Jonathan Eisen was the PI on a project to sequence and analyze the macronuclear genome of the model ciliate Tetrahymena thermophila. This project was supported by grants from NIH-NIGMS and NSF. It was a collaboration with Ed Orias, Eileen Hamilton and many others in the Tetrahymena community. Some links of relevance to this project:
Publications supported by these grants
- Macronuclear Genome Sequence of the Ciliate Tetrahymena … (Eisen et al. PLoS Biology 2006)
- Tetrahymena Genome Database (TGD): a new genomic resource for … Stover et al. NAR
- Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure.
- Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome.
Other links of relevance
- Welcome to TGD Wiki
- Tetrahymena Genome Project
- Tetrahymena – Wikipedia, the free encyclopedia
- TGED
- Tackling a hairy beast (press release when grants were awarded)
- Jonathan Eisen blog post about genome project
- Ars Technica story on the genome:
- Slashdot discussion
- Structure and Strangeness Blog
- Open Source Pimp Blog
- mAd is an idiot blog
- Muton Blog
- Cognitive Labs
- Press release from TIGR
Jonathan Eisen's Lab 
A client is working with plasmodium and/or toxoplasma. He is trying to Sanger sequence something in one of those organisms, but keep getting hits to Tetrahymena and not to the other protozoa he works with. Specifically, the hits are always to “Tetrahymena thermophila DNA polymerase family B containing protein, mRNA, NCBI Reference Sequence: XM_001017761.1” (http://www.ncbi.nlm.nih.gov/nucleotide/118369111?report=genbank&log$=nuclalign&blast_rank=1&RID=36D1FY8B01R). Also, each time he tries to sequence it he gets hits to different regions of that same entry. Is it possible this is some sort of retrovirus that could infect other protozoa? I’d attach the BLAST result to this if I knew how. Sorry for the silly question…
LikeLike
Well, how similar are the hits to Tetrahymena?
LikeLike
Score:577 bits (312); Exp: 3e -161 Identical: 374/404 Gaps: 4/404
LikeLike
Can you post the sequence of the query here? Or is it private? If not, I would suggest using the “create a tree” option from Blast
LikeLike