Fungal Genomic Cosmid and cDNA Sequencing

Fungal (Aspergillus nidulans, Aspergillus parasiticus and Neurospora crassa) Cosmid and cDNA Sequencing

Fungal Genomic (Cosmid Cloned) DNA Sequencing

Aspergillus nidulans Cosmids

Cosmid swe06e08 - AC000133

Cosmid 30b1 - AC004395

Cosmid 2h2 - AC005299

Aspergillus parasiticus Cosmids

Cosmid ap0 - AC005991

Cosmid pyj7 - AC007872

Neurospora crassaCosmids

Cosmid nc14 - AC007959

Cosmid nc17 - AC007960

Cosmid nc19 - AC025046

Fungal (Aspergillus nidulans, Aspergillus flavus and Neurospora crassa) cDNA Sequencing

To date, we have isolated over 14,900 cDNA clones from a mixed vegatative and 24 hour asexual development culture of Aspergillus nidulans Strain FGSC A26(biA1) constructed in lambda zap by Dr. Rodolfo Aramayo, at Texas A&M University, College Station, Texas raramayo@bio.tamu.edu and over 6000 cDNA clones from an evening Neurospora crassa cDNA library and over 7000 cDNA clones from a morning cDNA library, constructed by Jay Dunlap at Dartmouth College, New Hampshire Jay.C.Dunlap@Dartmouth.edu

Table 1 from Zhu, et. al. Genetics, in press 2001.

We recently also have sequenced ca. 1400 cDNA clones from a wild type, Aspergillus flavus vegetative mycelia cDNA library created by Nancy Keller at Department of Plant Pathology, Texas A&M University who recently moved to the Department of Plant Pathology, University of Wisconson-Madison npk@plantpath.wisc.edu
We recently also have sequenced ca. 1500 cDNA clones from a wild type, Neurospora crassa perathecia (fruting bodies) from a cDNA library created by Mary Ann Nelson at Department of Biology, University of New Mexico, Albuquerque, New Mexico manelson@unm.edu from RNA isolated five days after fertilization.

Aspergillus nidulans Eighth Data Release - March 11, 1999

The Aspergillus nidulans EST's are being generated by Doris Kupfer with technical help from Wendy Martin, Jennifer Lewis, and Jennifer Gray in collaboration with Rolf Prade and Rodolfo Aramayo.
We now have end sequenced approximately 6000 templates (ca. 12,000 reactions) from both ends of the directionally cloned inserts after excision into pBlueScript SK-.
After screening out ribosomal RNA, mitochondrial RNA, vector and small inserts <100bp we have 12,485 sequences; 4,268,514 total bases.
We now have generated a unigene database and are making available the results of a blastx search of GenBank with this database.

Aspergillus flavus First Data Release - February 22, 2001

The Aspergillus flavus EST's are being generated by Doris Kupfer with the technical help of Laura Hern and Yuhong Tang in collaboration with Nancy Keller.
We now have end sequenced approximately 1400 templates from the 3' end of the directionally cloned inserts after excision into in pBlueScript SK-.
After screening out ribosomal RNA, mitochondrial RNA, vector and small inserts <100 bp, we have 1253 sequences; 591,872 total bases.
We now have generated a unigene database and are making available the results of a blastx search of GenBank with this database.

Neurospora crassa Fifth Data Release - December 16, 1999

The Neurospora crassa EST's are being generated by Hua Zhu in collaboration with Jay Dunlap and Jennifer Loros.
We now have end sequenced approximately 6000 templates (ca. 12,000 reactions) from both ends of the directionally cloned inserts from the evening cDNA library after excision into pBlueScript SK- and
We also have end sequenced approximately 7000 templates (ca. 14,000 reactions) from both ends of the directionally cloned inserts from the morning cDNA library after excision into pBlueScript SK-.
After screening out ribosomal RNA, mitochondrial RNA, vector and small inserts <100bp we have 9148 sequences; 3,034,174 total bases from the evening cDNA library and 10,871 sequences; 3,651,580 total bases from the morning cDNA library.

Neurospora crassa perathecia cDNAs - First Data Release Dec. 19, 2000

The Neurospora crassa perathecia cDNAs are being sequenced by Doris Kupfer, Hua Zhu, and Sara Downard in collaboration with Mary Ann Nelson's group at University of New Mexico.
We now have end sequenced approximately 1500 templates (ca. 3000 reactions) from both ends of the directionally cloned cDNAs which were directionally cloned into the EcoRI and XhoI sites of pbluescript sk- resulting in a total of 1,147,514 nucleotides.
The 3' end contains an XhoI linkerprimer site 5'CTCGAGTTTTTT... and the 5' end contains an EcoRI adaptor 5'GAATTCGGCACGAG...

