to which they impart numerous and profound fitness benefits, is a model for endophyte
research that is amenable to both Mendelian and molecular genetic analysis.
We presently are sequencing the Phymatotrichum omnivorum genome with funding for 6-fold coverage from the
Oklahoma Department of Agriculture, in collaboration with Steve Marek at Oklahoma State University and Rick
Dixon and collegues at the Noble Foundation, Ardmore, OK.
Search the Phymatotrichum omnivorum genome sequence data
-
Search the Phymatotrichum omnivorum genome sequence data using Blastall
- To view the blastx results for all Phymatotrichum omnivorum contigs greater than 2kb vs the GenBank NR Protein database
sorted by the top gene hit and contig containing that hit
Click here
Note that this is quite a large file and may take a minute or two to load in your browser.
Search the Phymatotrichum omnivorum EST sequence data
-
Search the Phymatotrichum omnivorum EST sequence data using Blastall
- To view the blastx results for all Phymatotrichum omnivorum EST contigs (Unigenes) and singlets vs the GenBank NR Protein database
sorted by the top gene hit and contig containing that hit
Click here
Note that this is quite a large file and may take a minute or two to load in your browser.
Search the Epichloe festucae genome sequence data
Obtaining the sequence data via ftp
All of our shotgun sequence data is available via ftp (see below) but at the present time,
the various contigs are in "random" order and do
not correspond to any specific relationship one to another.
Please be aware that the order and contig number will change with each new
release of data.
Please note that the 454 data not only is included in the 2368 assembly assembly along
with the ABI 3730 data but also is available as separate, 454 contigs assembled without 3730 data.
However, you should only search the 454 only data if your query sequence
did not find a match in the 2368 assembly.
Caution: the data has been neither proof read nor edited and thus should be
considered preliminary raw sequence data.
Also, because the sequence assembly program, Phrap,
has the tendency to include inaccurate sequence reads on the ends of contigs, be
cautious when using sequences within 1-200 bases of the ends of individual contigs.
Please take this into account when using this data
If you have determined which contig is of interest to you using the
above Blast search capability on the OU Server, this contig(s) are in the
appropriate directory:
- For Epichloe festucae, see the Kentucky, ef_454_all or ef_454_large directory
- For Phymatotrichum omnivorum, see the 454AllContigs, 454LargeContigs, or auto_crr directory.
on our ftp site.
If however, you determined which contig was of interest using the
'KeyWord Search' option, then the contig(s) of interest will be found
via the link above, presently only available for P. omnivorum.
The Epichloe festucae genome is being sequenced in collaboration with Chris Schardl and Uljana Hesse at the
University of Kentucky with funding from a National Science Foundation - USDA microbial genome sequencing grant.
Bruce Roe, broe@ou.edu