Search the Aspergillus nidulans or Neurospora crassa cDNA sequence data

Search the Aspergillus nidulans cDNA sequence data using blastn, tblastn or tblastx

Search the Aspergillus flavus cDNA sequence data using blastn, tblastn or tblastx

Search the Neurospora crassa Evening cDNA sequence data using blastn, tblastn or tblastx

Search the Neurospora crassa Morning cDNA sequence data using blastn, tblastn or tblastx

Search the combined Neurospora crassa Morning and Evening cDNA sequence databases using blastn, tblastn or tblastx

Search the Neurospora crassa perathecia cDNA sequence data using blastn, tblastn or tblastx

Search the results of a BlastX search of the GenBank nr database with the latest Aspergillus nidulans, Aspergillus flavus or Neurospora crassa cDNA data using Key Words.

For Aspergillus nidulans enter your keyword here:

For Aspergillus flavus enter your keyword here:

For Neurospora crassa Evening library enter your keyword here:

For Neurospora crassa Morning library enter your keyword here:

For Neurospora crassa combined morning and evening libraries enter your keyword here:

For Neurospora crassa perathecia library, enter your keyword here:

Obtaining the sequence data via ftp

All of the cDNA sequence data we have obtained to date is available from our ftp site directly, by anonymous ftp to ftp.genome.ou.edu (logon as anonymous with password your e-mail address), cd to /pub/asper or /pub/nc_evening or /pub/nc_morning or /pub/nc_combined and get either the ascii data file called asper_est_with_anno.fa or asper_est_wo_anno.fa, or nc_evening_est_with_anno.fa or nc_evening_est_wo_anno.fa or nc_morning_est_with_anno.fa or nc_morning_est_wo_anno.fa or nc_all_est_wo_anno.fa files contains all the EST's sequenced to date concatenated into a flat file either with or without annotation, respectively.

Aspergillus nidulans Sequencing Data via ftp

Aspergillus flavus Sequencing Data via ftp

Neurospora crassa Evening cDNA Library EST Sequencing Data via ftp

Neurospora crassaMorning cDNA Library EST Sequencing Data via ftp

Neurospora crassa combined morning and evening cDNA Library EST Sequencing Data via ftp

Neurospora crassa perathecia cDNA Library EST Sequencing Data via ftp

Clarification of our naming convention
For Aspergillus nidulans

The 3' end sequences have the notation .f1 at the end of the clone name
The 5' end sequences have the notation .r1 at the end of the clone name
For Neurospora crassa

The 3' end sequences have the notation .r1 at the end of the clone name
The 5' end sequences have the notation .f1 at the end of the clone name
For Neurospora crassa perathecia

The 3' end sequences have the notation .f1 at the end of the clone name
The 5' end sequences have the notation .r1 at the end of the clone name

Clone Availability

At the present time, many of our cDNA clones are available through the Fungal Genetics Stock Center. Since not all the clones have been deposited at the FGSC yet, if you cannot find the clone you are interested in there, please contact us directly and we will make it available to you.

Other Sites of Related Interest

Rolf Prade's Web Page at Oklahoma State Univ.

Aspergillus nidulans Genomic Home Page at Aspergillus-Genomics.org

Mycology: The Study of Fungi

The Neurospora Genome Project at Univ. New Mexico

Fungal Genome Resource at the University of Georgia

Candida albicans information

Acknowledgment

Should you find this data useful and wish to reference it, please acknowledge the Aspergillus nidulans and the Neurospora crassa cDNA Sequencing Project, and B. A. Roe, D. Kupfer, H. Zhu, J. Gray, S. Clifton, R. Prade, J. Loros J. Dunlap, M. Nelson; this project is supported by funds from the NSF-EPSCoR program.

If possible, please send us both the literature citation once published, and a copy of the manuscript.

Thanks, Bruce Roe, Doris Kupfer, Hua Zhu, Jennifer Gray, Sandy Clifton, Rolf Prade, Jennifer Loros, Jay Dunlap and Mary Anne Nelson.
The University of Oklahoma, Department of Chemistry and Biochemistry, Norman, Oklahoma 73019, Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, Oklahoma, Dartmouth College, Hanover, New Hampshire, and Department of Biology, University of New Mexico, Albuquerque, New Mexico.

Bruce Roe, broe@ou.edu

Fungal (Aspergillus nidulans, Aspergillus parasiticus and Neurospora crassa) Cosmid and cDNA Sequencing